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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL maftools
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘maftools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c ntcounts.c -o ntcounts.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c snpcounts.c -o snpcounts.o
snpcounts.c: In function ‘snpcounts’:
snpcounts.c:56:26: warning: passing argument 1 of ‘countlines’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   56 |   int nloci = countlines(bedfile);
      |                          ^~~~~~~
snpcounts.c:13:22: note: expected ‘char *’ but argument is of type ‘const char *’
   13 | int countlines(char *filename){
      |                ~~~~~~^~~~~~~~
snpcounts.c:89:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
   89 |   fprintf(tsv_fp, "#idxstats_mapped_reads\t%llu\n", tot_mapped);
      |                                            ~~~^     ~~~~~~~~~~
      |                                               |     |
      |                                               |     uint64_t {aka long unsigned int}
      |                                               long long unsigned int
      |                                            %lu
snpcounts.c:56:7: warning: unused variable ‘nloci’ [-Wunused-variable]
   56 |   int nloci = countlines(bedfile);
      |       ^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c somaticfreq.c -o somaticfreq.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-maftools/00new/maftools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maftools)