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This page was generated on 2021-12-03 13:05:00 -0500 (Fri, 03 Dec 2021).

INSTALL results for Rsamtools on nebbiolo2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsamtools.git to
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raw results

Package 1659/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.10.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/Rsamtools
git_branch: RELEASE_3_14
git_last_commit: b19738e
git_last_commit_date: 2021-10-26 11:55:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Rsamtools
Version: 2.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rsamtools
StartedAt: 2021-12-02 03:16:18 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 03:16:54 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 36.3 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rsamtools
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ResultManager.cpp -o ResultManager.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c as_bam.c -o as_bam.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam.c -o bam.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_data.c -o bam_data.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
                 from Template.h:9,
                 from BamIterator.h:10,
                 from BamRangeIterator.h:7,
                 from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
  138 |         (void) bam_seek(bfile, pos, SEEK_SET);
      |                ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
   87 |         (void) bam_seek(bfile, 0, 0);
      |                ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_sort.c -o bam_sort.o
In file included from /usr/include/string.h:495,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam_sort.c:34,
                 from bam_sort.c:1:
In function ‘strncpy’,
    inlined from ‘bam_sort_core_ext’ at /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam_sort.c:2065:9:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bambuffer.c -o bambuffer.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bamfile.c -o bamfile.o
bamfile.c: In function ‘bamfile_isincomplete’:
bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  168 |             (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function ‘bamfile_open’:
bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   29 |         index = hts_idx_load2(file, indexname);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c:73:17: note: ‘cfile’ was declared here
   73 |     const char *cfile;
      |                 ^~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bcffile.c -o bcffile.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c encode.c -o encode.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fafile.c -o fafile.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c idxstats.c -o idxstats.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
   20 |     (void) bam_seek(fp, 0, 0);
      |            ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c io_sam.c -o io_sam.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
                 from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:12: note: in expansion of macro ‘bam_seek’
  304 |     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
      |            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pileup.cpp -o pileup.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pileupbam.c -o pileupbam.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam.c -o sam.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam_opts.c -o sam_opts.o
In file included from /usr/include/stdio.h:867,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam_opts.c:27,
                 from sam_opts.c:1:
In function ‘fprintf’,
    inlined from ‘parse_sam_global_opt’ at /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam_opts.c:85:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:100:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
  100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  101 |    __va_arg_pack ());
      |    ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam_utils.c -o sam_utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c samtools_patch.c -o samtools_patch.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scan_bam_data.c -o scan_bam_data.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tabixfile.c -o tabixfile.o
tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  190 |     if (bgzf_is_bgzf(fn) != 1)
      |     ^~
In file included from tabixfile.c:3:
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
  243 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
      |         ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tagfilter.c -o tagfilter.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c zip_compression.c -o zip_compression.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-Rsamtools/00new/Rsamtools/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 (Rsamtools)