| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:48 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the Rsamtools package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1714/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsamtools 2.15.0 (landing page) Bioconductor Package Maintainer
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: Rsamtools |
| Version: 2.15.0 |
| Command: rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=Rsamtools.buildbin-libdir Rsamtools_2.15.0.tar.gz |
| StartedAt: 2022-12-29 05:40:33 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 05:41:53 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 80.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rsamtools_2.15.0.zip |
| PackageFileSize: 7.548 MiB |
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### Running command:
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### rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=Rsamtools.buildbin-libdir Rsamtools_2.15.0.tar.gz
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* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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 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-3.17-bioc/R/library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #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-3.17-bioc/R/library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function '_bam_tryindexload',
inlined from '_bamfile_open_r' at bamfile.c:89:24,
inlined from 'bamfile_open' at bamfile.c:127:17:
bamfile.c:29:17: warning: 'cfile' may be used uninitialized [-Wmaybe-uninitialized]
29 | index = hts_idx_load2(file, indexname);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function 'bamfile_open':
bamfile.c:73:17: note: 'cfile' was declared here
73 | const char *cfile;
| ^~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bedidx.c -o bedidx.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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 bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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 io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/library/Rhtslib/include/htslib/bgzf.h:270:9: note: declared here
270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
| ^~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.17-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_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.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-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rsamtools.buildbin-libdir/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
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_2.15.0.zip
* DONE (Rsamtools)