############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Rbwa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘Rbwa’ ... ** using staged installation ** libs ** arch - gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kthread.c -o kthread.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kstring.c -o kstring.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c ksw.c -o ksw.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt.c -o bwt.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bntseq.c -o bntseq.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwa.c -o bwa.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem.c -o bwamem.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c QSufSort.c -o QSufSort.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:879:10: 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:953:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] 953 | unsigned int bitsInWordMinusBitPerChar; | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c rope.c -o rope.o rope.c: In function ‘rope_restore_node’: rope.c:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function ‘rope_restore’: rope.c:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c is.c -o is.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c 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 ar: `u' modifier ignored since `D' is the default (see `U') gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwashm.c -o bwashm.o bwashm.c: In function ‘bwa_shm_stage’: bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] 29 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] 66 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwase.c -o bwase.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtgap.c -o bwtgap.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtaln.c -o bwtaln.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bamlite.c -o bamlite.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwape.c -o bwape.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kopen.c -o kopen.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c pemerge.c -o pemerge.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c maxk.c -o maxk.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c fastmap.c -o fastmap.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c main.c -o main.o gcc -g -Wall -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 mkdir -p ../inst cp bwa ../inst/bwa rm -f gmon.out *.o a.out bwa *~ *.a rm -f bwa ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbwa)