Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:11 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for Rsamtools on palomino3


To the developers/maintainers of the Rsamtools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsamtools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1706/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.12.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Rsamtools
git_branch: RELEASE_3_15
git_last_commit: d6a65dd
git_last_commit_date: 2022-04-26 11:04:33 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Rsamtools
Version: 2.12.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsamtools
StartedAt: 2022-10-18 15:53:21 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 15:54:39 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 78.3 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsamtools
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PosCacheColl.cpp -o PosCacheColl.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ResultManager.cpp -o ResultManager.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c as_bam.c -o as_bam.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam.c -o bam.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam_data.c -o bam_data.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from F:/biocbuild/bbs-3.15-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)':
F:/biocbuild/bbs-3.15-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*)':
F:/biocbuild/bbs-3.15-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"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam_plbuf.c -o bam_plbuf.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'bam_sort_core_ext':
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2065:9: warning: 'strncpy' specified bound 2 equals destination size [-Wstringop-truncation]
 2065 |         strncpy(g_sort_tag, sort_by_tag, 2);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bambuffer.c -o bambuffer.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bcffile.c -o bcffile.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c encode.c -o encode.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fafile.c -o fafile.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c idxstats.c -o idxstats.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/sam.h:29,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
F:/biocbuild/bbs-3.15-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"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io_sam.c -o io_sam.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/sam.h:29,
                 from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
F:/biocbuild/bbs-3.15-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++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pileup.cpp -o pileup.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pileupbam.c -o pileupbam.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam.c -o sam.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam_opts.c -o sam_opts.o
In file included from sam_opts.c:1:
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/sam_opts.c: In function 'parse_sam_global_opt':
F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/sam_opts.c:85:9: warning: '%s' directive argument is null [-Wformat-overflow=]
   85 |         fprintf(stderr, "Unexpected global option: %s\n", lopt->name);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam_utils.c -o sam_utils.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c samtools_patch.c -o samtools_patch.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c scan_bam_data.c -o scan_bam_data.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:
F:/biocbuild/bbs-3.15-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"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tagfilter.c -o tagfilter.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c zip_compression.c -o zip_compression.o
g++ -std=gnu++11 -shared -s -static-libgcc -o Rsamtools.dll tmp.def 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 F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rsamtools/00new/Rsamtools/libs/x64
** 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 (Rsamtools)