installing dependencies ‘msa’ * installing *source* package ‘msa’ ... ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic -g -O2 -Wall -pedantic -mtune=native -c R_init_msa.cpp -o R_init_msa.o In file included from ./Muscle/RMuscle.h:4, from R_init_msa.cpp:3: ./Muscle/muscle.h:54:9: warning: "assert" redefined 54 | #define assert(exp) ((void)0) | ^~~~~~ In file included from /usr/include/c++/14/cassert:44, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include/Rcpp/utils/tinyformat.h:40, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:74, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from ./ClustalOmega/src/RClustalOmega.h:4, from R_init_msa.cpp:1: /usr/include/assert.h:50:10: note: this is the location of the previous definition 50 | # define assert(expr) (__ASSERT_VOID_CAST (0)) | ^~~~~~ In file included from ./Muscle/muscle.h:38: ./Muscle/intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic -g -O2 -Wall -pedantic -mtune=native -c SplitCharVector2List.cpp -o SplitCharVector2List.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic -g -O2 -Wall -pedantic -mtune=native -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o make --file=msaMakefile --directory=gc-8.2.2 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/gc-8.2.2' ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared=no --with-pic checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking GC version numbers... major=8 minor=2 micro=2 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking dependency style of gcc... gcc3 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3145728 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for emscripten... no checking for inline... inline configure: WARNING: "Explicit GC_INIT() calls may be required." checking for pthread_self in -lpthread... yes checking for clock_gettime without additional libraries... yes checking whether compiler supports -Wextra... yes checking whether compiler supports -Wpedantic... yes checking for xlc... no checking whether compiler supports -fno-strict-aliasing... yes checking for getcontext... yes checking for dl_iterate_phdr... yes checking for dlopen in -ldl... yes checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking whether to build shared libraries... no checking which machine-dependent code should be used... checking whether AIX gcc optimization fix is necessary... no checking whether -Wno-frame-address works... yes checking for dladdr... yes checking for sigsetjmp... yes checking for pthread_setname_np... yes (with tid) checking sys/dg_sys_info.h usability... no checking sys/dg_sys_info.h presence... no checking for sys/dg_sys_info.h... no checking for compiler intrinsics support... yes checking which libatomic_ops to use... none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bdw-gc.pc config.status: creating include/config.h config.status: include/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands config.status: executing default commands make make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/gc-8.2.2' make[3]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/gc-8.2.2' depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include 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cord/.deps/libcord_la-cordprnt.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT cord/libcord_la-cordxtra.lo -MD -MP -MF cord/.deps/libcord_la-cordxtra.Tpo -c -o cord/libcord_la-cordxtra.lo `test -f 'cord/cordxtra.c' || echo './'`cord/cordxtra.c libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT cord/libcord_la-cordxtra.lo -MD -MP -MF cord/.deps/libcord_la-cordxtra.Tpo -c cord/cordxtra.c -fPIC -DPIC -o cord/libcord_la-cordxtra.o mv -f cord/.deps/libcord_la-cordxtra.Tpo cord/.deps/libcord_la-cordxtra.Plo /bin/bash ./libtool --tag=CC --mode=link gcc -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -version-info 6:0:5 -no-undefined -o libcord.la -rpath /usr/local/lib cord/libcord_la-cordbscs.lo cord/libcord_la-cordprnt.lo cord/libcord_la-cordxtra.lo libgc.la libtool: link: ar cru .libs/libcord.a cord/libcord_la-cordbscs.o cord/libcord_la-cordprnt.o cord/libcord_la-cordxtra.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libcord.a libtool: link: ( cd ".libs" && rm -f "libcord.la" && ln -s "../libcord.la" "libcord.la" ) make[3]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/gc-8.2.2' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/gc-8.2.2' cp .libs/libgc.a ../ cp .libs/libgccpp.a ../ make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/gc-8.2.2' ---------------------------------------- ------------------ GC ----------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=Muscle make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/Muscle' export PKG_CXXFLAGS=" -I../gc-8.2.2/include" /home/hornik/tmp/R-d-gcc-14/bin/R CMD SHLIB -o libMuscle.so aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/Muscle' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aligngivenpath.cpp -o aligngivenpath.o aligngivenpath.cpp: In function ‘void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)’: aligngivenpath.cpp:186:24: warning: unused variable ‘uLengthA’ [-Wunused-variable] 186 | const unsigned uLengthA = msaA.GetColCount(); | ^~~~~~~~ aligngivenpath.cpp:187:24: warning: unused variable ‘uLengthB’ [-Wunused-variable] 187 | const unsigned uLengthB = msaB.GetColCount(); | ^~~~~~~~ aligngivenpath.cpp: In function ‘void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)’: aligngivenpath.cpp:335:40: warning: unused variable ‘uColA’ [-Wunused-variable] 335 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpath.cpp:336:40: warning: unused variable ‘uColB’ [-Wunused-variable] 336 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ aligngivenpath.cpp:346:40: warning: unused variable ‘uColA’ [-Wunused-variable] 346 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpath.cpp:354:40: warning: unused variable ‘uColB’ [-Wunused-variable] 354 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ In file included from muscle.h:38, from aligngivenpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aligngivenpathsw.cpp -o aligngivenpathsw.o aligngivenpathsw.cpp: In function ‘void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)’: aligngivenpathsw.cpp:58:24: warning: unused variable ‘uLengthA’ [-Wunused-variable] 58 | const unsigned uLengthA = msaA.GetColCount(); | ^~~~~~~~ aligngivenpathsw.cpp:59:24: warning: unused variable ‘uLengthB’ [-Wunused-variable] 59 | const unsigned uLengthB = msaB.GetColCount(); | ^~~~~~~~ aligngivenpathsw.cpp: In function ‘void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)’: aligngivenpathsw.cpp:204:40: warning: unused variable ‘uColA’ [-Wunused-variable] 204 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpathsw.cpp:205:40: warning: unused variable ‘uColB’ [-Wunused-variable] 205 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ aligngivenpathsw.cpp:215:40: warning: unused variable ‘uColA’ [-Wunused-variable] 215 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpathsw.cpp:223:40: warning: unused variable ‘uColB’ [-Wunused-variable] 223 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ In file included from muscle.h:38, from aligngivenpathsw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aligntwomsas.cpp -o aligntwomsas.o In file included from muscle.h:38, from aligntwomsas.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aligntwoprofs.cpp -o aligntwoprofs.o In file included from muscle.h:38, from aligntwoprofs.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aln.cpp -o aln.o In file included from muscle.h:38, from aln.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c alpha.cpp -o alpha.o alpha.cpp: In function ‘unsigned int GetAlphaSize(ALPHA)’: alpha.cpp:84:16: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch] 84 | switch (Alpha) | ^ In file included from muscle.h:38, from alpha.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c anchors.cpp -o anchors.o anchors.cpp: In function ‘void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)’: anchors.cpp:162:34: warning: unused variable ‘uWindowCenter’ [-Wunused-variable] 162 | unsigned uWindowCenter = uBestColIndex + uWindowLength/2; | ^~~~~~~~~~~~~ anchors.cpp: At global scope: anchors.cpp:105:13: warning: ‘void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)’ defined but not used [-Wunused-function] 105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], | ^~~~~~~~~~~~ anchors.cpp:53:13: warning: ‘void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)’ defined but not used [-Wunused-function] 53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount, | ^~~~~~~~~~~~~~~~~ In file included from muscle.h:38, from anchors.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bittraceback.cpp -o bittraceback.o bittraceback.cpp: In function ‘void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)’: bittraceback.cpp:146:14: warning: unused variable ‘Bits’ [-Wunused-variable] 146 | char Bits = TraceBack[uLengthA][uLengthB]; | ^~~~ bittraceback.cpp: At global scope: bittraceback.cpp:15:20: warning: ‘const char* BitsToStr(char)’ defined but not used [-Wunused-function] 15 | static const char *BitsToStr(char Bits) | ^~~~~~~~~ In file included from muscle.h:38, from bittraceback.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c blosum62.cpp -o blosum62.o In file included from muscle.h:38, from blosum62.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c blosumla.cpp -o blosumla.o blosumla.cpp:7:14: warning: ‘Blosum62LA’ defined but not used [-Wunused-variable] 7 | static float Blosum62LA[20][20] = | ^~~~~~~~~~ In file included from muscle.h:38, from blosumla.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c clust.cpp -o clust.o clust.cpp: In member function ‘void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)’: clust.cpp:167:16: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch] 167 | switch (m_JoinStyle) | ^ clust.cpp: In member function ‘void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’: clust.cpp:184:24: warning: unused variable ‘uClusterCount’ [-Wunused-variable] 184 | const unsigned uClusterCount = GetClusterCount(); | ^~~~~~~~~~~~~ clust.cpp: In member function ‘void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’: clust.cpp:204:24: warning: unused variable ‘uClusterCount’ [-Wunused-variable] 204 | const unsigned uClusterCount = GetClusterCount(); | ^~~~~~~~~~~~~ clust.cpp: In member function ‘float Clust::ComputeDist(unsigned int, unsigned int)’: clust.cpp:295:16: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch [-Wswitch] 295 | switch (m_CentroidStyle) | ^ clust.cpp: In member function ‘float Clust::ComputeDistMAFFT(unsigned int, unsigned int)’: clust.cpp:360:21: warning: unused variable ‘dDistLR’ [-Wunused-variable] 360 | const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); | ^~~~~~~ clust.cpp: In member function ‘float Clust::ComputeMetric(unsigned int, unsigned int) const’: clust.cpp:611:16: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch] 611 | switch (m_JoinStyle) | ^ In file included from muscle.h:38, from clust.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cluster.cpp -o cluster.o cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’: cluster.cpp:284:22: warning: variable ‘bFound’ set but not used [-Wunused-but-set-variable] 284 | bool bFound = false; | ^~~~~~ cluster.cpp:267:16: warning: unused variable ‘dMaxDist’ [-Wunused-variable] 267 | double dMaxDist = 0.0; | ^~~~~~~~ In file included from muscle.h:38, from cluster.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’: cluster.cpp:307:47: warning: ‘uIndexClosest1’ may be used uninitialized [-Wmaybe-uninitialized] 307 | ClusterNode &Child1 = m_Nodes[uIndexClosest1]; | ^~~~~~~~~~~~~~ cluster.cpp:282:26: note: ‘uIndexClosest1’ was declared here 282 | unsigned uIndexClosest1; | ^~~~~~~~~~~~~~ cluster.cpp:308:47: warning: ‘uIndexClosest2’ may be used uninitialized [-Wmaybe-uninitialized] 308 | ClusterNode &Child2 = m_Nodes[uIndexClosest2]; | ^~~~~~~~~~~~~~ cluster.cpp:283:26: note: ‘uIndexClosest2’ was declared here 283 | unsigned uIndexClosest2; | ^~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c clwwt.cpp -o clwwt.o In file included from muscle.h:38, from clwwt.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c color.cpp -o color.o color.cpp:72:12: warning: ‘int BlosumScore(char, char)’ defined but not used [-Wunused-function] 72 | static int BlosumScore(char c1, char c2) | ^~~~~~~~~~~ In file included from muscle.h:38, from color.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cons.cpp -o cons.o In file included from muscle.h:38, from cons.cpp:7: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c diaglist.cpp -o diaglist.o In file included from muscle.h:38, from diaglist.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ diaglist.cpp: In member function ‘void DiagList::FromPath(const PWPath&)’: diaglist.cpp:70:36: warning: ‘uStartPosA’ may be used uninitialized [-Wmaybe-uninitialized] 70 | Add(uStartPosA, uStartPosB, uLength); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diaglist.cpp:51:18: note: ‘uStartPosA’ was declared here 51 | unsigned uStartPosA; | ^~~~~~~~~~ diaglist.cpp:70:36: warning: ‘uStartPosB’ may be used uninitialized [-Wmaybe-uninitialized] 70 | Add(uStartPosA, uStartPosB, uLength); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diaglist.cpp:52:18: note: ‘uStartPosB’ was declared here 52 | unsigned uStartPosB; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c diffobjscore.cpp -o diffobjscore.o diffobjscore.cpp: In function ‘SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)’: diffobjscore.cpp:76:24: warning: unused variable ‘uSeqCount’ [-Wunused-variable] 76 | const unsigned uSeqCount = msa.GetSeqCount(); | ^~~~~~~~~ diffobjscore.cpp:77:24: warning: unused variable ‘uColCount’ [-Wunused-variable] 77 | const unsigned uColCount = msa.GetColCount(); | ^~~~~~~~~ In file included from muscle.h:38, from diffobjscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c diffpaths.cpp -o diffpaths.o In file included from muscle.h:38, from diffpaths.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c difftrees.cpp -o difftrees.o difftrees.cpp: In function ‘void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)’: difftrees.cpp:161:24: warning: unused variable ‘uLeafCount2’ [-Wunused-variable] 161 | const unsigned uLeafCount2 = Tree2.GetLeafCount(); | ^~~~~~~~~~~ In file included from muscle.h:38, from difftrees.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c difftreese.cpp -o difftreese.o In file included from muscle.h:38, from difftreese.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distcalc.cpp -o distcalc.o In file included from muscle.h:38, from distcalc.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distfunc.cpp -o distfunc.o In file included from muscle.h:38, from distfunc.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distpwkimura.cpp -o distpwkimura.o In file included from muscle.h:38, from distpwkimura.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c domuscle.cpp -o domuscle.o domuscle.cpp: In function ‘void DoMuscle(MuscleInput*, MuscleOutput*)’: domuscle.cpp:169:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 169 | if (g_bClusterOnly) | ^~ domuscle.cpp:172:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 172 | return; | ^~~~~~ domuscle.cpp:180:13: warning: unused variable ‘PNlength’ [-Wunused-variable] 180 | int PNlength = (msaInput->inputSeqs).Length(); | ^~~~~~~~ In file included from muscle.h:38, from RMuscle.h:4, from domuscle.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dosp.cpp -o dosp.o In file included from muscle.h:38, from dosp.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dpreglist.cpp -o dpreglist.o dpreglist.cpp: In function ‘void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)’: dpreglist.cpp:82:40: warning: unused variable ‘uDiagLengthMinusCaps’ [-Wunused-variable] 82 | const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; | ^~~~~~~~~~~~~~~~~~~~ In file included from muscle.h:38, from dpreglist.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c drawtree.cpp -o drawtree.o In file included from muscle.h:38, from drawtree.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c edgelist.cpp -o edgelist.o In file included from muscle.h:38, from edgelist.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c enumopts.cpp -o enumopts.o In file included from muscle.h:38, from enumopts.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c enumtostr.cpp -o enumtostr.o In file included from muscle.h:38, from enumtostr.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c estring.cpp -o estring.o estring.cpp:464:13: warning: ‘bool CanMultiplyEstrings(const short int*, const short int*)’ defined but not used [-Wunused-function] 464 | static bool CanMultiplyEstrings(const short es1[], const short es2[]) | ^~~~~~~~~~~~~~~~~~~ In file included from muscle.h:38, from estring.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ estring.cpp: In function ‘void EstringsToPath(const short int*, const short int*, PWPath&)’: estring.cpp:409:17: warning: ‘cType’ may be used uninitialized [-Wmaybe-uninitialized] 409 | switch (cType) | ^~~~~~ estring.cpp:377:22: note: ‘cType’ was declared here 377 | char cType; | ^~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fasta.cpp -o fasta.o fasta.cpp: In member function ‘void MSA::FromFASTAFile(TextFile&)’: fasta.cpp:15:18: warning: unused variable ‘uSeqCount’ [-Wunused-variable] 15 | unsigned uSeqCount = 0; | ^~~~~~~~~ fasta.cpp:16:18: warning: unused variable ‘uColCount’ [-Wunused-variable] 16 | unsigned uColCount = uInsane; | ^~~~~~~~~ In file included from muscle.h:38, from fasta.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fasta2.cpp -o fasta2.o In file included from muscle.h:38, from fasta2.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastclust.cpp -o fastclust.o In file included from muscle.h:38, from fastclust.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastdist.cpp -o fastdist.o In file included from muscle.h:38, from fastdist.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastdistjones.cpp -o fastdistjones.o In file included from muscle.h:38, from fastdistjones.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastdistkbit.cpp -o fastdistkbit.o In file included from muscle.h:38, from fastdistkbit.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastdistkmer.cpp -o fastdistkmer.o fastdistkmer.cpp: In function ‘void FastDistKmer(const SeqVect&, DistFunc&)’: fastdistkmer.cpp:235:32: warning: unused variable ‘KD’ [-Wunused-variable] 235 | double KD = KimuraDist(EstimatedPctId); | ^~ In file included from muscle.h:38, from fastdistkmer.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastdistmafft.cpp -o fastdistmafft.o fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’: fastdistmafft.cpp:239:29: warning: unused variable ‘pName1’ [-Wunused-variable] 239 | const char *pName1 = s1.GetName(); | ^~~~~~ fastdistmafft.cpp: At global scope: fastdistmafft.cpp:104:13: warning: ‘void ListCount(const unsigned char*)’ defined but not used [-Wunused-function] 104 | static void ListCount(const unsigned char Count[]) | ^~~~~~~~~ In file included from muscle.h:38, from fastdistmafft.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastdistnuc.cpp -o fastdistnuc.o fastdistnuc.cpp: In function ‘void DistKmer4_6(const SeqVect&, DistFunc&)’: fastdistnuc.cpp:223:29: warning: unused variable ‘pName1’ [-Wunused-variable] 223 | const char *pName1 = s1.GetName(); | ^~~~~~ fastdistnuc.cpp: At global scope: fastdistnuc.cpp:85:13: warning: ‘void ListCount(const unsigned char*)’ defined but not used [-Wunused-function] 85 | static void ListCount(const unsigned char Count[]) | ^~~~~~~~~ fastdistnuc.cpp:33:17: warning: ‘uResidueGroupCount’ defined but not used [-Wunused-variable] 33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); | ^~~~~~~~~~~~~~~~~~ In file included from muscle.h:38, from fastdistnuc.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastscorepath2.cpp -o fastscorepath2.o In file included from muscle.h:38, from fastscorepath2.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c finddiags.cpp -o finddiags.o finddiags.cpp:11:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function] 11 | static char *TupleToStr(int t) | ^~~~~~~~~~ In file included from muscle.h:38, from finddiags.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c finddiagsn.cpp -o finddiagsn.o finddiagsn.cpp: In function ‘char* TupleToStr(int)’: finddiagsn.cpp:16:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 16 | for (int i = 0; i < K; ++i) | ~~^~~ finddiagsn.cpp: At global scope: finddiagsn.cpp:12:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function] 12 | static char *TupleToStr(int t) | ^~~~~~~~~~ In file included from muscle.h:38, from finddiagsn.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalign.cpp -o glbalign.o In file included from muscle.h:38, from glbalign.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalign352.cpp -o glbalign352.o In file included from muscle.h:38, from glbalign352.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbaligndiag.cpp -o glbaligndiag.o In file included from muscle.h:38, from glbaligndiag.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalignle.cpp -o glbalignle.o In file included from muscle.h:38, from glbalignle.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignle.cpp: In function ‘SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’: glbalignle.cpp:431:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 431 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignle.cpp:404:18: note: ‘uInsertPos’ was declared here 404 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalignsimple.cpp -o glbalignsimple.o glbalignsimple.cpp:52:13: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function] 52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, | ^~~~~~ glbalignsimple.cpp:28:13: warning: ‘void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function] 28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, | ^~~~~~ In file included from muscle.h:38, from glbalignsimple.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalignsp.cpp -o glbalignsp.o In file included from muscle.h:38, from glbalignsp.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignsp.cpp: In function ‘SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’: glbalignsp.cpp:305:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 305 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignsp.cpp:272:26: note: ‘uInsertPos’ was declared here 272 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignsp.cpp:366:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 366 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignsp.cpp:339:18: note: ‘uInsertPos’ was declared here 339 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalignspn.cpp -o glbalignspn.o In file included from muscle.h:38, from glbalignspn.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignspn.cpp: In function ‘SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’: glbalignspn.cpp:340:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 340 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignspn.cpp:307:26: note: ‘uInsertPos’ was declared here 307 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignspn.cpp:401:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 401 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignspn.cpp:374:18: note: ‘uInsertPos’ was declared here 374 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalignss.cpp -o glbalignss.o glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’: glbalignss.cpp:177:30: warning: unused variable ‘ptrRowA’ [-Wunused-variable] 177 | const SCORE *ptrRowA = MxRowA[i]; | ^~~~~~~ glbalignss.cpp:119:24: warning: unused variable ‘uPrefixCountA’ [-Wunused-variable] 119 | const unsigned uPrefixCountA = uLengthA + 1; | ^~~~~~~~~~~~~ glbalignss.cpp:120:24: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable] 120 | const unsigned uPrefixCountB = uLengthB + 1; | ^~~~~~~~~~~~~ glbalignss.cpp: At global scope: glbalignss.cpp:11:14: warning: ‘SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)’ defined but not used [-Wunused-function] 11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) | ^~~~~ In file included from muscle.h:38, from glbalignss.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’: glbalignss.cpp:252:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 252 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignss.cpp:221:26: note: ‘uInsertPos’ was declared here 221 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignss.cpp:310:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 310 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignss.cpp:283:18: note: ‘uInsertPos’ was declared here 283 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glbalndimer.cpp -o glbalndimer.o glbalndimer.cpp: In function ‘SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)’: glbalndimer.cpp:123:16: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch] 123 | switch (g_PPScore) | ^ glbalndimer.cpp:123:16: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch [-Wswitch] glbalndimer.cpp: At global scope: glbalndimer.cpp:14:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function] 14 | static const char *LocalScoreToStr(SCORE s) | ^~~~~~~~~~~~~~~ In file included from muscle.h:38, from glbalndimer.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c globals.cpp -o globals.o In file included from muscle.h:38, from globals.cpp:6: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c globalslinux.cpp -o globalslinux.o globalslinux.cpp: In function ‘double GetNAN()’: globalslinux.cpp:17:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 17 | double dNAN = *( double* )nan; | ^~~~~~~~~~~~~~ In file included from muscle.h:38, from globalslinux.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c globalsosx.cpp -o globalsosx.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c globalsother.cpp -o globalsother.o In file included from muscle.h:38, from globalsother.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c globalswin32.cpp -o globalswin32.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gonnet.cpp -o gonnet.o gonnet.cpp:137:14: warning: ‘Gonnet160’ defined but not used [-Wunused-variable] 137 | static SCORE Gonnet160[20][20] = | ^~~~~~~~~ In file included from muscle.h:38, from gonnet.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c henikoffweight.cpp -o henikoffweight.o In file included from muscle.h:38, from henikoffweight.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c henikoffweightpb.cpp -o henikoffweightpb.o In file included from muscle.h:38, from henikoffweightpb.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c html.cpp -o html.o In file included from muscle.h:38, from html.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hydro.cpp -o hydro.o In file included from muscle.h:38, from hydro.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c intmath.cpp -o intmath.o In file included from muscle.h:38, from intmath.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c local.cpp -o local.o In file included from muscle.h:38, from local.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c main.cpp -o main.o In file included from muscle.h:38, from main.cpp:3: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c makerootmsa.cpp -o makerootmsa.o makerootmsa.cpp: In function ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’: makerootmsa.cpp:18:24: warning: unused variable ‘uSeqLength’ [-Wunused-variable] 18 | const unsigned uSeqLength = s.Length(); | ^~~~~~~~~~ makerootmsa.cpp: In function ‘short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)’: makerootmsa.cpp:94:31: warning: unused variable ‘Path’ [-Wunused-variable] 94 | const PWPath &Path = Nodes[uNodeIndex].m_Path; | ^~~~ makerootmsa.cpp: In function ‘void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)’: makerootmsa.cpp:168:24: warning: unused variable ‘uTreeNodeCount’ [-Wunused-variable] 168 | const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); | ^~~~~~~~~~~~~~ makerootmsa.cpp: At global scope: makerootmsa.cpp:12:13: warning: ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’ defined but not used [-Wunused-function] 12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) | ^~~~~~~ In file included from muscle.h:38, from makerootmsa.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c makerootmsab.cpp -o makerootmsab.o In file included from muscle.h:38, from makerootmsab.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c maketree.cpp -o maketree.o In file included from muscle.h:38, from maketree.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mhack.cpp -o mhack.o In file included from muscle.h:38, from mhack.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mpam200.cpp -o mpam200.o In file included from muscle.h:38, from mpam200.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c msa.cpp -o msa.o msa.cpp:419:13: warning: ‘void FmtPad(unsigned int)’ defined but not used [-Wunused-function] 419 | static void FmtPad(unsigned n) | ^~~~~~ msa.cpp:407:13: warning: ‘void FmtInt0(unsigned int, unsigned int)’ defined but not used [-Wunused-function] 407 | static void FmtInt0(unsigned u, unsigned uWidth) | ^~~~~~~ msa.cpp:392:13: warning: ‘void FmtInt(unsigned int, unsigned int)’ defined but not used [-Wunused-function] 392 | static void FmtInt(unsigned u, unsigned uWidth) | ^~~~~~ msa.cpp:385:13: warning: ‘void FmtChar(char, unsigned int)’ defined but not used [-Wunused-function] 385 | static void FmtChar(char c, unsigned uWidth) | ^~~~~~~ In file included from muscle.h:38, from msa.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c msa2.cpp -o msa2.o msa2.cpp: In function ‘void SetMSAWeightsMuscle(MSA&)’: msa2.cpp:357:16: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch [-Wswitch] 357 | switch (Method) | ^ msa2.cpp: In function ‘void MSAAppend(MSA&, const MSA&)’: msa2.cpp:476:24: warning: unused variable ‘uColCountCat’ [-Wunused-variable] 476 | const unsigned uColCountCat = uColCount1 + uColCount2; | ^~~~~~~~~~~~ In file included from muscle.h:38, from msa2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c msadistkimura.cpp -o msadistkimura.o In file included from muscle.h:38, from msadistkimura.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c msf.cpp -o msf.o msf.cpp:24:20: warning: ‘const char* strfind(const char*, const char*)’ defined but not used [-Wunused-function] 24 | static const char *strfind(const char *s, const char *t) | ^~~~~~~ In file included from muscle.h:38, from msf.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c muscle.cpp -o muscle.o In file included from muscle.h:38, from muscle.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c muscleout.cpp -o muscleout.o In file included from muscle.h:38, from muscleout.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nucmx.cpp -o nucmx.o In file included from muscle.h:38, from nucmx.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nwdasimple.cpp -o nwdasimple.o In file included from muscle.h:38, from nwdasimple.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nwdasimple2.cpp -o nwdasimple2.o In file included from muscle.h:38, from nwdasimple2.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nwdasmall.cpp -o nwdasmall.o In file included from muscle.h:38, from nwdasmall.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nwrec.cpp -o nwrec.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nwsmall.cpp -o nwsmall.o In file included from muscle.h:38, from nwsmall.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c objscore.cpp -o objscore.o objscore.cpp: In function ‘SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)’: objscore.cpp:31:16: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch [-Wswitch] 31 | switch (OS) | ^ objscore.cpp:31:16: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch [-Wswitch] In file included from muscle.h:38, from objscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c objscore2.cpp -o objscore2.o objscore2.cpp: In function ‘SCORE TermGapScore(bool)’: objscore2.cpp:22:16: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch [-Wswitch] 22 | switch (g_TermGaps) | ^ objscore2.cpp: In function ‘SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)’: objscore2.cpp:62:15: warning: unused variable ‘scoreGaps’ [-Wunused-variable] 62 | SCORE scoreGaps = 0; | ^~~~~~~~~ objscore2.cpp:63:14: warning: unused variable ‘bGapping1’ [-Wunused-variable] 63 | bool bGapping1 = false; | ^~~~~~~~~ objscore2.cpp:64:14: warning: unused variable ‘bGapping2’ [-Wunused-variable] 64 | bool bGapping2 = false; | ^~~~~~~~~ objscore2.cpp:67:14: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable] 67 | bool bLeftTermGap = false; | ^~~~~~~~~~~~ objscore2.cpp:82:14: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable] 82 | bool bRightTermGap = false; | ^~~~~~~~~~~~~ objscore2.cpp: In function ‘SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)’: objscore2.cpp:140:14: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable] 140 | bool bLeftTermGap = false; | ^~~~~~~~~~~~ objscore2.cpp:155:14: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable] 155 | bool bRightTermGap = false; | ^~~~~~~~~~~~~ objscore2.cpp: In function ‘SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)’: objscore2.cpp:314:24: warning: unused variable ‘uColCount2’ [-Wunused-variable] 314 | const unsigned uColCount2 = msa2.GetColCount(); | ^~~~~~~~~~ objscore2.cpp: In function ‘SCORE ObjScoreXP(const MSA&, const MSA&)’: objscore2.cpp:493:38: warning: unused variable ‘w’ [-Wunused-variable] 493 | const WEIGHT w = w1*w2; | ^ In file included from muscle.h:38, from objscore2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c objscoreda.cpp -o objscoreda.o In file included from muscle.h:38, from objscoreda.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c onexception.cpp -o onexception.o In file included from muscle.h:38, from onexception.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c options.cpp -o options.o In file included from muscle.h:38, from options.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c outweights.cpp -o outweights.o In file included from muscle.h:38, from outweights.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pam200mafft.cpp -o pam200mafft.o pam200mafft.cpp:6:14: warning: ‘PAM200’ defined but not used [-Wunused-variable] 6 | static float PAM200[23][23] = | ^~~~~~ In file included from muscle.h:38, from pam200mafft.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c params.cpp -o params.o params.cpp: In function ‘void SetPPScore(bool)’: params.cpp:441:16: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch] 441 | switch (g_PPScore) | ^ In file included from muscle.h:38, from params.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phy.cpp -o phy.o phy.cpp: In member function ‘void Tree::RootUnrootedTree(ROOT)’: phy.cpp:665:16: warning: unused variable ‘dEdgeLength’ [-Wunused-variable] 665 | double dEdgeLength = GetEdgeLength(uNode1, uNode2); | ^~~~~~~~~~~ In file included from muscle.h:38, from phy.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phy2.cpp -o phy2.o In file included from muscle.h:38, from phy2.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phy3.cpp -o phy3.o phy3.cpp: In function ‘void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)’: phy3.cpp:125:22: warning: unused variable ‘dThisDist’ [-Wunused-variable] 125 | const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); | ^~~~~~~~~ phy3.cpp: In function ‘void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)’: phy3.cpp:167:24: warning: unused variable ‘uLeafCount’ [-Wunused-variable] 167 | const unsigned uLeafCount = tree.GetLeafCount(); | ^~~~~~~~~~ phy3.cpp:190:16: warning: unused variable ‘dAllMaxDist’ [-Wunused-variable] 190 | double dAllMaxDist = -1e20; | ^~~~~~~~~~~ phy3.cpp:191:18: warning: unused variable ‘uMaxFrom’ [-Wunused-variable] 191 | unsigned uMaxFrom = NULL_NEIGHBOR; | ^~~~~~~~ phy3.cpp:192:18: warning: unused variable ‘uMaxTo’ [-Wunused-variable] 192 | unsigned uMaxTo = NULL_NEIGHBOR; | ^~~~~~ phy3.cpp: In function ‘void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)’: phy3.cpp:263:18: warning: variable ‘uMostDistantLeaf’ set but not used [-Wunused-but-set-variable] 263 | unsigned uMostDistantLeaf = NULL_NEIGHBOR; | ^~~~~~~~~~~~~~~~ phy3.cpp: At global scope: phy3.cpp:45:13: warning: ‘void ListEIs(EdgeInfo**, unsigned int)’ defined but not used [-Wunused-function] 45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) | ^~~~~~~ In file included from muscle.h:38, from phy3.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phy4.cpp -o phy4.o In file included from muscle.h:38, from phy4.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phyfromclust.cpp -o phyfromclust.o In file included from muscle.h:38, from phyfromclust.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phyfromfile.cpp -o phyfromfile.o In file included from muscle.h:38, from phyfromfile.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c physeq.cpp -o physeq.o physeq.cpp: In member function ‘void MSA::ToPhySequentialFile(TextFile&) const’: physeq.cpp:60:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 60 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ physeq.cpp:71:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 71 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ physeq.cpp: In member function ‘void MSA::ToPhyInterleavedFile(TextFile&) const’: physeq.cpp:112:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 112 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ physeq.cpp:124:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 124 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ In file included from muscle.h:38, from physeq.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phytofile.cpp -o phytofile.o In file included from muscle.h:38, from phytofile.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c posgap.cpp -o posgap.o In file included from muscle.h:38, from posgap.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ppscore.cpp -o ppscore.o In file included from muscle.h:38, from ppscore.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c profdb.cpp -o profdb.o In file included from clustsetmsa.h:8, from profdb.cpp:9: msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’: msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch] 22 | switch(m_Distance) | ^ msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch] In file included from muscle.h:38, from profdb.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c profile.cpp -o profile.o In file included from muscle.h:38, from profile.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c profilefrommsa.cpp -o profilefrommsa.o profilefrommsa.cpp: In function ‘void ListProfile(const ProfPos*, unsigned int, const MSA*)’: profilefrommsa.cpp:131:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 131 | if (-1 == PP.m_uResidueGroup) | ~~~^~~~~~~~~~~~~~~~~~~~~ profilefrommsa.cpp: In function ‘unsigned int ResidueGroupFromFCounts(const FCOUNT*)’: profilefrommsa.cpp:230:16: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch] 230 | switch (g_Alpha) | ^ profilefrommsa.cpp: In function ‘ProfPos* ProfileFromMSA(const MSA&)’: profilefrommsa.cpp:245:24: warning: unused variable ‘uSeqCount’ [-Wunused-variable] 245 | const unsigned uSeqCount = a.GetSeqCount(); | ^~~~~~~~~ profilefrommsa.cpp:253:18: warning: unused variable ‘uHydrophobicRunLength’ [-Wunused-variable] 253 | unsigned uHydrophobicRunLength = 0; | ^~~~~~~~~~~~~~~~~~~~~ profilefrommsa.cpp: At global scope: profilefrommsa.cpp:15:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function] 15 | static const char *LocalScoreToStr(SCORE s) | ^~~~~~~~~~~~~~~ In file included from muscle.h:38, from profilefrommsa.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c progalign.cpp -o progalign.o progalign.cpp: In function ‘ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)’: progalign.cpp:41:24: warning: unused variable ‘uIterCount’ [-Wunused-variable] 41 | const unsigned uIterCount = uSeqCount - 1; | ^~~~~~~~~~ In file included from muscle.h:38, from progalign.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c progress.cpp -o progress.o In file included from muscle.h:38, from progress.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c progressivealign.cpp -o progressivealign.o In file included from muscle.h:38, from progressivealign.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwpath.cpp -o pwpath.o pwpath.cpp: In member function ‘void PWPath::Validate() const’: pwpath.cpp:80:23: warning: unused variable ‘LastEdge’ [-Wunused-variable] 80 | const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); | ^~~~~~~~ pwpath.cpp: In member function ‘void PWPath::FromFile(TextFile&)’: pwpath.cpp:213:18: warning: unused variable ‘uEdgeIndex’ [-Wunused-variable] 213 | unsigned uEdgeIndex = 0; | ^~~~~~~~~~ In file included from muscle.h:38, from pwpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c readmx.cpp -o readmx.o readmx.cpp: In function ‘float (* ReadMx(TextFile&))[32][32]’: readmx.cpp:83:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 83 | for (int i = 0; i < MAX_ALPHA; ++i) | ~~^~~~~~~~~~~ readmx.cpp:84:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 84 | for (int j = 0; j < MAX_ALPHA; ++j) | ~~^~~~~~~~~~~ readmx.cpp: In function ‘float (* ReadMxFromR(std::vector >, float (*)[32]))[32][32]’: readmx.cpp:184:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 184 | for (int i = 0; i < MAX_ALPHA; ++i) | ~~^~~~~~~~~~~ readmx.cpp:185:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 185 | for (int j = 0; j < MAX_ALPHA; ++j) | ~~^~~~~~~~~~~ readmx.cpp: At global scope: readmx.cpp:30:17: warning: ‘unsigned int MxCharToLetter(char)’ defined but not used [-Wunused-function] 30 | static unsigned MxCharToLetter(char c) | ^~~~~~~~~~~~~~ In file included from muscle.h:38, from readmx.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c realigndiffs.cpp -o realigndiffs.o In file included from muscle.h:38, from realigndiffs.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c realigndiffse.cpp -o realigndiffse.o realigndiffse.cpp: In function ‘void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)’: realigndiffse.cpp:77:34: warning: unused variable ‘uNewRight’ [-Wunused-variable] 77 | unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); | ^~~~~~~~~ realigndiffse.cpp:80:34: warning: unused variable ‘uOldRight’ [-Wunused-variable] 80 | unsigned uOldRight = OldTree.GetRight(uOld); | ^~~~~~~~~ In file included from muscle.h:38, from realigndiffse.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refine.cpp -o refine.o In file included from clustsetmsa.h:8, from refine.cpp:9: msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’: msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch] 22 | switch(m_Distance) | ^ msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch] In file included from muscle.h:38, from refine.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refinehoriz.cpp -o refinehoriz.o In file included from muscle.h:38, from refinehoriz.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ refinehoriz.cpp: In function ‘bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)’: refinehoriz.cpp:173:23: warning: ‘scoreBefore’ may be used uninitialized [-Wmaybe-uninitialized] 173 | SCORE scoreBefore; | ^~~~~~~~~~~ refinehoriz.cpp:174:23: warning: ‘scoreAfter’ may be used uninitialized [-Wmaybe-uninitialized] 174 | SCORE scoreAfter; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refinesubfams.cpp -o refinesubfams.o refinesubfams.cpp: In function ‘bool RefineSubfams(MSA&, const Tree&, unsigned int)’: refinesubfams.cpp:63:24: warning: unused variable ‘uNodeCount’ [-Wunused-variable] 63 | const unsigned uNodeCount = tree.GetNodeCount(); | ^~~~~~~~~~ In file included from muscle.h:38, from refinesubfams.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refinetree.cpp -o refinetree.o In file included from muscle.h:38, from refinetree.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refinetreee.cpp -o refinetreee.o In file included from muscle.h:38, from refinetreee.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refinevert.cpp -o refinevert.o In file included from muscle.h:38, from refinevert.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c refinew.cpp -o refinew.o refinew.cpp: In function ‘void AppendMSA(MSA&, const MSA&)’: refinew.cpp:22:24: warning: unused variable ‘uColCountCat’ [-Wunused-variable] 22 | const unsigned uColCountCat = uColCount1 + uColCount2; | ^~~~~~~~~~~~ refinew.cpp: In function ‘void RefineW(const MSA&, MSA&)’: refinew.cpp:125:34: warning: unused variable ‘uOutCols’ [-Wunused-variable] 125 | unsigned uOutCols = msaOut.GetColCount(); | ^~~~~~~~ In file included from muscle.h:38, from refinew.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c savebest.cpp -o savebest.o In file included from muscle.h:38, from savebest.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scoredist.cpp -o scoredist.o In file included from muscle.h:38, from scoredist.cpp:3: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scoregaps.cpp -o scoregaps.o scoregaps.cpp:80:14: warning: ‘SCORE Penalty(unsigned int, bool)’ defined but not used [-Wunused-function] 80 | static SCORE Penalty(unsigned Length, bool Term) | ^~~~~~~ scoregaps.cpp:37:13: warning: ‘void FreeGapInfo(GAPINFO*)’ defined but not used [-Wunused-function] 37 | static void FreeGapInfo(GAPINFO *GI) | ^~~~~~~~~~~ In file included from muscle.h:38, from scoregaps.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scorehistory.cpp -o scorehistory.o In file included from muscle.h:38, from scorehistory.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scorepp.cpp -o scorepp.o In file included from muscle.h:38, from scorepp.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c seq.cpp -o seq.o In file included from muscle.h:38, from seq.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c seqvect.cpp -o seqvect.o In file included from muscle.h:38, from seqvect.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c setblosumweights.cpp -o setblosumweights.o In file included from muscle.h:38, from setblosumweights.cpp:42: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c setgscweights.cpp -o setgscweights.o In file included from muscle.h:38, from setgscweights.cpp:104: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c setnewhandler.cpp -o setnewhandler.o In file included from muscle.h:38, from setnewhandler.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c spfast.cpp -o spfast.o spfast.cpp: In function ‘SCORE ObjScoreSPDimer(const MSA&)’: spfast.cpp:252:24: warning: unused variable ‘uSeqCount’ [-Wunused-variable] 252 | const unsigned uSeqCount = msa.GetSeqCount(); | ^~~~~~~~~ spfast.cpp: At global scope: spfast.cpp:59:14: warning: ‘SCORE SPColBrute(const MSA&, unsigned int)’ defined but not used [-Wunused-function] 59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) | ^~~~~~~~~~ spfast.cpp:14:20: warning: ‘const char* GapTypeToStr(int)’ defined but not used [-Wunused-function] 14 | static const char *GapTypeToStr(int GapType) | ^~~~~~~~~~~~ In file included from muscle.h:38, from spfast.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sptest.cpp -o sptest.o In file included from muscle.h:38, from sptest.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c stabilize.cpp -o stabilize.o In file included from muscle.h:38, from stabilize.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c subfam.cpp -o subfam.o subfam.cpp: In function ‘void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)’: subfam.cpp:173:13: warning: unused variable ‘NotUsed’ [-Wunused-variable] 173 | int NotUsed = system(CmdLine); | ^~~~~~~ In file included from muscle.h:38, from subfam.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c subfams.cpp -o subfams.o subfams.cpp:54:13: warning: ‘void Relax(DistFunc&, unsigned int, unsigned int)’ defined but not used [-Wunused-function] 54 | static void Relax(DistFunc &DF, unsigned u, unsigned v) | ^~~~~ subfams.cpp:42:13: warning: ‘void InitializeSingleSource(DistFunc&, unsigned int)’ defined but not used [-Wunused-function] 42 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) | ^~~~~~~~~~~~~~~~~~~~~~ subfams.cpp:12:13: warning: ‘void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)’ defined but not used [-Wunused-function] 12 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) | ^~~~~~~~~~~~~~~~~~ In file included from muscle.h:38, from subfams.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sw.cpp -o sw.o sw.cpp:20:13: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function] 20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, | ^~~~~~ In file included from muscle.h:38, from sw.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c termgaps.cpp -o termgaps.o In file included from muscle.h:38, from termgaps.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c textfile.cpp -o textfile.o textfile.cpp: In member function ‘void TextFile::PutChar(char)’: textfile.cpp:111:13: warning: unused variable ‘i’ [-Wunused-variable] 111 | int i = fputc(c, m_ptrFile); | ^ textfile.cpp: In member function ‘void TextFile::PutString(const char*)’: textfile.cpp:124:13: warning: unused variable ‘iError’ [-Wunused-variable] 124 | int iError = fputs(szLine, m_ptrFile); | ^~~~~~ In file included from muscle.h:38, from textfile.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c threewaywt.cpp -o threewaywt.o In file included from muscle.h:38, from threewaywt.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tomhydro.cpp -o tomhydro.o In file included from muscle.h:38, from tomhydro.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c traceback.cpp -o traceback.o traceback.cpp: In function ‘SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)’: traceback.cpp:21:24: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable] 21 | const unsigned uPrefixCountB = uLengthB + 1; | ^~~~~~~~~~~~~ In file included from muscle.h:38, from traceback.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tracebackopt.cpp -o tracebackopt.o In file included from muscle.h:38, from tracebackopt.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tracebacksw.cpp -o tracebacksw.o tracebacksw.cpp: In function ‘void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)’: tracebacksw.cpp:22:24: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable] 22 | const unsigned uPrefixCountB = uLengthB + 1; | ^~~~~~~~~~~~~ tracebacksw.cpp:29:15: warning: unused variable ‘scoreMax’ [-Wunused-variable] 29 | SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); | ^~~~~~~~ In file included from muscle.h:38, from tracebacksw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c treefrommsa.cpp -o treefrommsa.o In file included from clustsetmsa.h:8, from treefrommsa.cpp:5: msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’: msadist.h:22:23: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch] 22 | switch(m_Distance) | ^ msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch] In file included from muscle.h:38, from treefrommsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c typetostr.cpp -o typetostr.o In file included from muscle.h:38, from typetostr.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c upgma2.cpp -o upgma2.o upgma2.cpp:68:13: warning: ‘void ListState()’ defined but not used [-Wunused-function] 68 | static void ListState() | ^~~~~~~~~ In file included from muscle.h:38, from upgma2.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ upgma2.cpp: In function ‘void UPGMA2(const DistCalc&, Tree&, LINKAGE)’: upgma2.cpp:292:36: warning: ‘dtNewDist’ may be used uninitialized [-Wmaybe-uninitialized] 292 | g_Dist[vL] = dtNewDist; | ~~~~~~~~~~~^~~~~~~~~~~ upgma2.cpp:252:32: note: ‘dtNewDist’ was declared here 252 | dist_t dtNewDist; | ^~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c usage.cpp -o usage.o In file included from muscle.h:38, from usage.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c validateids.cpp -o validateids.o In file included from muscle.h:38, from validateids.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vtml2.cpp -o vtml2.o In file included from muscle.h:38, from vtml2.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c writescorefile.cpp -o writescorefile.o In file included from muscle.h:38, from writescorefile.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ In function ‘double GetColScore(const MSA&, unsigned int)’, inlined from ‘void WriteScoreFile(const MSA&)’ at writescorefile.cpp:59:29: writescorefile.cpp:40:30: warning: ‘Score’ may be used uninitialized [-Wmaybe-uninitialized] 40 | dSum += Score; | ~~~~~^~~~~~~~ writescorefile.cpp: In function ‘void WriteScoreFile(const MSA&)’: writescorefile.cpp:27:32: note: ‘Score’ was declared here 27 | double Score; | ^~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RMuscle.cpp -o RMuscle.o In file included from muscle.h:38, from RMuscle.h:4, from RMuscle.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o libMuscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/Muscle' ar rcs libMuscle.a aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o cp libMuscle.a ../ make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/Muscle' ---------------------------------------- ---------------- MUSCLE ---------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=ClustalW make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalW' ./configure; \ cd src; \ export PKG_CXXFLAGS="-DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result"; \ /home/hornik/tmp/R-d-gcc-14/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \ ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \ cp libClustalW.a ../../ checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu building for linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalW/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/FileReader.cpp -o fileInput/FileReader.o fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)’: fileInput/FileReader.cpp:421:17: warning: variable ‘maxAlnLength’ set but not used [-Wunused-but-set-variable] 421 | int maxAlnLength; // Get values from the Alignment object. | ^~~~~~~~~~~~ fileInput/FileReader.cpp: In member function ‘void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)’: fileInput/FileReader.cpp:692:21: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 692 | catch(exception ex) | ^~ fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)’: fileInput/FileReader.cpp:357:54: warning: ‘this’ pointer is null [-Wnonnull] 357 | seqRangeVector = fileParser->getSeqRangeR(1, noSeqs, offendingSeq, input); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from fileInput/FileReader.h:16, from fileInput/FileReader.cpp:29: fileInput/FileParser.h:44:26: note: in a call to non-static member function ‘std::vector clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)’ 44 | vector getSeqRangeR(int firstSeq, int num, string *offendingSeq, ClustalWInput *input); | ^~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/FileParser.cpp -o fileInput/FileParser.o fileInput/FileParser.cpp: In member function ‘std::vector clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)’: fileInput/FileParser.cpp:38:21: warning: unused variable ‘n’ [-Wunused-variable] 38 | int n = (*input).inputSeqs.size(); | ^ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/Tree.cpp -o tree/Tree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/ClusterTree.cpp -o tree/ClusterTree.o tree/ClusterTree.cpp: In member function ‘void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)’: tree/ClusterTree.cpp:580:9: warning: variable ‘rs’ set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; | ^~ tree/ClusterTree.cpp:580:17: warning: variable ‘rl’ set but not used [-Wunused-but-set-variable] 580 | int rs = 0, rl = 0; | ^~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/TreeInterface.cpp -o tree/TreeInterface.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/NJTree.cpp -o tree/NJTree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)’: substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable ‘inline1’ [-Wunused-variable] 1305 | char inline1[1024]; | ^~~~~~~ substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable ‘nmat’ [-Wunused-variable] 1307 | int nmat; | ^~~~ substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable ‘n’ [-Wunused-variable] 1308 | int n, llimit, ulimit; | ^ substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable ‘llimit’ [-Wunused-variable] 1308 | int n, llimit, ulimit; | ^~~~~~ substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable ‘ulimit’ [-Wunused-variable] 1308 | int n, llimit, ulimit; | ^~~~~~ substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)’: substitutionMatrix/SubMatrix.cpp:1361:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1361 | for (j = 0; j < curline.length(); j++) { | ~~^~~~~~~~~~~~~~~~~~ substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])’: substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable ‘maxRes’ set but not used [-Wunused-but-set-variable] 1845 | int maxRes; | ^~~~~~ substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])’: substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable ‘maxRes’ set but not used [-Wunused-but-set-variable] 1905 | int maxRes; | ^~~~~~ substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)’: substitutionMatrix/SubMatrix.cpp:1128:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 1128 | return (maxRes); | ^ substitutionMatrix/SubMatrix.cpp:1023:9: note: ‘n’ was declared here 1023 | int n, llimit, ulimit; | ^ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o multipleAlign/Iteration.cpp: In member function ‘bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)’: multipleAlign/Iteration.cpp:170:9: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 170 | int count; | ^~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o multipleAlign/MSA.cpp: In member function ‘int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)’: multipleAlign/MSA.cpp:340:11: warning: unused variable ‘alignmentScore’ [-Wunused-variable] 340 | int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 | ^~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/OutputFile.cpp -o general/OutputFile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/UserParameters.cpp -o general/UserParameters.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/Utility.cpp -o general/Utility.o general/Utility.cpp: In member function ‘bool clustalw::Utility::lineType(char*, const char*)’: general/Utility.cpp:251:8: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 251 | int n; | ^ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/InvalidCombination.cpp -o general/InvalidCombination.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/DebugLog.cpp -o general/DebugLog.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/ClustalWResources.cpp -o general/ClustalWResources.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/SymMatrix.cpp -o general/SymMatrix.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c general/Stats.cpp -o general/Stats.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c Help.cpp -o Help.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c alignment/Alignment.cpp -o alignment/Alignment.o alignment/Alignment.cpp: In member function ‘bool clustalw::Alignment::keepPortionOfSeqArray(int, int)’: alignment/Alignment.cpp:1715:24: warning: variable ‘posToAddTo’ set but not used [-Wunused-but-set-variable] 1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin(); | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion, ClustalWOutput*)’: alignment/AlignmentOutput.cpp:683:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 683 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)’: alignment/AlignmentOutput.cpp:878:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 878 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)’: alignment/AlignmentOutput.cpp:1037:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 1037 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)’: alignment/AlignmentOutput.cpp:1166:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 1166 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)’: alignment/AlignmentOutput.cpp:1455:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 1455 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)’: alignment/AlignmentOutput.cpp:1570:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 1570 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion, ClustalWOutput*)’: alignment/AlignmentOutput.cpp:2153:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 2153 | catch(VectorOutOfRange e) | ^ alignment/AlignmentOutput.cpp:2160:21: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 2160 | catch(exception e) | ^ alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)’: alignment/AlignmentOutput.cpp:2410:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=] 2410 | catch(VectorOutOfRange e) | ^ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c alignment/Sequence.cpp -o alignment/Sequence.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c Clustal.cpp -o Clustal.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c RClustalWMain.cpp -o RClustalWMain.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fpic -g -O2 -Wall -pedantic -mtune=native -c RClustalW.cpp -o RClustalW.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o libClustalW.so pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR /usr/bin/ld: multipleAlign/Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': /home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231:(.text+0xfe1): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalW/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalW' ---------------------------------------- --------------- ClustalW --------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=ClustalOmega make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalOmega' ./configure `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \ export PKG_LIBS=" "; \ export PKG_CXXFLAGS=" `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \ export PKG_CFLAGS=" -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \ cd src; \ /home/hornik/tmp/R-d-gcc-14/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \ ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \ cp libClustalOmega.a ../../ configure: Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3145728 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 16 checking if malloc debugging is wanted... no checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/exceptions4c/Makefile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/argtable2/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: src/clustal-omega-config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalOmega/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/argtable2.c -o argtable2/argtable2.o In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:654:13, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:653:13, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:642:17, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:641:17, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:614:13, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:618:17, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ In function ‘arg_cat’, inlined from ‘arg_cat_option’ at argtable2/argtable2.c:617:17, inlined from ‘arg_print_syntax’ at argtable2/argtable2.c:828:9: argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 590 | *dest=0; | ~~~~~^~ argtable2/argtable2.c: In function ‘arg_print_syntax’: argtable2/argtable2.c:818:14: note: at offset 200 into destination object ‘syntax’ of size 200 818 | char syntax[200]=""; | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_end.c -o argtable2/arg_end.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_rem.c -o argtable2/arg_rem.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_lit.c -o argtable2/arg_lit.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_int.c -o argtable2/arg_int.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_str.c -o argtable2/arg_str.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c argtable2/arg_file.c -o argtable2/arg_file.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -pedantic -mtune=native -c kmpp/KMeans.cpp -o kmpp/KMeans.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -pedantic -mtune=native -c kmpp/KmTree.cpp -o kmpp/KmTree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -pedantic -mtune=native -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o In file included from clustal/hhalign_wrapper.c:22: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition clustal/hhalign_wrapper.c: In function ‘SanitiseUnknown’: clustal/hhalign_wrapper.c:85:9: warning: unused variable ‘iLen’ [-Wunused-variable] 85 | int iLen; /* length of sequence */ | ^~~~ clustal/hhalign_wrapper.c:84:9: warning: unused variable ‘iR’ [-Wunused-variable] 84 | int iR; /* iterator for residue */ | ^~ In file included from clustal/seq.h:24, from clustal/hhalign_wrapper.c:31: clustal/hhalign_wrapper.c: In function ‘ReAttachLeadingGaps’: clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:292:13: note: in expansion of macro ‘CKREALLOC’ 292 | CKREALLOC(prMSeq->seq[i], iLen+iCutHead+iCutTail+2); | ^~~~~~~~~ clustal/hhalign_wrapper.c:239:9: warning: variable ‘iSize2’ set but not used [-Wunused-but-set-variable] 239 | int iSize2 = 0; /* #seqs in 2nd profile */ | ^~~~~~ clustal/hhalign_wrapper.c:238:9: warning: variable ‘iSize1’ set but not used [-Wunused-but-set-variable] 238 | int iSize1 = 0; /* #seqs in 1st profile */ | ^~~~~~ clustal/hhalign_wrapper.c: In function ‘PrepareAlignment’: clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:366:13: note: in expansion of macro ‘CKREALLOC’ 366 | CKREALLOC(mseq->seq[piLeafListL[i]], iMaxLen); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:370:13: note: in expansion of macro ‘CKREALLOC’ 370 | CKREALLOC(mseq->seq[piLeafListR[i]], iMaxLen); | ^~~~~~~~~ clustal/hhalign_wrapper.c: In function ‘HHalignWrapper’: clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:555:31: note: in expansion of macro ‘CKCALLOC’ 555 | prHMM = (hmm_light *) CKCALLOC(1, sizeof(hmm_light)); | ^~~~~~~~ clustal/hhalign_wrapper.c:582:75: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 582 | Log(&rLog, LOG_DEBUG, "Dealigning aligned sequences (inside %s)", __FUNCTION__); | ^~~~~~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:593:19: note: in expansion of macro ‘CKCALLOC’ 593 | piLeafCount = CKCALLOC(iNodeCount, sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:594:19: note: in expansion of macro ‘CKCALLOC’ 594 | ppiLeafList = CKCALLOC(iNodeCount, sizeof(int *)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:595:19: note: in expansion of macro ‘CKCALLOC’ 595 | ppcProfile1 = CKCALLOC(prMSeq->nseqs*2-1, sizeof(char *)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:596:19: note: in expansion of macro ‘CKCALLOC’ 596 | ppcProfile2 = CKCALLOC(prMSeq->nseqs*2-1, sizeof(char *)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:597:19: note: in expansion of macro ‘CKCALLOC’ 597 | pdScores = CKCALLOC(iNodeCount, sizeof(double)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:598:19: note: in expansion of macro ‘CKCALLOC’ 598 | pdWeightsL = CKCALLOC(iNodeCount, sizeof(double)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:599:19: note: in expansion of macro ‘CKCALLOC’ 599 | pdWeightsR = CKCALLOC(iNodeCount, sizeof(double)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:613:33: note: in expansion of macro ‘CKMALLOC’ 613 | ppiLeafList[0] = (int *)CKMALLOC(iSizeProf1 * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:618:33: note: in expansion of macro ‘CKMALLOC’ 618 | ppiLeafList[1] = (int *)CKMALLOC(iSizeProf2 * sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:630:29: note: in expansion of macro ‘CKCALLOC’ 630 | piOrderLR = (int *)CKCALLOC(DIFF_NODE, sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:659:62: note: in expansion of macro ‘CKMALLOC’ 659 | ppiLeafList[piOrderLR[riAux+PRNT_NODE]] = (int *)CKMALLOC(1 * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:686:38: note: in expansion of macro ‘CKMALLOC’ 686 | ppiLeafList[iP] = (int *)CKMALLOC(piLeafCount[iP] * sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:732:30: note: in expansion of macro ‘CKCALLOC’ 732 | pcReprsnt1 = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:736:28: note: in expansion of macro ‘CKCALLOC’ 736 | ppcCopy1 = CKCALLOC(piLeafCount[iL], sizeof(char *)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:738:35: note: in expansion of macro ‘CKCALLOC’ 738 | ppcCopy1[j] = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char)); | ^~~~~~~~ clustal/hhalign_wrapper.c:786:33: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 786 | __FUNCTION__, __FILE__, __LINE__, iHHret, | ^~~~~~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:803:30: note: in expansion of macro ‘CKCALLOC’ 803 | pcConsens1 = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:820:30: note: in expansion of macro ‘CKCALLOC’ 820 | pcReprsnt2 = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:824:28: note: in expansion of macro ‘CKCALLOC’ 824 | ppcCopy2 = CKCALLOC(piLeafCount[iR], sizeof(char *)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:826:35: note: in expansion of macro ‘CKCALLOC’ 826 | ppcCopy2[j] = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char)); | ^~~~~~~~ clustal/hhalign_wrapper.c:874:33: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 874 | __FUNCTION__, __FILE__, __LINE__, iHHret, | ^~~~~~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:891:30: note: in expansion of macro ‘CKCALLOC’ 891 | pcConsens2 = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char)); | ^~~~~~~~ clustal/hhalign_wrapper.c:948:33: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 948 | __FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR], | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:983:37: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 983 | __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB, zcError); | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:987:77: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 987 | fprintf(stderr, "%s:%s:%d: 2nd attempt worked", __FUNCTION__, __FILE__, __LINE__); | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1010:33: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 1010 | __FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR], | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1037:37: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 1037 | __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB, zcError); | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1041:77: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 1041 | fprintf(stderr, "%s:%s:%d: 2nd attempt worked", __FUNCTION__, __FILE__, __LINE__); | ^~~~~~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1082:21: note: in expansion of macro ‘CKFREE’ 1082 | CKFREE(ppcCopy1[i]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1084:17: note: in expansion of macro ‘CKFREE’ 1084 | CKFREE(ppcCopy1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1085:17: note: in expansion of macro ‘CKFREE’ 1085 | CKFREE(pcReprsnt1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1086:17: note: in expansion of macro ‘CKFREE’ 1086 | CKFREE(pcConsens1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1091:21: note: in expansion of macro ‘CKFREE’ 1091 | CKFREE(ppcCopy2[i]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1093:17: note: in expansion of macro ‘CKFREE’ 1093 | CKFREE(ppcCopy2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1094:17: note: in expansion of macro ‘CKFREE’ 1094 | CKFREE(pcReprsnt2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1095:17: note: in expansion of macro ‘CKFREE’ 1095 | CKFREE(pcConsens2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1097:13: note: in expansion of macro ‘CKFREE’ 1097 | CKFREE(ppiLeafList[iL]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1099:13: note: in expansion of macro ‘CKFREE’ 1099 | CKFREE(ppiLeafList[iR]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1161:9: note: in expansion of macro ‘CKFREE’ 1161 | CKFREE(prHMM); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1163:5: note: in expansion of macro ‘CKFREE’ 1163 | CKFREE(ppcProfile2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1164:5: note: in expansion of macro ‘CKFREE’ 1164 | CKFREE(ppcProfile1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1165:5: note: in expansion of macro ‘CKFREE’ 1165 | CKFREE(ppiLeafList[piOrderLR[DIFF_NODE*(iNodeCount-1)+PRNT_NODE]]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1166:5: note: in expansion of macro ‘CKFREE’ 1166 | CKFREE(ppiLeafList); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1167:5: note: in expansion of macro ‘CKFREE’ 1167 | CKFREE(piLeafCount); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1168:5: note: in expansion of macro ‘CKFREE’ 1168 | CKFREE(pdScores); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1170:5: note: in expansion of macro ‘CKFREE’ 1170 | CKFREE(pdWeightsL); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/hhalign_wrapper.c:1171:5: note: in expansion of macro ‘CKFREE’ 1171 | CKFREE(pdWeightsR); | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o In file included from clustal/ktuple_pair.c:29: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal/ktuple_pair.c:45: clustal/ktuple_pair.c: In function ‘pair_align’: clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:411:23: note: in expansion of macro ‘CKCALLOC’ 411 | slopes = (char *) CKCALLOC(tl1+1, sizeof(char)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:412:21: note: in expansion of macro ‘CKCALLOC’ 412 | displ = (int *) CKCALLOC(tl1+1, sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:413:26: note: in expansion of macro ‘CKMALLOC’ 413 | diag_index = (int *) CKMALLOC((tl1+1) * sizeof(int)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:602:5: note: in expansion of macro ‘CKFREE’ 602 | CKFREE(displ); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:603:5: note: in expansion of macro ‘CKFREE’ 603 | CKFREE(slopes); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:604:5: note: in expansion of macro ‘CKFREE’ 604 | CKFREE(diag_index); | ^~~~~~ clustal/ktuple_pair.c: In function ‘KTuplePairDist’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:663:27: note: in expansion of macro ‘CKMALLOC’ 663 | seqlen_array = (int*) CKMALLOC((mseq->nseqs+1) * sizeof(int)); | ^~~~~~~~ clustal/ktuple_pair.c:681:79: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 681 | Log(&rLog, LOG_FATAL, "Internal error in %s: Unknown sequence type.", __FUNCTION__); | ^~~~~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:697:28: note: in expansion of macro ‘CKMALLOC’ 697 | seq_array = (char **) CKMALLOC((mseq->nseqs+1) * sizeof(char *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:703:35: note: in expansion of macro ‘CKMALLOC’ 703 | seq_array[i+1] = (char *) CKMALLOC((seqlen_array[i+1]+2) * sizeof (char));; | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:735:22: note: in expansion of macro ‘CKCALLOC’ 735 | accum = (int **) CKCALLOC(5, sizeof (int *)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:737:28: note: in expansion of macro ‘CKCALLOC’ 737 | accum[i] = (int *) CKCALLOC((2*max_aln_length+1), sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:739:19: note: in expansion of macro ‘CKCALLOC’ 739 | zza = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:740:19: note: in expansion of macro ‘CKCALLOC’ 740 | zzb = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:741:19: note: in expansion of macro ‘CKCALLOC’ 741 | zzc = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:742:19: note: in expansion of macro ‘CKCALLOC’ 742 | zzd = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); | ^~~~~~~~ clustal/ktuple_pair.c:758: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 758 | #pragma omp critical(ktuple) clustal/ktuple_pair.c:801: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 801 | #pragma omp critical(ktuple) clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:817:9: note: in expansion of macro ‘CKFREE’ 817 | CKFREE(accum[i]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:819:5: note: in expansion of macro ‘CKFREE’ 819 | CKFREE(accum); | ^~~~~~ clustal/ktuple_pair.c:822: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 822 | #pragma omp critical(ktuple) clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:830:5: note: in expansion of macro ‘CKFREE’ 830 | CKFREE(zza); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:831:5: note: in expansion of macro ‘CKFREE’ 831 | CKFREE(zzb); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:832:5: note: in expansion of macro ‘CKFREE’ 832 | CKFREE(zzc); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:833:5: note: in expansion of macro ‘CKFREE’ 833 | CKFREE(zzd); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:838:9: note: in expansion of macro ‘CKFREE’ 838 | CKFREE(seq_array[i]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/ktuple_pair.c:840:5: note: in expansion of macro ‘CKFREE’ 840 | CKFREE(seq_array); | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/list.c -o clustal/list.o In file included from clustal/list.c:32: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/log.c -o clustal/log.o In file included from clustal/log.c:22: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o In file included from clustal/muscle_upgma.c:53: clustal/muscle_upgma.c: In function ‘MuscleUpgma2’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:260:25: note: in expansion of macro ‘CKMALLOC’ 260 | g_Dist = (dist_t *) CKMALLOC(g_ulTriangleSize * sizeof(dist_t)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:262:28: note: in expansion of macro ‘CKMALLOC’ 262 | g_uNodeIndex = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:263:34: note: in expansion of macro ‘CKMALLOC’ 263 | g_uNearestNeighbor = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:264:28: note: in expansion of macro ‘CKMALLOC’ 264 | g_MinDist = (dist_t *) CKMALLOC(sizeof(dist_t) * g_uLeafCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:265:19: note: in expansion of macro ‘CKMALLOC’ 265 | Ids = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:272:24: note: in expansion of macro ‘CKMALLOC’ 272 | g_uLeft = (uint*) CKMALLOC(sizeof(uint) * g_uInternalNodeCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:273:25: note: in expansion of macro ‘CKMALLOC’ 273 | g_uRight = (uint*) CKMALLOC(sizeof(uint) * g_uInternalNodeCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:274:27: note: in expansion of macro ‘CKMALLOC’ 274 | g_Height = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:275:31: note: in expansion of macro ‘CKMALLOC’ 275 | g_LeftLength = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_upgma.c:276:32: note: in expansion of macro ‘CKMALLOC’ 276 | g_RightLength = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount); | ^~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/muscle_tree.c -o clustal/muscle_tree.o In file included from clustal/muscle_tree.c:37: clustal/muscle_tree.c: In function ‘FreeMuscleTree’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:300:13: note: in expansion of macro ‘CKFREE’ 300 | CKFREE(tree->m_ptrName[i]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:303:5: note: in expansion of macro ‘CKFREE’ 303 | CKFREE(tree->m_ptrName); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:305:5: note: in expansion of macro ‘CKFREE’ 305 | CKFREE(tree->m_uNeighbor1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:306:5: note: in expansion of macro ‘CKFREE’ 306 | CKFREE(tree->m_uNeighbor2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:307:5: note: in expansion of macro ‘CKFREE’ 307 | CKFREE(tree->m_uNeighbor3); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:309:5: note: in expansion of macro ‘CKFREE’ 309 | CKFREE(tree->m_Ids); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:311:5: note: in expansion of macro ‘CKFREE’ 311 | CKFREE(tree->m_dEdgeLength1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:312:5: note: in expansion of macro ‘CKFREE’ 312 | CKFREE(tree->m_dEdgeLength2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:313:5: note: in expansion of macro ‘CKFREE’ 313 | CKFREE(tree->m_dEdgeLength3); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:318:5: note: in expansion of macro ‘CKFREE’ 318 | CKFREE(tree->m_bHasEdgeLength1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:319:5: note: in expansion of macro ‘CKFREE’ 319 | CKFREE(tree->m_bHasEdgeLength2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:320:5: note: in expansion of macro ‘CKFREE’ 320 | CKFREE(tree->m_bHasEdgeLength3); | ^~~~~~ clustal/muscle_tree.c: In function ‘InitCache’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:610:35: note: in expansion of macro ‘CKMALLOC’ 610 | tree->m_uNeighbor1 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:611:35: note: in expansion of macro ‘CKMALLOC’ 611 | tree->m_uNeighbor2 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:612:35: note: in expansion of macro ‘CKMALLOC’ 612 | tree->m_uNeighbor3 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:614:28: note: in expansion of macro ‘CKMALLOC’ 614 | tree->m_Ids = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:616:39: note: in expansion of macro ‘CKMALLOC’ 616 | tree->m_dEdgeLength1 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:617:39: note: in expansion of macro ‘CKMALLOC’ 617 | tree->m_dEdgeLength2 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:618:39: note: in expansion of macro ‘CKMALLOC’ 618 | tree->m_dEdgeLength3 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:623:40: note: in expansion of macro ‘CKMALLOC’ 623 | tree->m_bHasEdgeLength1 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:624:40: note: in expansion of macro ‘CKMALLOC’ 624 | tree->m_bHasEdgeLength2 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:625:40: note: in expansion of macro ‘CKMALLOC’ 625 | tree->m_bHasEdgeLength3 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:627:33: note: in expansion of macro ‘CKMALLOC’ 627 | tree->m_ptrName = (char **) CKMALLOC(sizeof(char *) * tree->m_uCacheCount); | ^~~~~~~~ clustal/muscle_tree.c: In function ‘ExpandCache’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:949:30: note: in expansion of macro ‘CKMALLOC’ 949 | uNewNeighbor1 = (uint *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:951:30: note: in expansion of macro ‘CKMALLOC’ 951 | uNewNeighbor2 = (uint *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:953:30: note: in expansion of macro ‘CKMALLOC’ 953 | uNewNeighbor3 = (uint *) CKMALLOC( | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:956:24: note: in expansion of macro ‘CKCALLOC’ 956 | uNewIds = (uint *) CKCALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:959:34: note: in expansion of macro ‘CKMALLOC’ 959 | dNewEdgeLength1 = (double *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:961:35: note: in expansion of macro ‘CKMALLOC’ 961 | dNewEdgeLength2 = (double *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:963:34: note: in expansion of macro ‘CKMALLOC’ 963 | dNewEdgeLength3 = (double *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:972:35: note: in expansion of macro ‘CKMALLOC’ 972 | bNewHasEdgeLength1 = (bool *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:974:35: note: in expansion of macro ‘CKMALLOC’ 974 | bNewHasEdgeLength2 = (bool *) CKMALLOC( | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:976:35: note: in expansion of macro ‘CKMALLOC’ 976 | bNewHasEdgeLength3 = (bool *) CKMALLOC( | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/muscle_tree.c:978:28: note: in expansion of macro ‘CKCALLOC’ 978 | ptrNewName = (char **) CKCALLOC(uNewCacheCount, sizeof(char*)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1028:9: note: in expansion of macro ‘CKFREE’ 1028 | CKFREE(tree->m_ptrName); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1030:9: note: in expansion of macro ‘CKFREE’ 1030 | CKFREE(tree->m_uNeighbor1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1031:9: note: in expansion of macro ‘CKFREE’ 1031 | CKFREE(tree->m_uNeighbor2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1032:9: note: in expansion of macro ‘CKFREE’ 1032 | CKFREE(tree->m_uNeighbor3); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1034:9: note: in expansion of macro ‘CKFREE’ 1034 | CKFREE(tree->m_Ids); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1036:9: note: in expansion of macro ‘CKFREE’ 1036 | CKFREE(tree->m_dEdgeLength1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1037:9: note: in expansion of macro ‘CKFREE’ 1037 | CKFREE(tree->m_dEdgeLength2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1038:9: note: in expansion of macro ‘CKFREE’ 1038 | CKFREE(tree->m_dEdgeLength3); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1040:9: note: in expansion of macro ‘CKFREE’ 1040 | CKFREE(tree->m_bHasEdgeLength1); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1041:9: note: in expansion of macro ‘CKFREE’ 1041 | CKFREE(tree->m_bHasEdgeLength2); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1042:9: note: in expansion of macro ‘CKFREE’ 1042 | CKFREE(tree->m_bHasEdgeLength3); | ^~~~~~ clustal/muscle_tree.c: In function ‘AppendBranch’: clustal/muscle_tree.c:1449:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 1449 | Log(&rLog, LOG_FATAL, "%s(): %s", __FUNCTION__, "tree has not been created"); | ^~~~~~~~~~~~ clustal/muscle_tree.c: In function ‘GetNeighbor’: clustal/muscle_tree.c:1681:59: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 1681 | Log(&rLog, LOG_FATAL, "Internal error in %s: sub=%u", __FUNCTION__, uNeighborSubscript); | ^~~~~~~~~~~~ clustal/muscle_tree.c: In function ‘AppendTree’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1832:17: note: in expansion of macro ‘CKFREE’ 1832 | CKFREE(prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/muscle_tree.c:1860:17: note: in expansion of macro ‘CKFREE’ 1860 | CKFREE(prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]); | ^~~~~~ clustal/muscle_tree.c: At top level: clustal/muscle_tree.c:519:1: warning: ‘IsEdge’ defined but not used [-Wunused-function] 519 | IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree) | ^~~~~~ clustal/muscle_tree.c:42:21: warning: ‘VERY_NEGATIVE_DOUBLE’ defined but not used [-Wunused-const-variable=] 42 | static const double VERY_NEGATIVE_DOUBLE = -9e29; | ^~~~~~~~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/mbed.c -o clustal/mbed.o In file included from clustal/mbed.c:28: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal/muscle_tree.h:32, from clustal/mbed.h:22, from clustal/mbed.c:34: clustal/mbed.c: In function ‘FreeKMeansResult’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:163:5: note: in expansion of macro ‘CKFREE’ 163 | CKFREE((*prResult_p)->piNObjsPerCluster); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:165:9: note: in expansion of macro ‘CKFREE’ 165 | CKFREE((*prResult_p)->ppiObjIndicesPerCluster[iAux]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:166:9: note: in expansion of macro ‘CKFREE’ 166 | CKFREE((*prResult_p)->ppdClusterCenters[iAux]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:168:5: note: in expansion of macro ‘CKFREE’ 168 | CKFREE((*prResult_p)->ppiObjIndicesPerCluster); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:169:5: note: in expansion of macro ‘CKFREE’ 169 | CKFREE((*prResult_p)->ppdClusterCenters); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:172:5: note: in expansion of macro ‘CKFREE’ 172 | CKFREE(*prResult_p); | ^~~~~~ clustal/mbed.c: In function ‘NewKMeansResult’: clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:190:9: note: in expansion of macro ‘CKCALLOC’ 190 | CKCALLOC(1, sizeof(bisecting_kmeans_result_t)); | ^~~~~~~~ clustal/mbed.c: In function ‘SeqToVec’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:322:21: note: in expansion of macro ‘CKMALLOC’ 322 | piSortedSeeds = CKMALLOC(iNumSeeds * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:339:23: note: in expansion of macro ‘CKMALLOC’ 339 | restore = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:381:9: note: in expansion of macro ‘CKFREE’ 381 | CKFREE(piSortedSeeds); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:382:9: note: in expansion of macro ‘CKFREE’ 382 | CKFREE(restore); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:448:5: note: in expansion of macro ‘CKFREE’ 448 | CKFREE(piSortedSeeds); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:449:5: note: in expansion of macro ‘CKFREE’ 449 | CKFREE(restore); | ^~~~~~ clustal/mbed.c: In function ‘SeedSelection’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:498:9: note: in expansion of macro ‘CKFREE’ 498 | CKFREE(piPermArray); | ^~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:504:26: note: in expansion of macro ‘CKMALLOC’ 504 | int *piSeqLen = CKMALLOC(prMSeq->nseqs * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:505:24: note: in expansion of macro ‘CKMALLOC’ 505 | int *piOrder = CKMALLOC(prMSeq->nseqs * sizeof(int)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:525:9: note: in expansion of macro ‘CKFREE’ 525 | CKFREE(piSeqLen); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:530:9: note: in expansion of macro ‘CKFREE’ 530 | CKFREE(piOrder); | ^~~~~~ clustal/mbed.c: In function ‘BisectingKmeans’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:691:32: note: in expansion of macro ‘CKMALLOC’ 691 | piCurObjToUpdate = (int *) CKMALLOC(2 * sizeof(int)); | ^~~~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:697:36: note: in expansion of macro ‘CKCALLOC’ 697 | pdKClusterCenters = (double *) CKCALLOC(2 * iDim, sizeof(double)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:705:21: note: in expansion of macro ‘CKMALLOC’ 705 | (double **) CKMALLOC(1 * sizeof(double *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:707:20: note: in expansion of macro ‘CKMALLOC’ 707 | (double *) CKMALLOC(iDim * sizeof(double)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:710:17: note: in expansion of macro ‘CKMALLOC’ 710 | (int *) CKMALLOC(1 * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:714:18: note: in expansion of macro ‘CKMALLOC’ 714 | (int **) CKMALLOC(1 * sizeof(int *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:716:9: note: in expansion of macro ‘CKMALLOC’ 716 | CKMALLOC(iNObjs * sizeof(int)); | ^~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:739:45: note: in expansion of macro ‘CKREALLOC’ 739 | *ppcClusterSplits_p = (char **)CKREALLOC(*ppcClusterSplits_p, iNObjs*sizeof(char *)); | ^~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:740:45: note: in expansion of macro ‘CKMALLOC’ 740 | (*ppcClusterSplits_p)[0] = (char *)CKMALLOC(iNObjs*iLog2N2); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:806:13: note: in expansion of macro ‘CKMALLOC’ 806 | CKMALLOC(iNObjsInClusterToSplit * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:809:13: note: in expansion of macro ‘CKMALLOC’ 809 | CKMALLOC(iNObjsInClusterToSplit * iDim * sizeof(double)); | ^~~~~~~~ clustal/mbed.c:920:30: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 920 | __FUNCTION__, | ^~~~~~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:938:13: note: in expansion of macro ‘CKFREE’ 938 | CKFREE(piKClusterAssignments); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:939:13: note: in expansion of macro ‘CKFREE’ 939 | CKFREE(pdVectorsInClusterToSplit); | ^~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:956:13: note: in expansion of macro ‘CKREALLOC’ 956 | CKREALLOC((*prKMeansResult_p)->ppdClusterCenters, | ^~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:959:13: note: in expansion of macro ‘CKMALLOC’ 959 | CKMALLOC(iDim * sizeof(double)); | ^~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:982:13: note: in expansion of macro ‘CKREALLOC’ 982 | CKREALLOC((*prKMeansResult_p)->piNObjsPerCluster, | ^~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1025:46: note: in expansion of macro ‘CKMALLOC’ 1025 | piObjIndicesOfSplitCluster = (int *) CKMALLOC(iNObjsInClusterToSplit * sizeof(int)); | ^~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1031:13: note: in expansion of macro ‘CKREALLOC’ 1031 | CKREALLOC((*prKMeansResult_p)->ppiObjIndicesPerCluster, | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1036:21: note: in expansion of macro ‘CKREALLOC’ 1036 | (int *) CKREALLOC((*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot], | ^~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1040:21: note: in expansion of macro ‘CKMALLOC’ 1040 | (int *) CKMALLOC((*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] * sizeof(int)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1075:9: note: in expansion of macro ‘CKFREE’ 1075 | CKFREE(piObjIndicesOfSplitCluster); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1100:9: note: in expansion of macro ‘CKFREE’ 1100 | CKFREE(piKClusterAssignments); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1101:9: note: in expansion of macro ‘CKFREE’ 1101 | CKFREE(pdVectorsInClusterToSplit); | ^~~~~~ clustal/mbed.c:786:16: warning: variable ‘dCost’ set but not used [-Wunused-but-set-variable] 786 | double dCost = -1.0; | ^~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1117:5: note: in expansion of macro ‘CKFREE’ 1117 | CKFREE(pdKClusterCenters); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1118:5: note: in expansion of macro ‘CKFREE’ 1118 | CKFREE(piCurObjToUpdate); | ^~~~~~ clustal/mbed.c: In function ‘Mbed’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1213:23: note: in expansion of macro ‘CKMALLOC’ 1213 | piSeeds = (int *) CKMALLOC(iNumSeeds * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1218:29: note: in expansion of macro ‘CKMALLOC’ 1218 | ppdSeqVec = (double **) CKMALLOC(prMSeq->nseqs * sizeof(double *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1220:36: note: in expansion of macro ‘CKMALLOC’ 1220 | ppdSeqVec[iI] = (double *) CKMALLOC(iNumSeeds * sizeof(double)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1226:5: note: in expansion of macro ‘CKFREE’ 1226 | CKFREE(piSeeds); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1277:9: note: in expansion of macro ‘CKFREE’ 1277 | CKFREE(ppcClusterSplits[0]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1278:9: note: in expansion of macro ‘CKFREE’ 1278 | CKFREE(ppcClusterSplits); | ^~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1335:27: note: in expansion of macro ‘CKMALLOC’ 1335 | ppcLabels = (char **) CKMALLOC(prKMeansResult->iNClusters * sizeof(char*)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1337:34: note: in expansion of macro ‘CKMALLOC’ 1337 | ppcLabels[iI] = (char *) CKMALLOC(32 * sizeof(char)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1349:9: note: in expansion of macro ‘CKFREE’ 1349 | CKFREE(ppcLabels[iI]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1351:5: note: in expansion of macro ‘CKFREE’ 1351 | CKFREE(ppcLabels); | ^~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1375:9: note: in expansion of macro ‘CKMALLOC’ 1375 | CKMALLOC(prKMeansResult->iNClusters * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1445:13: note: in expansion of macro ‘CKMALLOC’ 1445 | CKMALLOC(prSubClusterMSeq->nseqs * sizeof(char *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1447:13: note: in expansion of macro ‘CKMALLOC’ 1447 | CKMALLOC(prSubClusterMSeq->nseqs * sizeof(char *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1449:13: note: in expansion of macro ‘CKMALLOC’ 1449 | CKMALLOC(prSubClusterMSeq->nseqs * sizeof(SQINFO)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/mbed.c:1530:30: note: in expansion of macro ‘CKMALLOC’ 1530 | ppcLabels = (char**) CKMALLOC(iNSeqInCluster * sizeof(char*)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1549:9: note: in expansion of macro ‘CKFREE’ 1549 | CKFREE(ppcLabels); /* don't free members, they just point */ | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1643:9: note: in expansion of macro ‘CKFREE’ 1643 | CKFREE(ppdSeqVec[iI]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1645:5: note: in expansion of macro ‘CKFREE’ 1645 | CKFREE(ppdSeqVec); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/mbed.c:1646:5: note: in expansion of macro ‘CKFREE’ 1646 | CKFREE(piClusterToTreeNode); | ^~~~~~ clustal/mbed.c: At top level: clustal/mbed.c:69:18: warning: ‘MAX_ALLOWED_SEQ_PER_PRECLUSTER’ defined but not used [-Wunused-const-variable=] 69 | static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/pair_dist.c -o clustal/pair_dist.o In file included from clustal/pair_dist.c:22: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition clustal/pair_dist.c: In function ‘KimuraCorrection’: clustal/pair_dist.c:137:68: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 137 | Log(&rLog, LOG_FATAL, "Internal error in %s:%s", __FILE__, __FUNCTION__); | ^~~~~~~~~~~~ clustal/pair_dist.c: In function ‘SquidIdPairDist’: clustal/pair_dist.c:185:68: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 185 | Log(&rLog, LOG_ERROR, "Sequences need to be aligned (%s)", __FUNCTION__); | ^~~~~~~~~~~~ clustal/pair_dist.c:206: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 206 | #pragma omp critical(squidid) clustal/pair_dist.c:218: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas] 218 | #pragma omp atomic clustal/pair_dist.c:228: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 228 | #pragma omp critical(squidid) clustal/pair_dist.c:177:10: warning: unused variable ‘bPrintCR’ [-Wunused-variable] 177 | bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; | ^~~~~~~~ clustal/pair_dist.c: In function ‘PairDistances’: clustal/pair_dist.c:336: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 336 | #pragma omp parallel for private(iChunk) schedule(dynamic) clustal/pair_dist.c:359: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 359 | #pragma omp parallel for private(iChunk) schedule(dynamic) clustal/pair_dist.c:376: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 376 | #pragma omp parallel for private(iChunk) schedule(dynamic) In file included from clustal/../clustal-omega.h:44, from clustal/pair_dist.c:31: clustal/../clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/pair_dist.c:400:26: note: in expansion of macro ‘CKMALLOC’ 400 | names = (char **)CKMALLOC(mseq->nseqs * sizeof(char*)); | ^~~~~~~~ clustal/../clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/pair_dist.c:409:9: note: in expansion of macro ‘CKFREE’ 409 | CKFREE(names); | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/progress.c -o clustal/progress.o In file included from clustal/progress.c:22: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal/progress.c:29: clustal/progress.c: In function ‘NewProgress’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/progress.c:61:37: note: in expansion of macro ‘CKMALLOC’ 61 | (*pprProgress) = (progress_t *) CKMALLOC(1*sizeof(progress_t)); | ^~~~~~~~ clustal/progress.c: In function ‘FreeProgress’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/progress.c:89:5: note: in expansion of macro ‘CKFREE’ 89 | CKFREE((*pprProgress)->pcPrefix); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/progress.c:92:5: note: in expansion of macro ‘CKFREE’ 92 | CKFREE(*pprProgress); | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/seq.c -o clustal/seq.o In file included from clustal/seq.c:30: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition clustal/seq.c: In function ‘AliStat’: clustal/seq.c:81:77: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 81 | "Cannot report all and sample at the same time. Skipping %s()", __FUNCTION__); | ^~~~~~~~~~~~ clustal/seq.c:86:57: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 86 | "Sequences are not aligned. Skipping %s()", __FUNCTION__); | ^~~~~~~~~~~~ clustal/seq.c:68:9: warning: unused variable ‘iAux’ [-Wunused-variable] 68 | int iAux; | ^~~~ In file included from clustal/seq.c:37: clustal/seq.c: In function ‘ShuffleMSeq’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:244:5: note: in expansion of macro ‘CKFREE’ 244 | CKFREE(piPermArray); | ^~~~~~ clustal/seq.c: In function ‘SeqTypeToStr’: clustal/seq.c:388:55: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 388 | Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__); | ^~~~~~~~~~~~ clustal/seq.c: In function ‘ReadSequences’: clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:487:13: note: in expansion of macro ‘CKREALLOC’ 487 | CKREALLOC(prMSeq->seq, (prMSeq->nseqs+1) * sizeof(char *)); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:492:13: note: in expansion of macro ‘CKREALLOC’ 492 | CKREALLOC(prMSeq->sqinfo, (prMSeq->nseqs+1) * sizeof(SQINFO)); | ^~~~~~~~~ clustal/seq.c:518:63: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 518 | Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__); | ^~~~~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:570:33: note: in expansion of macro ‘CKMALLOC’ 570 | prMSeq->orig_seq = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char *)); | ^~~~~~~~ clustal/seq.c: In function ‘ReadSequencesFromR’: clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:682:13: note: in expansion of macro ‘CKREALLOC’ 682 | CKREALLOC(prMSeq->seq, (prMSeq->nseqs+1) * sizeof(char *)); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:687:13: note: in expansion of macro ‘CKREALLOC’ 687 | CKREALLOC(prMSeq->sqinfo, (prMSeq->nseqs+1) * sizeof(SQINFO)); | ^~~~~~~~~ clustal/seq.c:714:63: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 714 | Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__); | ^~~~~~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:762:33: note: in expansion of macro ‘CKMALLOC’ 762 | prMSeq->orig_seq = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char *)); | ^~~~~~~~ clustal/seq.c: In function ‘NewMSeq’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:830:26: note: in expansion of macro ‘CKMALLOC’ 830 | *prMSeq = (mseq_t *) CKMALLOC(1 * sizeof(mseq_t)); | ^~~~~~~~ clustal/seq.c: In function ‘CopyMSeq’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:870:9: note: in expansion of macro ‘CKMALLOC’ 870 | CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:872:9: note: in expansion of macro ‘CKMALLOC’ 872 | CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:874:9: note: in expansion of macro ‘CKMALLOC’ 874 | CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(SQINFO)); | ^~~~~~~~ clustal/seq.c: In function ‘FreeRSeq’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:944:17: note: in expansion of macro ‘CKFREE’ 944 | CKFREE((*mseq)->filename); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:950:9: note: in expansion of macro ‘CKFREE’ 950 | CKFREE((*mseq)->orig_seq[i]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:953:9: note: in expansion of macro ‘CKFREE’ 953 | CKFREE((*mseq)->seq); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:956:9: note: in expansion of macro ‘CKFREE’ 956 | CKFREE((*mseq)->orig_seq); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:959:9: note: in expansion of macro ‘CKFREE’ 959 | CKFREE((*mseq)->sqinfo); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:964:9: note: in expansion of macro ‘CKFREE’ 964 | CKFREE((*mseq)->tree_order); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:970:5: note: in expansion of macro ‘CKFREE’ 970 | CKFREE((*mseq)); | ^~~~~~ clustal/seq.c: In function ‘SortMSeqByLength’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1180:24: note: in expansion of macro ‘CKMALLOC’ 1180 | piSeqLen = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1181:23: note: in expansion of macro ‘CKMALLOC’ 1181 | piOrder = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:1191:9: note: in expansion of macro ‘CKFREE’ 1191 | CKFREE(prMSeq->seq[iSeqIndex]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:1194:9: note: in expansion of macro ‘CKFREE’ 1194 | CKFREE(prMSeq->orig_seq[iSeqIndex]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:1200:5: note: in expansion of macro ‘CKFREE’ 1200 | CKFREE(piSeqLen); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/seq.c:1201:5: note: in expansion of macro ‘CKFREE’ 1201 | CKFREE(piOrder); | ^~~~~~ clustal/seq.c: In function ‘AddSeq’: clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1311:9: note: in expansion of macro ‘CKREALLOC’ 1311 | CKREALLOC((*prMSeqDest_p)->seq, (iSeqIdx+1) * sizeof(char *)); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1313:9: note: in expansion of macro ‘CKREALLOC’ 1313 | CKREALLOC((*prMSeqDest_p)->orig_seq, (iSeqIdx+1) * sizeof(char *)); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1315:9: note: in expansion of macro ‘CKREALLOC’ 1315 | CKREALLOC((*prMSeqDest_p)->sqinfo, (iSeqIdx+1) * sizeof(SQINFO)); | ^~~~~~~~~ clustal/seq.c: In function ‘JoinMSeqs’: clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1383:9: note: in expansion of macro ‘CKREALLOC’ 1383 | CKREALLOC((*prMSeqDest_p)->seq, iNewNSeq * sizeof(char *)); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1386:9: note: in expansion of macro ‘CKREALLOC’ 1386 | CKREALLOC((*prMSeqDest_p)->orig_seq, iNewNSeq * sizeof(char *)); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/seq.c:1389:9: note: in expansion of macro ‘CKREALLOC’ 1389 | CKREALLOC((*prMSeqDest_p)->sqinfo, iNewNSeq * sizeof(SQINFO)); | ^~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/symmatrix.c -o clustal/symmatrix.o In file included from clustal/symmatrix.c:30: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition clustal/symmatrix.c: In function ‘NewSymMatrix’: clustal/symmatrix.c:78:27: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 78 | __FILE__, __FUNCTION__); | ^~~~~~~~~~~~ clustal/symmatrix.c:85:27: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 85 | __FILE__, __FUNCTION__); | ^~~~~~~~~~~~ clustal/symmatrix.c:94:31: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 94 | __FILE__, __FUNCTION__); | ^~~~~~~~~~~~ clustal/symmatrix.c: In function ‘SymMatrixRead’: clustal/symmatrix.c:377:27: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 377 | __FILE__, __FUNCTION__, __LINE__); | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/tree.c -o clustal/tree.o In file included from clustal/tree.c:22: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal/tree.c:29: clustal/tree.c: In function ‘GuideTreeUpgma’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/tree.c:67:26: note: in expansion of macro ‘CKMALLOC’ 67 | (*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t)); | ^~~~~~~~ clustal/tree.c: In function ‘GuideTreeFromFile’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/tree.c:104:26: note: in expansion of macro ‘CKMALLOC’ 104 | (*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t)); | ^~~~~~~~ clustal/tree.c: In function ‘TraverseTree’: clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/tree.c:180:27: note: in expansion of macro ‘CKCALLOC’ 180 | *piOrderLR_p = (int *)CKCALLOC(DIFF_NODE * GetNodeCount(tree), sizeof(int)); | ^~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/util.c -o clustal/util.o In file included from clustal/util.c:22: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal/util.c:32: clustal/util.c: In function ‘CkStrdup’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/util.c:213:19: note: in expansion of macro ‘CKMALLOC’ 213 | cp = (char *) CKMALLOC(strlen(src) +1); | ^~~~~~~~ clustal/util.c: In function ‘PermutationArray’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/util.c:244:23: note: in expansion of macro ‘CKMALLOC’ 244 | (*perm) = (int *) CKMALLOC(len * sizeof(int)); | ^~~~~~~~ clustal/util.c: In function ‘RandomUniqueIntArray’: clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/util.c:300:24: note: in expansion of macro ‘CKCALLOC’ 300 | is_used = (bool *) CKCALLOC(max_value, sizeof(bool)); | ^~~~~~~~ clustal/util.c: In function ‘QSortAndTrackIndex’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/util.c:417:34: note: in expansion of macro ‘CKMALLOC’ 417 | prSort = (sortwithindex_t *) CKMALLOC(iArrayLen * sizeof(sortwithindex_t)); | ^~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal/weights.c -o clustal/weights.o In file included from clustal/weights.c:72: ./config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal/muscle_tree.h:32, from clustal/weights.c:77: clustal/weights.c: In function ‘CalcClustalWeights’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/weights.c:205:33: note: in expansion of macro ‘CKMALLOC’ 205 | (*pdWeights_p) = (double *) CKMALLOC(uNodeCount * sizeof(double)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/weights.c:220:9: note: in expansion of macro ‘CKFREE’ 220 | CKFREE(pdWeights_p); | ^~~~~~ clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/weights.c:233:34: note: in expansion of macro ‘CKCALLOC’ 233 | puLeavesUnderNode = (uint *) CKCALLOC(uNodeCount, sizeof(uint)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal/weights.c:246:30: note: in expansion of macro ‘CKMALLOC’ 246 | pdStrengths = (double *) CKMALLOC(uNodeCount * sizeof(double)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/weights.c:332:5: note: in expansion of macro ‘CKFREE’ 332 | CKFREE(puLeavesUnderNode); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal/weights.c:333:5: note: in expansion of macro ‘CKFREE’ 333 | CKFREE(pdStrengths); | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/a2m.c -o squid/a2m.o In file included from squid/squid.h:32, from squid/a2m.c:20: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition squid/a2m.c: In function ‘WriteA2M’: squid/a2m.c:113:9: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 113 | __FUNCTION__, __FILE__, __LINE__, cpl+20); | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/aligneval.c -o squid/aligneval.o In file included from squid/squid.h:32, from squid/aligneval.c:59: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/alignio.c -o squid/alignio.o In file included from squid/squid.h:32, from squid/alignio.c:21: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/clustal.c -o squid/clustal.o In file included from squid/squid.h:32, from squid/clustal.c:24: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition squid/clustal.c: In function ‘WriteClustal’: squid/clustal.c:226:11: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 226 | __FUNCTION__, __FILE__, __LINE__, msa->nseq); | ^~~~~~~~~~~~ squid/clustal.c:235:9: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 235 | __FUNCTION__, __FILE__, __LINE__, cpl+20); | ^~~~~~~~~~~~ squid/clustal.c:214:7: warning: unused variable ‘cons’ [-Wunused-variable] 214 | int cons; | ^~~~ squid/clustal.c: In function ‘WriteClustalForR’: squid/clustal.c:450:41: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 450 | __FUNCTION__, __FILE__, __LINE__, msa->nseq); | ^~~~~~~~~~~~ squid/clustal.c:459:33: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 459 | __FUNCTION__, __FILE__, __LINE__, cpl+20); | ^~~~~~~~~~~~ squid/clustal.c:438:13: warning: unused variable ‘cons’ [-Wunused-variable] 438 | int cons; | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/cluster.c -o squid/cluster.o In file included from squid/squid.h:32, from squid/cluster.c:124: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/dayhoff.c -o squid/dayhoff.o In file included from squid/squid.h:32, from squid/dayhoff.c:28: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/eps.c -o squid/eps.o In file included from squid/squid.h:32, from squid/eps.c:23: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/file.c -o squid/file.o In file included from squid/squid.h:32, from squid/file.c:28: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/getopt.c -o squid/getopt.o In file included from squid/squid.h:32, from squid/getopt.c:17: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/gki.c -o squid/gki.o In file included from squid/squid.h:32, from squid/gki.c:82: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/gsi.c -o squid/gsi.o In file included from squid/squid.h:32, from squid/gsi.c:35: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/gsi64.c -o squid/gsi64.o squid/gsi64.c:395: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/hsregex.c -o squid/hsregex.o In file included from squid/squid.h:32, from squid/hsregex.c:33: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/iupac.c -o squid/iupac.o In file included from squid/squid.h:32, from squid/iupac.c:17: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/msa.c -o squid/msa.o In file included from squid/squid.h:32, from squid/msa.c:22: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/msf.c -o squid/msf.o In file included from squid/squid.h:32, from squid/msf.c:25: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition squid/msf.c: In function ‘ReadMSF’: squid/msf.c:87:11: warning: variable ‘alleged_checksum’ set but not used [-Wunused-but-set-variable] 87 | int alleged_checksum; | ^~~~~~~~~~~~~~~~ squid/msf.c:85:11: warning: variable ‘alleged_alen’ set but not used [-Wunused-but-set-variable] 85 | int alleged_alen; | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/phylip.c -o squid/phylip.o In file included from squid/squid.h:32, from squid/phylip.c:23: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition squid/phylip.c: In function ‘ReadPhylip’: squid/phylip.c:80:15: warning: variable ‘alen’ set but not used [-Wunused-but-set-variable] 80 | int nseq, alen; | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/revcomp.c -o squid/revcomp.o In file included from squid/squid.h:32, from squid/revcomp.c:19: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/rk.c -o squid/rk.o In file included from squid/squid.h:32, from squid/rk.c:26: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/selex.c -o squid/selex.o In file included from squid/squid.h:32, from squid/selex.c:43: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/seqencode.c -o squid/seqencode.o In file included from squid/squid.h:32, from squid/seqencode.c:18: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/shuffle.c -o squid/shuffle.o In file included from squid/squid.h:32, from squid/shuffle.c:42: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/sqerror.c -o squid/sqerror.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/sqio.c -o squid/sqio.o In file included from squid/squid.h:32, from squid/sqio.c:57: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/squidcore.c -o squid/squidcore.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/sre_ctype.c -o squid/sre_ctype.o In file included from squid/squid.h:32, from squid/sre_ctype.c:19: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/sre_math.c -o squid/sre_math.o In file included from squid/squid.h:32, from squid/sre_math.c:19: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/sre_random.c -o squid/sre_random.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/sre_string.c -o squid/sre_string.o In file included from squid/squid.h:32, from squid/sre_string.c:23: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/ssi.c -o squid/ssi.o In file included from squid/squid.h:32, from squid/ssi.c:16: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition squid/ssi.c: In function ‘SSIAddPrimaryKeyToIndex’: squid/ssi.c:751:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=] 751 | fprintf(g->ptmp, "%s\t%d\t%" PRIu64 "\t%" PRIu64 "\t%lu\n", | ^~~~~~~~~~~ 752 | key, fh, (unsigned long long)r_off->off.i64, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int In file included from squid/ssi.c:20: /usr/include/inttypes.h:105:41: note: format string is defined here 105 | # define PRIu64 __PRI64_PREFIX "u" squid/ssi.c:751:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=] 751 | fprintf(g->ptmp, "%s\t%d\t%" PRIu64 "\t%" PRIu64 "\t%lu\n", | ^~~~~~~~~~~ 752 | key, fh, (unsigned long long)r_off->off.i64, 753 | d_off == NULL ? 0 : (unsigned long long) d_off->off.i64, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int /usr/include/inttypes.h:105:41: note: format string is defined here 105 | # define PRIu64 __PRI64_PREFIX "u" squid/ssi.c: In function ‘activate_external_sort’: squid/ssi.c:1407:24: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=] 1407 | fprintf(g->ptmp, "%s\t%u\t%" PRIu64 "\t%" PRIu64 "\t%lu\n", | ^~~~~~~~~~~ 1408 | g->pkeys[i].key, g->pkeys[i].fnum, 1409 | (unsigned long long) g->pkeys[i].r_off.off.i64, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int /usr/include/inttypes.h:105:41: note: format string is defined here 105 | # define PRIu64 __PRI64_PREFIX "u" squid/ssi.c:1407:24: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=] 1407 | fprintf(g->ptmp, "%s\t%u\t%" PRIu64 "\t%" PRIu64 "\t%lu\n", | ^~~~~~~~~~~ ...... 1410 | (unsigned long long) g->pkeys[i].d_off.off.i64, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int /usr/include/inttypes.h:105:41: note: format string is defined here 105 | # define PRIu64 __PRI64_PREFIX "u" gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/stack.c -o squid/stack.o In file included from squid/squid.h:32, from squid/stack.c:18: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/stockholm.c -o squid/stockholm.o In file included from squid/squid.h:32, from squid/stockholm.c:31: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/stopwatch.c -o squid/stopwatch.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/translate.c -o squid/translate.o In file included from squid/squid.h:32, from squid/translate.c:19: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/types.c -o squid/types.o In file included from squid/squid.h:32, from squid/types.c:20: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/vectorops.c -o squid/vectorops.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c squid/weight.c -o squid/weight.o In file included from squid/squid.h:32, from squid/weight.c:19: squid/../config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -pedantic -mtune=native -c hhalign/hhalign.cpp -o hhalign/hhalign.o In file included from hhalign/hhalign.cpp:68: hhalign/util-C.h: In function ‘float fast_log2(float)’: hhalign/util-C.h:94:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 94 | int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f; | ~^~~~~~~~~~ hhalign/util-C.h:95:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 95 | int b = ((*((int *)&x)) & 0x007FE000) >>13; | ~^~~~~~~~~~ hhalign/util-C.h:96:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 96 | int c = ((*((int *)&x)) & 0x00001FFF); | ~^~~~~~~~~~ hhalign/util-C.h: In function ‘float fpow2(float)’: hhalign/util-C.h:111:14: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 111 | int lx = *((int*)&tx) - 0x4b400000; // integer value of x | ~^~~~~~~~~~ hhalign/util-C.h: In function ‘float fast_pow2(float)’: hhalign/util-C.h:158:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 158 | pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024) | ~^~~~~~~~~~~~~~~~~~~~~ hhalign/util-C.h:202:12: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 202 | return *((float*)&y); | ~^~~~~~~~~~~ In file included from hhalign/hhalign.cpp:70: hhalign/hash-C.h: In member function ‘void Hash::Print()’: hhalign/hash-C.h:485:8: warning: ISO C++ forbids variable length array ‘key’ [-Wvla] 485 | char key[MaxLen()+1]; | ^~~ In file included from hhalign/hhalign.cpp:82: hhalign/hhhmm-C.h: In member function ‘int HMM::ReadHMMer3(FILE*, char*)’: hhalign/hhhmm-C.h:1141:12: warning: variable ‘dAlphaInv’ set but not used [-Wunused-but-set-variable] 1141 | double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */ | ^~~~~~~~~ hhalign/hhhmm-C.h: In member function ‘void HMM::UseSecStrucDependentGapPenalties()’: hhalign/hhhmm-C.h:1734:17: warning: ISO C++ forbids variable length array ‘iis’ [-Wvla] 1734 | unsigned char iis[par.maxResLen]; // inside-integer array | ^~~ hhalign/hhhmm-C.h: In member function ‘void HMM::WriteToFileHMMER(char*)’: hhalign/hhhmm-C.h:2206:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2206 | for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n"); | ^~~ hhalign/hhhmm-C.h:2206:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2206 | for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n"); | ^~~~~~~ In file included from hhalign/hhalign.cpp:83: hhalign/hhalignment-C.h: In member function ‘void Alignment::Read(FILE*, char*, char*)’: hhalign/hhalignment-C.h:245:32: warning: variable ‘ptr2’ set but not used [-Wunused-but-set-variable] 245 | char *ptr1, *ptr2; | ^~~~ hhalign/hhalignment-C.h: In member function ‘int Alignment::FilterWithCoreHMM(char*, float, HMM&)’: hhalign/hhalignment-C.h:1429:19: warning: variable ‘score_M’ set but not used [-Wunused-but-set-variable] 1429 | float score_M=0.0; | ^~~~~~~ hhalign/hhalignment-C.h:1430:19: warning: variable ‘score_prev’ set but not used [-Wunused-but-set-variable] 1430 | float score_prev=0.0; | ^~~~~~~~~~ hhalign/hhalignment-C.h: In member function ‘void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)’: hhalign/hhalignment-C.h:1905:18: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1905 | if (ncol=NCOLMIN) | ^ hhalign/hhalignment-C.h: In member function ‘void Alignment::Transitions_from_D_state(HMM&, char*)’: hhalign/hhalignment-C.h:2344:32: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2344 | if (ncol='a' && q.fam[0]<='k' && q.fam[1]=='.') | ~~^~~ In file included from hhalign/hhalign.cpp:76: hhalign/hhhmm.h:53:8: note: ‘HMM::fam’ declared here 53 | char fam[NAMELEN]; // family ID (derived from name) (FAM field) | ^~~ hhalign/hhhitlist-C.h: In member function ‘void HitList::CalculateHHblastCorrelation(HMM&)’: hhalign/hhhitlist-C.h:840:9: warning: the address of ‘HMM::fam’ will never be NULL [-Waddress] 840 | if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') | ~~^~~ hhalign/hhhmm.h:53:8: note: ‘HMM::fam’ declared here 53 | char fam[NAMELEN]; // family ID (derived from name) (FAM field) | ^~~ hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring()’: hhalign/hhhitlist-C.h:1259:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable] 1259 | size_t unused; /* disable fread gcc warning */ | ^~~~~~ hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring2()’: hhalign/hhhitlist-C.h:1624:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable] 1624 | size_t unused; /* disable fread gcc warning */ | ^~~~~~ hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring3()’: hhalign/hhhitlist-C.h:1994:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable] 1994 | size_t unused; /* disable fread gcc warning */ | ^~~~~~ hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring4()’: hhalign/hhhitlist-C.h:2359:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable] 2359 | size_t unused; /* disable fread gcc warning */ | ^~~~~~ In file included from hhalign/hhalign.cpp:88: hhalign/hhfunc-C.h: In function ‘void AddBackgroundFrequencies(float**, float**, float**, int, hmm_light*, char**, char*, int, char*)’: hhalign/hhfunc-C.h:74:9: warning: unused variable ‘iT’ [-Wunused-variable] 74 | int iT; /* transition state iterator */ | ^~ hhalign/hhfunc-C.h:80:11: warning: unused variable ‘fGThgiew’ [-Wunused-variable] 80 | float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */ | ^~~~~~~~ hhalign/hhfunc-C.h:85:11: warning: unused variable ‘zf1SeqTrans’ [-Wunused-variable] 85 | float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75}; | ^~~~~~~~~~~ hhalign/hhfunc-C.h:86:11: warning: unused variable ‘zf1SeqInit’ [-Wunused-variable] 86 | float zf1SeqInit[] = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01}; | ^~~~~~~~~~ hhalign/hhfunc-C.h:87:11: warning: unused variable ‘zf1SeqDel’ [-Wunused-variable] 87 | float zf1SeqDel[] = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01}; | ^~~~~~~~~ hhalign/hhfunc-C.h:88:11: warning: unused variable ‘zf1SeqRevrt’ [-Wunused-variable] 88 | float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01}; | ^~~~~~~~~~~ hhalign/hhfunc-C.h: In function ‘int ReadAndPrepare(int, char**, int, hmm_light*, char*, char*, double*, char*, HMM&, Alignment*)’: hhalign/hhfunc-C.h:328:17: warning: unused variable ‘NEFF_SCORE’ [-Wunused-variable] 328 | const int NEFF_SCORE = 10; /* FIXME: Magic Number */ | ^~~~~~~~~~ hhalign/hhfunc-C.h:511:17: warning: unused variable ‘NEFF_SCORE’ [-Wunused-variable] 511 | const int NEFF_SCORE = 10; /* FIXME: Magic Number */ | ^~~~~~~~~~ hhalign/hhfunc-C.h:561:30: warning: format ‘%p’ expects argument of type ‘void*’, but argument 5 has type ‘char**’ [-Wformat=] 561 | "\tppcProf=%p, #seq=%d, ppcProf[0][0]=%c\n" | ~^ | | | void* 562 | , __FUNCTION__, __FILE__, __LINE__ 563 | , ppcProf, iCnt, ppcProf[0][0]); | ~~~~~~~ | | | char** hhalign/hhalign.cpp: In function ‘int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)’: hhalign/hhalign.cpp:727:9: warning: variable ‘Nali’ set but not used [-Wunused-but-set-variable] 727 | int Nali; /* number of normally backtraced alignments | ^~~~ hhalign/hhhmm-C.h: In member function ‘int HMM::Read(FILE*, char*)’: hhalign/hhhmm-C.h:294:20: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ output may be truncated copying between 0 and 510 bytes from a string of length 262139 [-Wstringop-truncation] 294 | strncat(file,ptr,NAMELEN-1-strlen(file)); // append file name read from file to path | ^ hhalign/hhhmm-C.h:285:27: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 254 bytes from a string of length 262140 [-Wstringop-truncation] 285 | if (ptr) strncpy(fam,ptr,IDLEN-1); else strcpy(fam,""); //copy family name to basename | ^ hhalign/hhhmm-C.h:269:22: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation] 269 | strncpy(longname,ptr,DESCLEN-1); //copy full name to longname | ^ hhalign/hhhmm-C.h: In member function ‘int HMM::ReadHMMer(FILE*, char*)’: hhalign/hhhmm-C.h:668:18: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation] 668 | strncpy(name,ptr,NAMELEN-1); // copy full name to name | ^ hhalign/hhhmm-C.h:684:22: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation] 684 | strncpy(desc,ptr,DESCLEN-1); // copy description to name... | ^ hhalign/hhhmm-C.h:676:18: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation] 676 | strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname... | ^ hhalign/hhhmm-C.h:1006:10: warning: ‘char* __builtin_strncat(char*, const char*, long unsigned int)’ output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation] 1006 | strncat(longname,desc,DESCLEN-strlen(longname)-1); | ^ hhalign/hhhmm-C.h: In member function ‘int HMM::ReadHMMer3(FILE*, char*)’: hhalign/hhhmm-C.h:1167:25: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation] 1167 | strncpy(name,ptr,NAMELEN-1); // copy full name to name | ^ hhalign/hhhmm-C.h:1183:33: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation] 1183 | strncpy(desc,ptr,DESCLEN-1); // copy description to name... | ^ hhalign/hhhmm-C.h:1175:25: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation] 1175 | strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname... | ^ hhalign/hhhmm-C.h:1500:9: warning: ‘char* __builtin_strncat(char*, const char*, long unsigned int)’ output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation] 1500 | strncat(longname,desc,DESCLEN-strlen(longname)-1); | ^ hhalign/hhhmm-C.h: In member function ‘void HMM::UseSecStrucDependentGapPenalties()’: hhalign/hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1748 | iis[0]=iis[L]=0; | ~~~~~~^~ hhalign/hhhmm-C.h:1734:17: note: at offset [-2147483648, -1] into destination object ‘iis’ of size [0, 2147483647] 1734 | unsigned char iis[par.maxResLen]; // inside-integer array | ^~~ hhalign/hhalignment-C.h: In member function ‘void Alignment::Read(FILE*, char*, char*)’: hhalign/hhalignment-C.h:247:26: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 32764 bytes from a string of length 262142 [-Wstringop-truncation] 247 | strncpy(longname,ptr1,DESCLEN-1); // copy whole commentary line after '# ' into longname | ^ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -pedantic -mtune=native -c RClustalOmega.cpp -o RClustalOmega.o In file included from RClustalOmega.cpp:27: config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mymain.c -o mymain.o In file included from mymain.c:22: config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal-omega.h:44, from mymain.c:35: mymain.c: In function ‘FreeUserOpts’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ mymain.c:228:9: note: in expansion of macro ‘CKFREE’ 228 | CKFREE(user_opts->pcSeqInfile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ mymain.c:231:9: note: in expansion of macro ‘CKFREE’ 231 | CKFREE(user_opts->pcProfile1Infile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ mymain.c:234:9: note: in expansion of macro ‘CKFREE’ 234 | CKFREE(user_opts->pcProfile2Infile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ mymain.c:237:9: note: in expansion of macro ‘CKFREE’ 237 | CKFREE(user_opts->pcAlnOutfile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ mymain.c:240:9: note: in expansion of macro ‘CKFREE’ 240 | CKFREE(user_opts->pcLogFile); | ^~~~~~ mymain.c: In function ‘ParseCommandLine’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ mymain.c:762:53: note: in expansion of macro ‘CKMALLOC’ 762 | user_opts->aln_opts.ppcHMMInput = (char **) CKMALLOC( | ^~~~~~~~ mymain.c: In function ‘executeClustalOmega’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ mymain.c:1171:41: note: in expansion of macro ‘CKMALLOC’ 1171 | prMSeq->tree_order = (int *)CKMALLOC(prMSeq->nseqs * sizeof(int)); | ^~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clustal-omega.c -o clustal-omega.o In file included from clustal-omega.c:22: config.h:132:9: warning: "NDEBUG" redefined 132 | #define NDEBUG /**/ | ^~~~~~ : note: this is the location of the previous definition In file included from clustal-omega.h:44, from clustal-omega.c:27: clustal-omega.c: In function ‘FreeAlnOpts’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:165:9: note: in expansion of macro ‘CKFREE’ 165 | CKFREE(prAlnOpts->pcGuidetreeInfile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:168:9: note: in expansion of macro ‘CKFREE’ 168 | CKFREE(prAlnOpts->pcGuidetreeOutfile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:171:9: note: in expansion of macro ‘CKFREE’ 171 | CKFREE(prAlnOpts->pcDistmatOutfile); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:174:9: note: in expansion of macro ‘CKFREE’ 174 | CKFREE(prAlnOpts->pcDistmatInfile); | ^~~~~~ clustal-omega.c: At top level: clustal-omega.c:321:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 321 | HmmerVersion() | ^~~~~~~~~~~~ clustal-omega.c: In function ‘AlnToHHMFile’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:417:9: note: in expansion of macro ‘CKFREE’ 417 | CKFREE(tmp_aln); | ^~~~~~ clustal-omega.c: In function ‘AlnToHMMFile’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:515:9: note: in expansion of macro ‘CKFREE’ 515 | CKFREE(tmp_aln); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:528:9: note: in expansion of macro ‘CKFREE’ 528 | CKFREE(tmp_aln); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:536:9: note: in expansion of macro ‘CKFREE’ 536 | CKFREE(tmp_hmm); | ^~~~~~ clustal-omega.c: In function ‘AlnToHMM’: clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:575:9: note: in expansion of macro ‘CKFREE’ 575 | CKFREE(pcHMM); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:584:9: note: in expansion of macro ‘CKFREE’ 584 | CKFREE(pcHMM); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:602:9: note: in expansion of macro ‘CKFREE’ 602 | CKFREE(pcHMM); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:609:5: note: in expansion of macro ‘CKFREE’ 609 | CKFREE(pcHMM); | ^~~~~~ clustal-omega.c: In function ‘SequentialAlignmentOrder’: clustal/util.h:30:43: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 30 | #define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal-omega.c:671:29: note: in expansion of macro ‘CKCALLOC’ 671 | (*piOrderLR_p) = (int *)CKCALLOC(DIFF_NODE * uNodes, sizeof(int)); | ^~~~~~~~ clustal-omega.c: In function ‘AlignmentOrder’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal-omega.c:786:33: note: in expansion of macro ‘CKMALLOC’ 786 | (*piOrderLR_p) = (int*) CKMALLOC(DIFF_NODE * 3 * sizeof(int)); | ^~~~~~~~ clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal-omega.c:848:35: note: in expansion of macro ‘CKMALLOC’ 848 | labels = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char*)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:856:17: note: in expansion of macro ‘CKFREE’ 856 | CKFREE(labels); | ^~~~~~ clustal-omega.c: In function ‘Align’: clustal/util.h:29:35: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 29 | #define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal-omega.c:1038:32: note: in expansion of macro ‘CKMALLOC’ 1038 | prHMMs = (hmm_light *) CKMALLOC(prOpts->iHMMInputFiles * sizeof(hmm_light)); | ^~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1073:13: note: in expansion of macro ‘CKFREE’ 1073 | CKFREE(prOpts->ppcHMMInput[iHMMInfileIndex]); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1075:9: note: in expansion of macro ‘CKFREE’ 1075 | CKFREE(prOpts->ppcHMMInput); | ^~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal-omega.c:1102:36: note: in expansion of macro ‘CKREALLOC’ 1102 | prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light))); | ^~~~~~~~~ clustal/util.h:31:45: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 31 | #define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) | ^~~~~~~~~~~~ clustal-omega.c:1127:36: note: in expansion of macro ‘CKREALLOC’ 1127 | prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light))); | ^~~~~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1259:17: note: in expansion of macro ‘CKFREE’ 1259 | CKFREE(piOrderLR); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1261:17: note: in expansion of macro ‘CKFREE’ 1261 | CKFREE(pdSeqWeights); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1365:9: note: in expansion of macro ‘CKFREE’ 1365 | CKFREE(piOrderLR); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1368:9: note: in expansion of macro ‘CKFREE’ 1368 | CKFREE(pdSeqWeights); | ^~~~~~ clustal/util.h:32:36: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic] 32 | #define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) | ^~~~~~~~~~~~ clustal-omega.c:1374:9: note: in expansion of macro ‘CKFREE’ 1374 | CKFREE(prHMMs); | ^~~~~~ clustal-omega.c: At top level: clustal-omega.c:134:18: warning: ‘ITERATION_SCORE_IMPROVEMENT_THRESHOLD’ defined but not used [-Wunused-const-variable=] 134 | static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o libClustalOmega.so exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR /usr/bin/ld: clustal-omega.o: in function `AlnToHHMFile': /home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalOmega/src/clustal-omega.c:389:(.text+0x53c): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalOmega/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalOmega' ---------------------------------------- ------------- ClustalOmega ------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o msa.so R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive -lpthread -L/home/hornik/tmp/R-d-gcc-14/lib -lR /usr/bin/ld: ./libClustalW.a(Iteration.o): in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': /home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231:(.text+0xfe1): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /usr/bin/ld: ./libClustalOmega.a(clustal-omega.o): in function `AlnToHHMFile': /home/hornik/tmp/scratch/RtmpfN91UL/R.INSTALL351602f3ed760/msa/src/ClustalOmega/src/clustal-omega.c:389:(.text+0x53c): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-msa/00new/msa/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (msa) checking bio3d_2.4-5.tar.gz ... Depends: Package: bio3d Depends: R (>= 3.1.0) Imports: Rcpp, parallel, grid, graphics, grDevices, stats, utils LinkingTo: Rcpp Timings: user system elapsed bio3d 124.311 7.287 134.383 Results: Check status summary: NOTE Source packages 1 Check results summary: bio3d ... NOTE * checking CRAN incoming feasibility ... [7s/8s] NOTE