downloading reverse dependencies ... downloading aplotExtra_0.0.3.tar.gz ... ok downloading fanyi_0.0.7.tar.gz ... ok downloading ggfun_0.1.8.tar.gz ... ok downloading ggplotify_0.1.2.tar.gz ... ok downloading ggtangle_0.0.6.tar.gz ... ok downloading ggVennDiagram_1.5.2.tar.gz ... ok downloading mirrorselect_0.0.3.tar.gz ... ok downloading rvcheck_0.2.1.tar.gz ... ok downloading scatterpie_0.2.4.tar.gz ... ok downloading seqmagick_0.1.7.tar.gz ... ok downloading shinyTempSignal_0.0.8.tar.gz ... ok downloading tidytree_0.4.6.tar.gz ... ok downloading wget_0.0.3.tar.gz ... ok downloading wikiprofiler_0.1.5.tar.gz ... ok installing dependencies ‘ggprism’, ‘ggstar’, ‘maftools’, ‘muscle’, ‘pillar’, ‘SSEparser’, ‘yulab.utils’ begin installing package ‘maftools’ begin installing package ‘pillar’ begin installing package ‘SSEparser’ begin installing package ‘muscle’ begin installing package ‘yulab.utils’ * installing *source* package ‘SSEparser’ ... ** package ‘SSEparser’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SSEparser) * installing *source* package ‘yulab.utils’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (yulab.utils) * installing *source* package ‘pillar’ ... ** package ‘pillar’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pillar) begin installing package ‘ggstar’ begin installing package ‘ggprism’ * installing *source* package ‘ggstar’ ... ** package ‘ggstar’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggstar) * installing *source* package ‘ggprism’ ... ** package ‘ggprism’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggprism) make: *** [Makefile:20: muscle.ts] Error 1 * installing *source* package ‘maftools’ ... ** package ‘maftools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7HPkjR/R.INSTALL1a966b11f7b9d3/maftools/src' gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ntcounts.c -o ntcounts.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c snpcounts.c -o snpcounts.o snpcounts.c: In function ‘snpcounts’: snpcounts.c:89:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 89 | fprintf(tsv_fp, "#idxstats_mapped_reads\t%llu\n", tot_mapped); | ~~~^ ~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c somaticfreq.c -o somaticfreq.o gcc-14 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7HPkjR/R.INSTALL1a966b11f7b9d3/maftools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-maftools/00new/maftools/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 (maftools) make: Target 'all' not remade because of errors. * installing *source* package ‘muscle’ ... ** package ‘muscle’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmWIiNt/R.INSTALL1a96724531d855/muscle/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c aligntwomsas.cpp -o aligntwomsas.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c aligntwoprofs.cpp -o aligntwoprofs.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c aln.cpp -o aln.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c blosum62.cpp -o blosum62.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c clwwt.cpp -o clwwt.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c cons.cpp -o cons.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c diaglist.cpp -o diaglist.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c diffpaths.cpp -o diffpaths.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c difftreese.cpp -o difftreese.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c distcalc.cpp -o distcalc.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c distfunc.cpp -o distfunc.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c distpwkimura.cpp -o distpwkimura.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c domuscle.cpp -o domuscle.o In file included from muscle.h:34, from domuscle.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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dosp.cpp -o dosp.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c drawtree.cpp -o drawtree.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c edgelist.cpp -o edgelist.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c enumopts.cpp -o enumopts.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c enumtostr.cpp -o enumtostr.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fasta2.cpp -o fasta2.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastclust.cpp -o fastclust.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastdist.cpp -o fastdist.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastdistjones.cpp -o fastdistjones.o In file included from muscle.h:34, from fastdistjones.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ fastdistjones.cpp: In function ‘void DistKmer20_3(const SeqVect&, DistFunc&)’: fastdistjones.cpp:158:18: warning: ‘void operator delete [](void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 158 | delete[] SeqList; | ^~~~~~~ fastdistjones.cpp:121:60: note: returned from ‘void* malloc(size_t)’ 121 | unsigned short *SeqList = (unsigned short *) malloc(uSeqListBytes); | ~~~~~~^~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastdistkbit.cpp -o fastdistkbit.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastdistmafft.cpp -o fastdistmafft.o fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’: fastdistmafft.cpp:238:29: warning: unused variable ‘pName1’ [-Wunused-variable] 238 | 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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastscorepath2.cpp -o fastscorepath2.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalign.cpp -o glbalign.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalign352.cpp -o glbalign352.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbaligndiag.cpp -o glbaligndiag.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalignla.cpp -o glbalignla.o In file included from muscle.h:34, from glbalignla.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignla.cpp: In function ‘SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’: glbalignla.cpp:363:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 363 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignla.cpp:330:26: note: ‘uInsertPos’ was declared here 330 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignla.cpp:424:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 424 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignla.cpp:397:18: note: ‘uInsertPos’ was declared here 397 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalignle.cpp -o glbalignle.o In file included from muscle.h:34, 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:427:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 427 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignle.cpp:400:18: note: ‘uInsertPos’ was declared here 400 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalignns.cpp -o glbalignns.o In file included from muscle.h:34, from glbalignns.cpp:1: intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignns.cpp: In function ‘SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’: glbalignns.cpp:305:52: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 305 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignns.cpp:272:26: note: ‘uInsertPos’ was declared here 272 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignns.cpp:366:30: warning: ‘uInsertPos’ may be used uninitialized [-Wmaybe-uninitialized] 366 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignns.cpp:339:18: note: ‘uInsertPos’ was declared here 339 | unsigned uInsertPos; | ^~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalignsp.cpp -o glbalignsp.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c glbalignspn.cpp -o glbalignspn.o In file included from muscle.h:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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:34, 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/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c globals.cpp -o globals.o globals.cpp: In function ‘void Quit(const char*, ...)’: globals.cpp:107:9: error: ‘error’ was not declared in this scope; did you mean ‘perror’? 107 | error("error in muscle\n"); | ^~~~~ | perror In file included from muscle.h:34, from globals.cpp:6: 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) | ^~~~~~~~~~~~~ make[1]: *** [/home/hornik/tmp/R/etc/Makeconf:202: globals.o] Error 1 make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmWIiNt/R.INSTALL1a96724531d855/muscle/src' ERROR: compilation failed for package ‘muscle’ * removing ‘/home/hornik/tmp/CRAN_recheck/Library/muscle’ Warning in (function (pkgs, lib, repos = getOption("repos"), contriburl = contrib.url(repos, : installation of package ‘muscle’ failed Calls: -> do.call -> checking yulab.utils_0.1.9.tar.gz ... checking aplotExtra_0.0.3.tar.gz ... checking fanyi_0.0.7.tar.gz ... checking ggfun_0.1.8.tar.gz ... checking ggplotify_0.1.2.tar.gz ... checking ggtangle_0.0.6.tar.gz ... checking ggVennDiagram_1.5.2.tar.gz ... checking mirrorselect_0.0.3.tar.gz ... checking rvcheck_0.2.1.tar.gz ... checking scatterpie_0.2.4.tar.gz ... checking seqmagick_0.1.7.tar.gz ... checking shinyTempSignal_0.0.8.tar.gz ... checking tidytree_0.4.6.tar.gz ... checking wget_0.0.3.tar.gz ... checking wikiprofiler_0.1.5.tar.gz ... Depends: Package: yulab.utils Imports: cli, digest, fs, rlang, tools, utils Timings: user system elapsed yulab.utils 20.924 2.693 25.391 Results: Check status summary: OK Source packages 1 Reverse depends 14 Check results summary: yulab.utils ... OK rdepends_aplotExtra ... OK rdepends_fanyi ... OK rdepends_ggfun ... OK rdepends_ggplotify ... OK rdepends_ggtangle ... OK rdepends_ggVennDiagram ... OK rdepends_mirrorselect ... OK rdepends_rvcheck ... OK rdepends_scatterpie ... OK rdepends_seqmagick ... OK rdepends_shinyTempSignal ... OK rdepends_tidytree ... OK rdepends_wget ... OK rdepends_wikiprofiler ... OK