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INSTALL report for Rsamtools on malbec2

This page was generated on 2020-10-17 11:55:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Rsamtools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1539/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.4.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Rsamtools
Branch: RELEASE_3_11
Last Commit: 3871cc8
Last Changed Date: 2020-04-27 14:21:43 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsamtools
Version: 2.4.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rsamtools
StartedAt: 2020-10-16 16:41:54 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 16:42:43 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 48.4 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rsamtools
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ResultManager.cpp -o ResultManager.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam.c -o bam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_data.c -o bam_data.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rhtslib/include/sam.h:29:0,
                 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-3.11-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]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:9: note: in expansion of macro ‘bam_seek’
         bam_seek(bfile, pos, SEEK_SET);
         ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
/home/biocbuild/bbs-3.11-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]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:9: note: in expansion of macro ‘bam_seek’
         bam_seek(bfile, 0, 0);
         ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_sort.c -o bam_sort.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bambuffer.c -o bambuffer.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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:168:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
             bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function ‘bamfile_open’:
bamfile.c:29:15: warning: ‘cfile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         index = hts_idx_load2(file, indexname);
         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c:73:17: note: ‘cfile’ was declared here
     const char *cfile;
                 ^~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bcffile.c -o bcffile.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c encode.c -o encode.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fafile.c -o fafile.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rhtslib/include/sam.h:29:0,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:5: note: in expansion of macro ‘bam_seek’
     bam_seek(fp, 0, 0);
     ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rhtslib/include/sam.h:29:0,
                 from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:5: note: in expansion of macro ‘bam_seek’
     bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
     ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pileup.cpp -o pileup.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pileupbam.c -o pileupbam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam.c -o sam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam_opts.c -o sam_opts.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-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]
     if (bgzf_is_bgzf(fn) != 1)
     ^~
In file included from tabixfile.c:3:0:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
         ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tagfilter.c -o tagfilter.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c zip_compression.c -o zip_compression.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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)