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This page was generated on 2022-03-18 11:08:33 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 1667/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.11.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/Rsamtools
git_branch: master
git_last_commit: badd3a3
git_last_commit_date: 2021-10-26 11:55:47 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
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: 2.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsamtools
StartedAt: 2022-03-17 15:47:49 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 15:49:07 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 77.6 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsamtools
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c PileupBuffer.cpp -o PileupBuffer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c PosCacheColl.cpp -o PosCacheColl.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ResultManager.cpp -o ResultManager.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c as_bam.c -o as_bam.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam.c -o bam.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam_data.c -o bam_data.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from D:/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)':
D:/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]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro 'bam_seek'
         (void) bam_seek(bfile, pos, SEEK_SET);
                ^~~~~~~~
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
D:/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]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro 'bam_seek'
         (void) bam_seek(bfile, 0, 0);
                ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam_plbuf.c -o bam_plbuf.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:26: warning: unknown conversion type character 'z' in format [-Wformat=]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
                          ^
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
                            ~^
                            %I64d
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13:
             max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
             ~~~~~~~          
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:74: warning: unknown conversion type character 'z' in format [-Wformat=]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
                                                                          ^
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:1: warning: too many arguments for format [-Wformat-extra-args]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:26: warning: unknown conversion type character 'z' in format [-Wformat=]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
                          ^
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
                            ~^
                            %I64d
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13:
             max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
             ~~~~~~~          
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:74: warning: unknown conversion type character 'z' in format [-Wformat=]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
                                                                          ^
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2256:1: warning: too many arguments for format [-Wformat-extra-args]
 "[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'bam_sort_core_ext':
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/bam_sort.c:2065:9: warning: 'strncpy' specified bound 2 equals destination size [-Wstringop-truncation]
         strncpy(g_sort_tag, sort_by_tag, 2);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bambuffer.c -o bambuffer.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
             (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]
         index = hts_idx_load2(file, indexname);
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c:73:17: note: 'cfile' was declared here
     const char *cfile;
                 ^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bcffile.c -o bcffile.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c encode.c -o encode.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fafile.c -o fafile.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c idxstats.c -o idxstats.o
In file included from D:/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':
D:/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]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro 'bam_seek'
     (void) bam_seek(fp, 0, 0);
            ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c io_sam.c -o io_sam.o
In file included from D:/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':
D:/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]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:12: note: in expansion of macro 'bam_seek'
     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c pileup.cpp -o pileup.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c pileupbam.c -o pileupbam.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sam.c -o sam.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sam_opts.c -o sam_opts.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sam_utils.c -o sam_utils.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c samtools_patch.c -o samtools_patch.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c scan_bam_data.c -o scan_bam_data.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:
D:/biocbuild/bbs-3.15-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");
         ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c tagfilter.c -o tagfilter.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c utilities.c -o utilities.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c zip_compression.c -o zip_compression.o
C:/rtools40/mingw64/bin/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 D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/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
  converting help for package 'Rsamtools'
    finding HTML links ... done
    ApplyPileupsParam-class                 html  
    BamFile-class                           html  
    finding level-2 HTML links ... done

    BamViews-class                          html  
    BcfFile-class                           html  
    FaFile-class                            html  
    PileupFiles-class                       html  
    Rsamtools-package                       html  
    RsamtoolsFile-class                     html  
    RsamtoolsFileList-class                 html  
    ScanBamParam-class                      html  
    ScanBcfParam-class                      html  
    TabixFile-class                         html  
    applyPileups                            html  
    defunct                                 html  
    deprecated                              html  
    headerTabix                             html  
    indexTabix                              html  
    pileup                                  html  
    quickBamFlagSummary                     html  
    readPileup                              html  
    scanBam                                 html  
    scanBcf                                 html  
    scanFa                                  html  
    scanTabix                               html  
    seqnamesTabix                           html  
    testPairedEndBam                        html  
    zip                                     html  
** 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)
Making 'packages.html' ... done