The following packages will be installed: bwa Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching bwa.SlackBuild... 0%100%100%100%100%100%Done Fetching bwa.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done bwa-0.7.17/ bwa-0.7.17/bntseq.c bwa-0.7.17/utils.c bwa-0.7.17/bwt.h bwa-0.7.17/bwamem.h bwa-0.7.17/bwtsw2_core.c bwa-0.7.17/bwase.h bwa-0.7.17/bwt.c bwa-0.7.17/bwt_lite.h bwa-0.7.17/README.md bwa-0.7.17/khash.h bwa-0.7.17/main.c bwa-0.7.17/bwtsw2.h bwa-0.7.17/bwt_lite.c bwa-0.7.17/ksort.h bwa-0.7.17/bwtgap.h bwa-0.7.17/NEWS.md bwa-0.7.17/bwa.1 bwa-0.7.17/rle.c bwa-0.7.17/bwtaln.c bwa-0.7.17/bwamem_extra.c bwa-0.7.17/bwtaln.h bwa-0.7.17/rope.c bwa-0.7.17/rle.h bwa-0.7.17/kopen.c bwa-0.7.17/kthread.c bwa-0.7.17/bamlite.h bwa-0.7.17/bwtsw2_chain.c bwa-0.7.17/is.c bwa-0.7.17/QSufSort.h bwa-0.7.17/maxk.c bwa-0.7.17/bwtsw2_aux.c bwa-0.7.17/bwtgap.c bwa-0.7.17/ChangeLog bwa-0.7.17/Makefile bwa-0.7.17/bamlite.c bwa-0.7.17/bwamem_pair.c bwa-0.7.17/COPYING bwa-0.7.17/utils.h bwa-0.7.17/pemerge.c bwa-0.7.17/fastmap.c bwa-0.7.17/ksw.c bwa-0.7.17/kstring.c bwa-0.7.17/kstring.h bwa-0.7.17/bwase.c bwa-0.7.17/bntseq.h bwa-0.7.17/xa2multi.pl bwa-0.7.17/bwaseqio.c bwa-0.7.17/example.c bwa-0.7.17/kseq.h bwa-0.7.17/QSufSort.c bwa-0.7.17/bwape.c bwa-0.7.17/bwashm.c bwa-0.7.17/kbtree.h bwa-0.7.17/rope.h bwa-0.7.17/bwamem.c bwa-0.7.17/bwakit/ bwa-0.7.17/bwakit/README.md bwa-0.7.17/bwakit/typeHLA.js bwa-0.7.17/bwakit/bwa-postalt.js bwa-0.7.17/bwakit/run-gen-ref bwa-0.7.17/bwakit/run-bwamem bwa-0.7.17/bwakit/typeHLA-selctg.js bwa-0.7.17/bwakit/typeHLA.sh bwa-0.7.17/bwakit/run-HLA bwa-0.7.17/malloc_wrap.c bwa-0.7.17/bwt_gen.c bwa-0.7.17/.travis.yml bwa-0.7.17/bwa.c bwa-0.7.17/bwtsw2_main.c bwa-0.7.17/kvec.h bwa-0.7.17/ksw.h bwa-0.7.17/README-alt.md bwa-0.7.17/malloc_wrap.h bwa-0.7.17/bwtsw2_pair.c bwa-0.7.17/bwtindex.c bwa-0.7.17/bwa.h bwa-0.7.17/qualfa2fq.pl gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o bwamem.c: In function ‘mem_align1_core’: bwamem.c:1075:33: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 1075 | err_printf("* %ld chains remain after removing duplicated chains\n", regs.n); | ~~^ ~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o bwamem_pair.c: In function ‘mem_pestat’: bwamem_pair.c:65:106: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:111: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:116: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:121: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:879:17: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] 879 | bgint_t oldInverseSa0RelativeRank = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~ bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:953:22: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] 953 | unsigned int bitsInWordMinusBitPerChar; | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o fastmap.c: In function ‘main_fastmap’: fastmap.c:413:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 413 | err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o gcc -O2 -march=i586 -mtune=i686 -msse2 -fcommon -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/bwa/bwa-0.7.17-i586-2salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/bwa usr/doc/ usr/doc/bwa-0.7.17/ usr/doc/bwa-0.7.17/COPYING usr/doc/bwa-0.7.17/ChangeLog usr/doc/bwa-0.7.17/README.md usr/doc/bwa-0.7.17/References usr/doc/bwa-0.7.17/bwa.SlackBuild usr/man/ usr/man/man1/ usr/man/man1/bwa.1.gz usr/share/ usr/share/bwa/ usr/share/bwa/qualfa2fq.pl usr/share/bwa/xa2multi.pl Slackware package /usr/src/slapt-src/academic/bwa/bwa-0.7.17-i586-2salix15.0.txz created. Installing package bwa-0.7.17-i586-2salix15.0... | bwa (Burrows-Wheeler Aligner) | | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns | relatively short nucleotide sequences against a long reference | sequence such as the human genome. It implements two algorithms, | bwa-short and BWA-SW. The former works for query sequences shorter | than 200bp and the latter for longer sequences up to around 100kbp. | | Home: http://bio-bwa.sourceforge.net/ | | | |