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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Rbwa
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘Rbwa’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bntseq.c -o bntseq.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwamem.c -o bwamem.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/home/biocbuild/R/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:879:17: 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 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c is.c -o is.o
gcc -I"/home/biocbuild/R/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
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwape.c -o bwape.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c kopen.c -o kopen.o
In function ‘cmd2argv’,
    inlined from ‘kopen’ at kopen.c:306:13:
kopen.c:248:9: warning: ‘strncpy’ specified bound between 18446744071562067969 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  248 |         strncpy(argv[0], cmd + beg, end - beg);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kopen.c:247:32: warning: argument 1 range [18446744071562067970, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  247 |         argv[0] = str = (char*)calloc(end - beg + 1, 1);
      |                                ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kopen.c:7:
/usr/include/stdlib.h: In function ‘kopen’:
/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)
      |              ^~~~~~
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
gcc -I"/home/biocbuild/R/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)