Michael Stadler
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/QuasR |
| Branch: RELEASE_3_6 |
| Last Commit: aa0bdbc |
| Last Changed Date: 2017-10-30 12:39:58 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:22:26 -0400 (Thu, 12 Apr 2018).
| Package 1104/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| QuasR 1.18.0 Michael Stadler
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | [ OK ] | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: QuasR |
| Version: 1.18.0 |
| Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.18.0.tar.gz |
| StartedAt: 2018-04-12 04:58:33 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 05:00:04 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 91.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: QuasR_1.18.0.zip |
| PackageFileSize: 1.97 MiB |
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### Running command:
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### rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.18.0.tar.gz
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* installing *source* package 'QuasR' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_init_QuasR.cpp -o R_init_QuasR.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c cat_bam.c -o cat_bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c count_alignments.c -o count_alignments.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c count_alignments_subregions.c -o count_alignments_subregions.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c count_junctions.cpp -o count_junctions.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c export_wig.c -o export_wig.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c extract_unmapped_reads.c -o extract_unmapped_reads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c idxstats_bam.c -o idxstats_bam.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c merge_reorder_sam.cpp -o merge_reorder_sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c profile_alignments.c -o profile_alignments.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c quantify_methylation.cpp -o quantify_methylation.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c split_sam_chr.c -o split_sam_chr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/QuasR.buildbin-libdir/QuasR/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'QuasR'
finding HTML links ... done
QuasR-package html
alignmentStats html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/alignmentStats.Rd:51: missing file link 'qProject'
preprocessReads html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/preprocessReads.Rd:98: missing file link 'clusterMap'
qAlign html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qAlign.Rd:85: missing file link 'parallel'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qAlign.Rd:180: missing file link 'qProject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qAlign.Rd:195: missing file link 'qProject'
qCount html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:30: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:31: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:32: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:83: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:124: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:133: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:145: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:227: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qCount.Rd:241: missing file link 'clusterMap'
qExportWig html
qMeth html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qMeth.Rd:118: missing file link 'clusterApplyLB'
qProfile html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qProfile.Rd:31: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qProfile.Rd:80: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcxWnjc/R.INSTALL377c2e41437/QuasR/man/qProfile.Rd:121: missing file link 'GRanges'
qProject-class html
qQCReport html
finding level-2 HTML links ... done
** building package indices
** installing vignettes
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuasR' as QuasR_1.18.0.zip
* DONE (QuasR)
In R CMD INSTALL