installing dependencies ‘dada2’, ‘DECIPHER’ also installing the dependency ‘ShortRead’ begin installing package ‘ShortRead’ begin installing package ‘DECIPHER’ * installing *source* package ‘ShortRead’ ... ** this is package ‘ShortRead’ version ‘1.67.1’ ** package ‘ShortRead’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc-15 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-15 accepts -g... yes checking for gcc-15 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc-15 -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 size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-4) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIayC6I/R.INSTALL105b8d368368a8/ShortRead/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_ShortRead.c -o R_init_ShortRead.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphabet.c -o alphabet.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c count.c -o count.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io.c -o io.o io.c: In function ‘read_prb_as_character’: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function ‘_read_solexa_export_file’: io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_bowtie.c -o io_bowtie.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_soap.c -o io_soap.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler.c -o sampler.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trim.c -o trim.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xsnap.c -o xsnap.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIayC6I/R.INSTALL105b8d368368a8/ShortRead/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-ShortRead/00new/ShortRead/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 (ShortRead) begin installing package ‘dada2’ * installing *source* package ‘DECIPHER’ ... ** this is package ‘DECIPHER’ version ‘3.5.0’ ** package ‘DECIPHER’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-4) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWI1aOB/R.INSTALL105b8f73926db0/DECIPHER/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’: AlignProfiles.c:438:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized] 438 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:51: note: ‘lGs’ was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:436:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized] 436 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:46: note: ‘lGp’ was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’: AlignProfiles.c:1291:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized] 1291 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:51: note: ‘lGs’ was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1289:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized] 1289 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:46: note: ‘lGp’ was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfiles’: AlignProfiles.c:82:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized] 82 | double *subM; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c AssignIndels.c -o AssignIndels.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CalculateDeltaG.c -o CalculateDeltaG.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CalculateFISH.c -o CalculateFISH.o CalculateFISH.c: In function ‘calculateFISH’: CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces] 25 | double dH_DR[4][4] = { | ^ 26 | -11.5, -7.8, -7, -8.3, | { } 27 | -10.4, -12.8, -16.3, -9.1, | { } 28 | -8.6, -8, -9.3, -5.9, | { } 29 | -7.8, -5.5, -9, -7.8 | { 30 | }; | } CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces] 31 | double dS_DR[4][4] = { | ^ 32 | -36.4, -21.6, -19.7, -23.9, | { } 33 | -28.4, -31.9, -47.1, -23.5, | { } 34 | -22.9, -17.1, -23.2, -12.3, | { } 35 | -23.2, -13.5, -26.1, -21.9 | { 36 | }; | } CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces] 37 | double dH_DD[4][4] = { | ^ 38 | -7.9, -8.4, -7.8, -7.2, | { } 39 | -8.5, -8, -10.6, -7.8, | { } 40 | -8.2, -9.8, -8, -8.4, | { } 41 | -7.2, -8.2, -8.5, -7.9 | { 42 | }; | } CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces] 43 | double dS_DD[4][4] = { | ^ 44 | -22.2, -22.4, -21, -20.4, | { } 45 | -22.7, -19.9, -27.2, -21, | { } 46 | -22.2, -24.4, -19.9, -22.4, | { } 47 | -21.3, -22.2, -22.7, -22.2 | { 48 | }; | } CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces] 49 | double dH_RR[4][4] = { | ^ 50 | -6.6, -10.17, -7.65, -5.76, | { } 51 | -10.56, -12.21, -7.95, -7.65, | { } 52 | -13.37, -14.21, -12.21, -10.17, | { } 53 | -8.11, -13.37, -10.56, -6.6 | { 54 | }; | } CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces] 55 | double dS_RR[4][4] = { | ^ 56 | -18.38, -26.03, -19.18, -15.67, | { } 57 | -28.25, -30.02, -19.18, -19.18, | { } 58 | -35.68, -34.85, -30.02, -26.03, | { } 59 | -22.59, -35.68, -28.25, -18.38 | { 60 | }; | } gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ChainSegments.c -o ChainSegments.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Cluster.c -o Cluster.o Cluster.c: In function ‘cluster._omp_fn.0’: Cluster.c:439:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 439 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster._omp_fn.1’: Cluster.c:469:50: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 469 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster._omp_fn.2’: Cluster.c:493:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 493 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster’: Cluster.c:277:14: warning: ‘minCols’ may be used uninitialized [-Wmaybe-uninitialized] 277 | int *minCols; | ^~~~~~~ Cluster.c:916:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 916 | *rPercentComplete = floor(100*soFar/total); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ Cluster.c:248:25: note: ‘rPercentComplete’ was declared here 248 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Cluster.c:916:45: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized] 916 | *rPercentComplete = floor(100*soFar/total); | ^~~~~~~~~~~~~~~~~~~~~~ Cluster.c:249:23: note: ‘total’ was declared here 249 | double soFar, total, minHeight, *cut, *rans, *distanceMatrix, minH; | ^~~~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from Cluster.c:11: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval Cluster.c:920:33: note: in expansion of macro ‘eval’ 920 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ Cluster.c:250:36: note: ‘utilsPackage’ was declared here 250 | SEXP ans, percentComplete, utilsPackage; | ^~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval Cluster.c:920:33: note: in expansion of macro ‘eval’ 920 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ Cluster.c:250:19: note: ‘percentComplete’ was declared here 250 | SEXP ans, percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Cluster.c:283:17: warning: ‘nDiv’ may be used uninitialized [-Wmaybe-uninitialized] 283 | double *nDiv; | ^~~~ Cluster.c:413:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 413 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ClusterME.c -o ClusterME.o ClusterME.c: In function ‘clusterME’: ClusterME.c:322:101: warning: ‘LLRL’ may be used uninitialized [-Wmaybe-uninitialized] 322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:284:24: note: ‘LLRL’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:322:101: warning: ‘LRRL’ may be used uninitialized [-Wmaybe-uninitialized] 322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:284:30: note: ‘LRRL’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:323:101: warning: ‘LLRR’ may be used uninitialized [-Wmaybe-uninitialized] 323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:284:36: note: ‘LLRR’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:323:101: warning: ‘LRRR’ may be used uninitialized [-Wmaybe-uninitialized] 323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:284:42: note: ‘LRRR’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ClusterML.c -o ClusterML.o ClusterML.c: In function ‘clusterML’: ClusterML.c:1913:17: warning: ‘node’ may be used uninitialized [-Wmaybe-uninitialized] 1913 | double *node; | ^~~~ ClusterML.c:1959:14: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 1959 | int *Up; | ^~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function ‘clusterMP._omp_fn.0’: ClusterMP.c:190:71: warning: ‘temp_nodes’ may be used uninitialized [-Wmaybe-uninitialized] 190 | temp_nodes[j] = 0; | ~~~~~~~~~~~~~~^~~ ClusterMP.c:163:34: note: ‘temp_nodes’ was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~~ ClusterMP.c:465:49: warning: ‘temp_lengths’ may be used uninitialized [-Wmaybe-uninitialized] 465 | *(temp_lengths + j) += *(S + w*c + m)*weight; | ^~~~~~~~~~~~~~~~~~~ ClusterMP.c:162:38: note: ‘temp_lengths’ was declared here 162 | double *temp_score, *temp_lengths; | ^~~~~~~~~~~~ ClusterMP.c:485:73: warning: ‘temp_subM’ may be used uninitialized [-Wmaybe-uninitialized] 485 | *(temp_subM + c*m + w - 1) += weight; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:163:22: note: ‘temp_subM’ was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~ ClusterMP.c:202:49: warning: ‘P’ may be used uninitialized [-Wmaybe-uninitialized] 202 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:185:38: note: ‘P’ was declared here 185 | int *P; | ^ ClusterMP.c:385:61: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 385 | *(R + 3*c*n + m) = 0; | ^ ClusterMP.c:105:22: note: ‘m’ was declared here 105 | int i, j, k, m, w; | ^ ClusterMP.c: In function ‘clusterMP’: ClusterMP.c:159:17: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:128:17: note: ‘lengths’ was declared here 128 | double *lengths, *score; | ^~~~~~~ ClusterMP.c:159:17: warning: ‘nodes’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:20: note: ‘nodes’ was declared here 129 | int size, *nodes, *subM; | ^~~~~ ClusterMP.c:159:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:28: note: ‘subM’ was declared here 129 | int size, *nodes, *subM; | ^~~~ ClusterMP.c:159:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:145:14: note: ‘Up’ was declared here 145 | int *Up; | ^~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Compositions.c -o Compositions.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Compression.c -o Compression.o Compression.c: In function ‘nbit._omp_fn.0’: Compression.c:1242:71: warning: ‘lastTriplet’ may be used uninitialized [-Wmaybe-uninitialized] 1242 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:632:26: note: ‘lastTriplet’ was declared here 632 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1012:62: warning: ‘word’ may be used uninitialized [-Wmaybe-uninitialized] 1012 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:545:37: note: ‘word’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1013:54: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized] 1013 | count++; | ~~~~~^~ Compression.c:545:43: note: ‘count’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:1215:56: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized] 1215 | p[c++] = rev == 0 ? 254 : 255; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ Compression.c:546:41: note: ‘rev’ was declared here 546 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ConsensusSequence.c -o ConsensusSequence.o In function ‘runsAA’, inlined from ‘consensusProfileAA’ at ConsensusSequence.c:1836:3: ConsensusSequence.c:454:50: warning: ‘lastPos’ may be used uninitialized [-Wmaybe-uninitialized] 454 | if (lastGap < (s - 2)) // ensure continuity before the run | ~~~^~~~ ConsensusSequence.c: In function ‘consensusProfileAA’: ConsensusSequence.c:397:30: note: ‘lastPos’ was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c: In function ‘colScores’: ConsensusSequence.c:2043:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized] 2043 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:1930:37: note: ‘curr’ was declared here 1930 | double weight, total, prev, curr; | ^~~~ ConsensusSequence.c: In function ‘colScoresAA’: ConsensusSequence.c:2186:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized] 2186 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:2073:37: note: ‘curr’ was declared here 2073 | double weight, total, prev, curr; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function ‘designProbes’: DesignProbes.c:71:27: warning: missing braces around initializer [-Wmissing-braces] 71 | double NN[4][4] = { | ^ 72 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 73 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 74 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 75 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 76 | }; | } DesignProbes.c:78:27: warning: missing braces around initializer [-Wmissing-braces] 78 | double PM[4][4] = { | ^ 79 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 80 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 81 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 82 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 83 | }; | } DesignProbes.c:85:34: warning: missing braces around initializer [-Wmissing-braces] 85 | double sMM[4][5][5][4] = { | ^ 86 | 0,0,0,0 | {{{ 87 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 88 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 89 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 90 | ,0.75,0.65,0.69,0.78 | }{ 91 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 92 | ,0,0,0,0 | }{ 93 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 94 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 95 | ,0.75,0.65,0.69,0.78 | }{ 96 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 97 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 98 | ,0,0,0,0 | }{ 99 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 100 | ,0.75,0.65,0.69,0.78 | }{ 101 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 102 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 103 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 104 | ,0,0,0,0 | }{ 105 | ,0.75,0.65,0.69,0.78 | }{ 106 | ,0.75,0.65,0.69,0.78 | - | }},{{ 107 | ,0.75,0.65,0.69,0.78 | }{ 108 | ,0.75,0.65,0.69,0.78 | }{ 109 | ,0.76,0.65,0.69,0.78 | }{ 110 | ,0,0,0,0 | }{ 111 | ,0,0,0,0 | - | }}},{{{ 112 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 113 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 114 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 115 | ,0.65,0.55,0.48,0.69 | }{ 116 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 117 | ,0,0,0,0 | }{ 118 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 119 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 120 | ,0.65,0.56,0.49,0.69 | }{ 121 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 122 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 123 | ,0,0,0,0 | }{ 124 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 125 | ,0.65,0.56,0.49,0.69 | }{ 126 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 127 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 128 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 129 | ,0,0,0,0 | }{ 130 | ,0.65,0.55,0.48,0.69 | }{ 131 | ,0.65,0.55,0.48,0.69 | - | }},{{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.56,0.49,0.69 | }{ 134 | ,0.65,0.55,0.48,0.69 | }{ 135 | ,0,0,0,0 | }{ 136 | ,0,0,0,0 | - | }}},{{{ 137 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 138 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 139 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 140 | ,0.68,0.46,0.55,0.65 | }{ 141 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 142 | ,0,0,0,0 | }{ 143 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 144 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 145 | ,0.68,0.47,0.56,0.65 | }{ 146 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 147 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 148 | ,0,0,0,0 | }{ 149 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 150 | ,0.68,0.47,0.56,0.65 | }{ 151 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 152 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 153 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 154 | ,0,0,0,0 | }{ 155 | ,0.68,0.46,0.55,0.65 | }{ 156 | ,0.68,0.46,0.55,0.65 | - | }},{{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.47,0.56,0.65 | }{ 159 | ,0.68,0.46,0.55,0.65 | }{ 160 | ,0,0,0,0 | }{ 161 | ,0,0,0,0 | - | }}},{{{ 162 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 163 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 164 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 165 | ,0.85,0.68,0.65,0.76 | }{ 166 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 167 | ,0,0,0,0 | }{ 168 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 169 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 170 | ,0.85,0.68,0.65,0.75 | }{ 171 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 172 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 173 | ,0,0,0,0 | }{ 174 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 175 | ,0.85,0.68,0.65,0.75 | }{ 176 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 177 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 178 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 179 | ,0,0,0,0 | }{ 180 | ,0.85,0.68,0.65,0.75 | }{ 181 | ,0.85,0.68,0.65,0.75 | - | }},{{ 182 | ,0.85,0.68,0.65,0.75 | }{ 183 | ,0.85,0.68,0.65,0.75 | }{ 184 | ,0.85,0.68,0.65,0.75 | }{ 185 | ,0,0,0,0 | }{ 186 | }; | }}} DesignProbes.c: In function ‘designProbes._omp_fn.0’: DesignProbes.c:838:60: warning: ‘lastCycle’ may be used uninitialized [-Wmaybe-uninitialized] 838 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:270:58: note: ‘lastCycle’ was declared here 270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Diff.c -o Diff.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function ‘firstSeqsPosEqual’: DistanceMatrix.c:1009:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1009 | if (!ci) | ^~ DistanceMatrix.c:1012:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1012 | while (i < ex) { | ^~~~~ DistanceMatrix.c:1031:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1031 | if (!cj) | ^~ DistanceMatrix.c:1034:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1034 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’: DistanceMatrix.c:1587:66: warning: ‘OV’ may be used uninitialized [-Wmaybe-uninitialized] 1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:1096:92: note: ‘OV’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1587:66: warning: ‘off’ may be used uninitialized [-Wmaybe-uninitialized] 1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:1096:96: note: ‘off’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~~ DistanceMatrix.c:1266:53: warning: ‘one’ may be used uninitialized [-Wmaybe-uninitialized] 1266 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1241:29: note: ‘one’ was declared here 1241 | int one, two; | ^~~ DistanceMatrix.c:1603:52: warning: ‘o’ may be used uninitialized [-Wmaybe-uninitialized] 1603 | if (o == 1) { | ^ DistanceMatrix.c:1096:112: note: ‘o’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^ DistanceMatrix.c:1606:91: warning: ‘ov’ may be used uninitialized [-Wmaybe-uninitialized] 1606 | sim[i] = (double)pos/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:1096:88: note: ‘ov’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1335:40: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1335 | keep = (int *) calloc(n, sizeof(int)); // initialized to zero (thread-safe on Windows) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from DistanceMatrix.c:32: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ DistanceMatrix.c: In function ‘distMatrix._omp_fn.0’: DistanceMatrix.c:137:25: warning: ‘m2’ may be used uninitialized [-Wmaybe-uninitialized] 137 | int i, j, I, J, m2, *counts; | ^~ DistanceMatrix.c:137:30: warning: ‘counts’ may be used uninitialized [-Wmaybe-uninitialized] 137 | int i, j, I, J, m2, *counts; | ^~~~~~ DistanceMatrix.c: In function ‘distMatrix’: DistanceMatrix.c:624:33: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads) | ^~~ DistanceMatrix.c:545:13: note: ‘m’ was declared here 545 | int m, *lkup_row, *lkup_col; | ^ DistanceMatrix.c:545:17: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized] 545 | int m, *lkup_row, *lkup_col; | ^~~~~~~~ DistanceMatrix.c:545:28: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized] 545 | int m, *lkup_row, *lkup_col; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function ‘pop’: EnumerateSequence.c:546:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 546 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function ‘enumerateSequence’: EnumerateSequence.c:359:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized] 359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:318:14: note: ‘mN’ was declared here 318 | int *mN; | ^~ EnumerateSequence.c:319:13: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 319 | int tot; // total number of k-mers | ^~~ EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’: EnumerateSequence.c:908:14: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized] 908 | int *mN; | ^~ EnumerateSequence.c:909:13: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 909 | int tot; // total number of k-mers | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function ‘findFrameshifts’: FindFrameshifts.c:464:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 464 | *rPercentComplete = floor(100*(double)(s + 1)/f_length); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FindFrameshifts.c:160:25: note: ‘rPercentComplete’ was declared here 160 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’ 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’ 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ FindFrameshifts.c:317:34: warning: ‘I’ may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:28: note: ‘I’ was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:317:43: warning: ‘J’ may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:31: note: ‘J’ was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:376:28: warning: ‘K’ may be used uninitialized [-Wmaybe-uninitialized] 376 | if (k == 1) { | ^ FindFrameshifts.c:135:34: note: ‘K’ was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function ‘scoreCodonModel’: GeneFinding.c:422:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 422 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:389:22: note: ‘x_i.ptr’ was declared here 389 | Chars_holder x_i; | ^~~ GeneFinding.c:432:57: warning: ‘lastVal’ may be used uninitialized [-Wmaybe-uninitialized] 432 | if (val < 64 && lastVal < 64) | ~~~~~~~~^~~~ GeneFinding.c:372:32: note: ‘lastVal’ was declared here 372 | int i, j, s, fin, val, lastVal, dicodon; | ^~~~~~~ GeneFinding.c: In function ‘startCodonModel’: GeneFinding.c:798:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 798 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:772:22: note: ‘x_i.ptr’ was declared here 772 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreStartCodonModel’: GeneFinding.c:899:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 899 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:869:22: note: ‘x_i.ptr’ was declared here 869 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘initialCodonModel’: GeneFinding.c:952:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 952 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:929:22: note: ‘x_i.ptr’ was declared here 929 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreInitialCodonModel’: GeneFinding.c:1059:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1059 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1032:22: note: ‘x_i.ptr’ was declared here 1032 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘terminationCodonModel’: GeneFinding.c:1116:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1116 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1093:22: note: ‘x_i.ptr’ was declared here 1093 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreTerminationCodonModel’: GeneFinding.c:1216:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1189:22: note: ‘x_i.ptr’ was declared here 1189 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘getRegion’: GeneFinding.c:1317:81: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1317 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c:1253:22: note: ‘x_i.ptr’ was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c:1314:51: warning: ‘x_i.length’ may be used uninitialized [-Wmaybe-uninitialized] 1314 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1253:22: note: ‘x_i.length’ was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘autocorrelationModel’: GeneFinding.c:1379:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1351:22: note: ‘x_i.ptr’ was declared here 1351 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreAutocorrelationModel’: GeneFinding.c:1496:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1496 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1462:22: note: ‘x_i.ptr’ was declared here 1462 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘couplingModel’: GeneFinding.c:1598:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1598 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1574:22: note: ‘x_i.ptr’ was declared here 1574 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreCouplingModel’: GeneFinding.c:1712:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1712 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1682:22: note: ‘x_i.ptr’ was declared here 1682 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘nucleotideBiasModel’: GeneFinding.c:1827:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1827 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1789:22: note: ‘x_i.ptr’ was declared here 1789 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreNucleotideBiasModel’: GeneFinding.c:1914:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1914 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1883:22: note: ‘x_i.ptr’ was declared here 1883 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘upstreamMotifModel’: GeneFinding.c:1993:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1993 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:1951:22: note: ‘x_i.ptr’ was declared here 1951 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreUpstreamMotifModel’: GeneFinding.c:2093:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2093 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:2058:22: note: ‘x_i.ptr’ was declared here 2058 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreRunLengthModel’: GeneFinding.c:2308:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2308 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2277:22: note: ‘x_i.ptr’ was declared here 2277 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘stopCodonModel’: GeneFinding.c:2426:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2426 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:2400:22: note: ‘x_i.ptr’ was declared here 2400 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreStopCodonModel’: GeneFinding.c:2527:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2527 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:2497:22: note: ‘x_i.ptr’ was declared here 2497 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘codonFrequencies’: GeneFinding.c:2578:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2578 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2555:22: note: ‘x_i.ptr’ was declared here 2555 | Chars_holder x_i; | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c GetPools.c -o GetPools.o GetPools.c: In function ‘getPools’: GetPools.c:33:46: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 33 | snprintf(buf, sizeof(buf), "%p", s); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Import.c -o Import.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c InformationContent.c -o InformationContent.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IntDist.c -o IntDist.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ManipulateXStringSet.c -o ManipulateXStringSet.o ManipulateXStringSet.c: In function ‘mergePairs._omp_fn.0’: ManipulateXStringSet.c:1106:58: warning: ‘l2’ may be used uninitialized [-Wmaybe-uninitialized] 1106 | p2 = (l2 + pow(10, ((double)q2_i.ptr[s2 + 1] - 33)/-10))/2; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ManipulateXStringSet.c:1087:36: note: ‘l2’ was declared here 1087 | double l1, l2; // last probability | ^~ ManipulateXStringSet.c:1096:58: warning: ‘l1’ may be used uninitialized [-Wmaybe-uninitialized] 1096 | p1 = (l1 + pow(10, ((double)q1_i.ptr[s1 + 1] - 33)/-10))/2; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ManipulateXStringSet.c:1087:32: note: ‘l1’ was declared here 1087 | double l1, l2; // last probability | ^~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c MeltPolymer.c -o MeltPolymer.o MeltPolymer.c: In function ‘meltPolymer’: MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces] 79 | double dH[4][4] = { | ^ 80 | -7.9,-8.4,-7.8,-7.2 | { 81 | ,-8.5,-8.0,-10.6,-7.8 | }{ 82 | ,-8.2,-9.8,-8.0,-8.4 | }{ 83 | ,-7.2,-8.2,-8.5,-7.9 | }{ 84 | }; | } MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces] 88 | double dS[4][4] = { | ^ 89 | -22.2,-22.4,-21.0,-20.4 | { 90 | ,-22.7,-19.9,-27.2,-21.0 | }{ 91 | ,-22.2,-24.4,-19.9,-22.4 | }{ 92 | ,-21.3,-22.2,-22.7,-22.2 | }{ 93 | }; | } MeltPolymer.c:406:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 406 | SET_VECTOR_ELT(ret, s, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ MeltPolymer.c:53:19: note: ‘ans’ was declared here 53 | SEXP ret, ans; | ^~~ MeltPolymer.c:358:41: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~~~~~~~~~~~~~~~~ MeltPolymer.c:54:17: note: ‘rans’ was declared here 54 | double *rans; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c MovingAverage.c -o MovingAverage.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c NNLS.c -o NNLS.o NNLS.c: In function ‘NNLS’: NNLS.c:78:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 78 | *rPercentComplete = floor(100*((double)i + 1)/(double)l); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NNLS.c:40:34: note: ‘rPercentComplete’ was declared here 40 | int i, j, k, before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from NNLS.c:17: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro ‘eval’ 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:14: note: ‘percentComplete’ was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro ‘eval’ 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:31: note: ‘utilsPackage’ was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Order.c -o Order.o Order.c: In function ‘radixOrder’: Order.c:99:19: warning: ‘bounds’ may be used uninitialized [-Wmaybe-uninitialized] 99 | R_xlen_t *bounds; | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’: PairwiseAlignment.c:446:39: warning: ‘p3’ may be used uninitialized [-Wmaybe-uninitialized] 446 | p3[0] = l1; | ~~~~~~^~~~ PairwiseAlignment.c:176:24: note: ‘p3’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:447:39: warning: ‘p4’ may be used uninitialized [-Wmaybe-uninitialized] 447 | p4[0] = l2 - j1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:29: note: ‘p4’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:450:39: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized] 450 | p1[0] = l2; | ~~~~~~^~~~ PairwiseAlignment.c:176:14: note: ‘p1’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:451:39: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized] 451 | p2[0] = l1 - i1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:19: note: ‘p2’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function ‘alignPairs’: PairwiseAlignment.c:1036:25: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 1036 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PairwiseAlignment.c:1038:14: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ PairwiseAlignment.c:1038:31: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PopulationGenetics.c -o PopulationGenetics.o PopulationGenetics.c: In function ‘correlationProfile’: PopulationGenetics.c:140:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 140 | *rPercentComplete = floor(100*soFar/tot); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ PopulationGenetics.c:40:68: note: ‘rPercentComplete’ was declared here 40 | int i, j, k, p, I, J, minL, warn = NA_INTEGER, v, before, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PopulationGenetics.c:140:53: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 140 | *rPercentComplete = floor(100*soFar/tot); | ^~~~~~~~~~~~~~~~~~~~ PopulationGenetics.c:41:31: note: ‘tot’ was declared here 41 | double weight, soFar, tot; | ^~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from PopulationGenetics.c:11: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’ 143 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ PopulationGenetics.c:50:14: note: ‘percentComplete’ was declared here 50 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’ 143 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ PopulationGenetics.c:50:31: note: ‘utilsPackage’ was declared here 50 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PredictDBN.c -o PredictDBN.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PredictHEC.c -o PredictHEC.o PredictHEC.c: In function ‘predictHEC’: PredictHEC.c:51:31: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized] 51 | double HEC[N], temp, *rans; | ^~~~ PredictHEC.c:247:43: warning: ‘states’ may be used uninitialized [-Wmaybe-uninitialized] 247 | states[j] = nms[0]; | ~~~~~~~~~~^~~~~~~~ PredictHEC.c:52:15: note: ‘states’ was declared here 52 | char *states; | ^~~~~~ PredictHEC.c:273:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 273 | SET_VECTOR_ELT(ret, i, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictHEC.c:59:19: note: ‘ans’ was declared here 59 | SEXP ret, ans; | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_decipher.c -o R_init_decipher.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Search.c -o Search.o Search.c: In function ‘searchIndex._omp_fn.0’: Search.c:578:92: warning: ‘subScores’ may be used uninitialized [-Wmaybe-uninitialized] 578 | if (lkup != NA_INTEGER && subScores[p1*l_i.length + lkup] != NA_REAL) | ^ Search.c:317:33: note: ‘subScores’ was declared here 317 | double *subScores; // substitution scores (if maxIt > 0) | ^~~~~~~~~ Search.c:449:66: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 449 | score2[j] = score[o1[j]]; | ^ Search.c:282:33: note: ‘score’ was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~ Search.c:450:72: warning: ‘addScore’ may be used uninitialized [-Wmaybe-uninitialized] 450 | addScore2[j] = addScore[o1[j]]; | ^ Search.c:282:41: note: ‘addScore’ was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~~~~ Search.c:587:83: warning: ‘maxLen’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (deltaTarget >= maxSep + maxLen) { | ~~~~~~~^~~~~~~~ Search.c:560:45: note: ‘maxLen’ was declared here 560 | int maxLen; // maximum observed length | ^~~~~~ Search.c:555:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 555 | Chars_holder p_i, s_j; | ^~~ Search.c:626:55: warning: ‘s_j.length’ may be used uninitialized [-Wmaybe-uninitialized] 626 | bound = s_j.length - 1; // right bound | ~~~~~~^~~~~~~~~~~~~~~~ Search.c:555:59: note: ‘s_j.length’ was declared here 555 | Chars_holder p_i, s_j; | ^~~ Search.c:882:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 882 | Chars_holder p_i, s_j; | ^~~ Search.c:371:30: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 371 | int *res; // indices of results | ^~~ Search.c:1150:72: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized] 1150 | anchor[k++] = posQuery[p] + len[p] - 1; | ^ Search.c:370:30: note: ‘len’ was declared here 370 | int *len; // length of each hit | ^~~ Search.c:1139:58: warning: ‘chain’ may be used uninitialized [-Wmaybe-uninitialized] 1139 | while (p != chain[p]) { | ^ Search.c:369:30: note: ‘chain’ was declared here 369 | int *chain; // set of joined hits per match | ^~~~~ Search.c: In function ‘searchIndex’: Search.c:224:17: warning: ‘sM’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:17: note: ‘sM’ was declared here 111 | double *sM, dS; | ^~ Search.c:224:17: warning: ‘dS’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:21: note: ‘dS’ was declared here 111 | double *sM, dS; | ^~ Search.c:112:14: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized] 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:112:25: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized] 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:112:36: warning: ‘pwv’ may be used uninitialized [-Wmaybe-uninitialized] 112 | int *lkup_row, *lkup_col, *pwv; | ^~~ Search.c:113:17: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized] 113 | double *scores, *addScores; | ^~~~~~ Search.c:224:17: warning: ‘addScores’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:113:26: note: ‘addScores’ was declared here 113 | double *scores, *addScores; | ^~~~~~~~~ Search.c:224:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:174:25: note: ‘rPercentComplete’ was declared here 174 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Search.c:176:14: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Search.c:176:31: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ Search.c:224:17: warning: ‘matrices’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:217:16: note: ‘matrices’ was declared here 217 | int ***matrices; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TerminalMismatch.c -o TerminalMismatch.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Translate.c -o Translate.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Utils.c -o Utils.o Utils.c: In function ‘splitPartitions’: Utils.c:990:35: warning: ‘change’ may be used uninitialized [-Wmaybe-uninitialized] 990 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ Utils.c:984:13: note: ‘change’ was declared here 984 | int change; // index before start of partition | ^~~~~~ Utils.c: In function ‘matchColumns’: Utils.c:1198:55: warning: ‘lkup’ may be used uninitialized [-Wmaybe-uninitialized] 1198 | int val = lkup[(unsigned char)x_i.ptr[o[j]]]; | ^ Utils.c:1130:14: note: ‘lkup’ was declared here 1130 | int *lkup; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c VectorSums.c -o VectorSums.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PopulationGenetics.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWI1aOB/R.INSTALL105b8f73926db0/DECIPHER/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-DECIPHER/00new/DECIPHER/libs ** R ** data ** 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 (DECIPHER) * installing *source* package ‘dada2’ ... ** this is package ‘dada2’ version ‘1.37.0’ ** package ‘dada2’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpE0Bgvk/R.INSTALL105ff765a91e90/dada2/src' g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from ../inst/include/dada2.h:7, from RcppExports.cpp:4: ../inst/include/dada2_RcppExports.h:14:14: warning: ‘void dada2::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function] 14 | void validateSignature(const char* sig) { | ^~~~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rmain.cpp -o Rmain.o Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’: Rmain.cpp:71:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 71 | if(quals.nrow() != maxlen) { | ~~~~~~~~~~~~~^~~~~~~~~ Rmain.cpp: In function ‘B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)’: Rmain.cpp:316:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 316 | while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) { | ~~~~~~~~~~~^~~~~~~~~~~ Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’: Rmain.cpp:288:9: warning: ‘k8’ may be used uninitialized [-Wmaybe-uninitialized] 288 | free(k8); | ~~~~^~~~ Rmain.cpp:122:12: note: ‘k8’ was declared here 122 | uint8_t *k8; | ^~ Rmain.cpp:289:9: warning: ‘k16’ may be used uninitialized [-Wmaybe-uninitialized] 289 | free(k16); | ~~~~^~~~~ Rmain.cpp:123:13: note: ‘k16’ was declared here 123 | uint16_t *k16; | ^~~ Rmain.cpp:290:9: warning: ‘kord’ may be used uninitialized [-Wmaybe-uninitialized] 290 | free(kord); | ~~~~^~~~~~ Rmain.cpp:124:13: note: ‘kord’ was declared here 124 | uint16_t *kord; | ^~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c chimera.cpp -o chimera.o chimera.cpp: In function ‘bool C_is_bimera(std::string, std::vector >, bool, int, int, int, int, int)’: chimera.cpp:25:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 25 | for(i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 29 | if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents" | ~~~~~~~~~~~~~^~~~~~~~~~~~ chimera.cpp:44:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 44 | if((max_right+max_left)>=sq.size()) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ chimera.cpp:48:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ chimera.cpp:48:83: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ chimera.cpp: In function ‘void get_lr(char**, int&, int&, int&, int&, bool, int)’: chimera.cpp:231:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 231 | while(al[0][pos] == '-' && pos+(len-max_shift)) { | ~~~^~~~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/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 function ‘void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’: cluster.cpp:17:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable] 17 | unsigned int index, cind, center_reads; | ^~~~ cluster.cpp: In function ‘void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’: cluster.cpp:166:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 166 | for(row=0;rownclust;i++) { | ~^~~~~~~~~~ cluster.cpp:285:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 285 | for(r=1; rbi[i]->nraw; r++) { // r=0 is the center | ~^~~~~~~~~~~~~~~ cluster.cpp:288:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 288 | if(raw->reads < min_abund) { continue; } | ~~~~~~~~~~~^~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c containers.cpp -o containers.o containers.cpp: In function ‘void b_free(B*)’: containers.cpp:141:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 141 | for(int i=0;inclust;i++) { bi_free(b->bi[i]); } | ~^~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c error.cpp -o error.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c evaluate.cpp -o evaluate.o evaluate.cpp: In function ‘Rcpp::IntegerVector C_eval_pair(std::string, std::string)’: evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 88 | } while((s1gap || s2gap) && start::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 133 | for(i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 152 | for(i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for(i=0;i >, std::vector >, int)’: evaluate.cpp:219:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 219 | for(int i=0;i >, std::vector >, int, int)’: evaluate.cpp:243:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 243 | for(int i=0;i >, std::vector >, int)’: evaluate.cpp:286:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 286 | for(int i=0;i >, std::vector >, int)’: evaluate.cpp:338:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 338 | for(i=0;i >, std::string, unsigned int, bool)’: filter.cpp:16:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 16 | for(i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20 | for(i=0;i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); } | ~~^~~~~~ kmers.cpp:174:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 174 | for(i=0; i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); } | ~~^~~~~~ kmers.cpp:221:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | for(i=0; i= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); } | ~~^~~~~~ kmers.cpp:255:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for(i=0;i=0 && (band=0 && (bandlen2) { r = len2; } | ~^~~~~ nwalign_endsfree.cpp:130:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 130 | if (i == len1) { | ~~^~~~~~~ nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 137 | if (j == len2) { | ~~^~~~~~~ nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; } | ~^~~~~ nwalign_endsfree.cpp:305:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 305 | if (i == len1) { | ~~^~~~~~~ nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 314 | if (j == len2) { | ~~^~~~~~~ nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 379 | for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; } | ~^~~~~ nwalign_endsfree.cpp:522:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 522 | for (i=0;insubs;s++) { | ~^~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nwalign_vectorized.cpp -o nwalign_vectorized.o nwalign_vectorized.cpp: In function ‘char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)’: nwalign_vectorized.cpp:96:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | start_col = 1 + (1+(band >, std::vector >, int16_t, int16_t, int16_t, int, bool)’: nwalign_vectorized.cpp:329:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 329 | for(i=0;insubs;s++) { | ~^~~~~~~~~~~ pval.cpp:123:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 123 | if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); } | ~~~~~^~~~~~~~~~~~ pval.cpp: In function ‘double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)’: pval.cpp:177:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 177 | for(s=0;snsubs;s++) { | ~^~~~~~~~~~~ pval.cpp:179:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 179 | if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); } | ~~~~~^~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c taxonomy.cpp -o taxonomy.o taxonomy.cpp: In function ‘void tax_kvec(const char*, unsigned int, unsigned char*)’: taxonomy.cpp:48:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | if(kmer>=0 && kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)’: taxonomy.cpp:221:45: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) { taxonomy.cpp:251:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 251 | for(kmer=0;kmer= 3.5.0) Imports: dplyr, plyr, magrittr, broom, phyloseq, vegan, rlang, ggplot2, ggpubr, DESeq2, SummarizedExperiment, S4Vectors, rstatix, tidyr, phangorn, randomForest, edgeR Timings: user system elapsed microbial 551.384 19.434 571.863 Results: Check status summary: OK Source packages 1 Check results summary: microbial ... OK