Rsamtools 1.29.0 Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools | Last Changed Rev: 129129 / Revision: 131943 | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] |  |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
##############################################################################
##############################################################################
###
### Running command:
###
### cd Rsamtools.buildbin-libdir/Rsamtools && zip -r ../../Rsamtools_1.29.0.zip . & cd ../..
###
##############################################################################
##############################################################################
adding: DESCRIPTION (332 bytes security) (deflated 42%)
adding: doc/ (372 bytes security) (stored 0%)
adding: doc/index.html (332 bytes security) (deflated 68%)
adding: doc/Rsamtools-Overview.pdf (332 bytes security) (deflated 13%)
adding: doc/Rsamtools-Overview.R (332 bytes security) (deflated 76%)
adding: doc/Rsamtools-Overview.Rnw (332 bytes security) (deflated 62%)
adding: doc/Rsamtools-UsingCLibraries.pdf (332 bytes security) (deflated 10%)
adding: doc/Rsamtools-UsingCLibraries.R (332 bytes security) (deflated 48%)
adding: doc/Rsamtools-UsingCLibraries.Rnw (332 bytes security) (deflated 57%)
adding: extdata/ (372 bytes security) (stored 0%)
adding: extdata/ce2dict1.fa (332 bytes security) (deflated 47%)
adding: extdata/ce2dict1.fa.fai (332 bytes security) (deflated 44%)
adding: extdata/ex1.bam (332 bytes security) (deflated 0%)
adding: extdata/ex1.bam.bai (332 bytes security) (deflated 63%)
adding: extdata/ex1.bcf (332 bytes security) (deflated 0%)
adding: extdata/ex1.bcf.bci (332 bytes security) (deflated 26%)
adding: extdata/ex1.sam (332 bytes security) (deflated 80%)
adding: extdata/example.gtf.gz (332 bytes security) (stored 0%)
adding: extdata/example.gtf.gz.tbi (332 bytes security) (deflated 5%)
adding: extdata/example_from_SAM_Spec.bam (332 bytes security) (deflated 7%)
adding: extdata/example_from_SAM_Spec.bam.bai (332 bytes security) (deflated 59%)
adding: extdata/example_from_SAM_Spec.sam (332 bytes security) (deflated 45%)
adding: extdata/no_which_buffered_pileup.bam (332 bytes security) (deflated 16%)
adding: extdata/no_which_buffered_pileup.bam.bai (332 bytes security) (deflated 69%)
adding: extdata/no_which_buffered_pileup.sam (332 bytes security) (deflated 60%)
adding: extdata/no_which_whole_file.bam (332 bytes security) (deflated 16%)
adding: extdata/no_which_whole_file.bam.bai (332 bytes security) (deflated 69%)
adding: extdata/no_which_whole_file.sam (332 bytes security) (deflated 47%)
adding: extdata/olaps.Rda (332 bytes security) (deflated 3%)
adding: extdata/pileup.txt (332 bytes security) (deflated 47%)
adding: extdata/querybins.bam (332 bytes security) (deflated 18%)
adding: extdata/querybins.bam.bai (332 bytes security) (deflated 59%)
adding: extdata/querybins.sam (332 bytes security) (deflated 31%)
adding: extdata/revbins.bam (332 bytes security) (deflated 5%)
adding: extdata/revbins.bam.bai (332 bytes security) (deflated 76%)
adding: extdata/revbins.sam (332 bytes security) (deflated 71%)
adding: extdata/samtools-github.txt (332 bytes security) (stored 0%)
adding: extdata/slxMaq09_urls.txt (332 bytes security) (deflated 91%)
adding: extdata/tagfilter.bam (332 bytes security) (deflated 7%)
adding: extdata/tagfilter.bam.bai (332 bytes security) (deflated 80%)
adding: extdata/tagfilter.sam (332 bytes security) (deflated 75%)
adding: extdata/tiny.bam (332 bytes security) (stored 0%)
adding: extdata/tiny.bam.bai (332 bytes security) (deflated 85%)
adding: extdata/tiny.sam (332 bytes security) (deflated 80%)
adding: extdata/tophat/ (372 bytes security) (stored 0%)
adding: extdata/tophat/accepted_hits.sam (332 bytes security) (deflated 90%)
adding: extdata/tophat/coverage.wig (332 bytes security) (deflated 78%)
adding: extdata/tophat/junctions.bed (332 bytes security) (deflated 34%)
adding: extdata/tophat/README (332 bytes security) (stored 0%)
adding: help/ (372 bytes security) (stored 0%)
adding: help/aliases.rds (332 bytes security) (stored 0%)
adding: help/AnIndex (332 bytes security) (deflated 84%)
adding: help/paths.rds (332 bytes security) (stored 0%)
adding: help/Rsamtools.rdb (332 bytes security) (deflated 1%)
adding: help/Rsamtools.rdx (332 bytes security) (stored 0%)
adding: html/ (372 bytes security) (stored 0%)
adding: html/00Index.html (332 bytes security) (deflated 92%)
adding: html/R.css (332 bytes security) (deflated 75%)
adding: include/ (548 bytes security) (stored 0%)
adding: include/samtools/ (548 bytes security) (stored 0%)
adding: include/samtools/bam.h (332 bytes security) (deflated 70%)
adding: include/samtools/bam_endian.h (332 bytes security) (deflated 68%)
adding: include/samtools/bcftools/ (548 bytes security) (stored 0%)
adding: include/samtools/bcftools/bcf.h (332 bytes security) (deflated 61%)
adding: include/samtools/bcftools/prob1.h (332 bytes security) (deflated 59%)
adding: include/samtools/bgzf.h (332 bytes security) (deflated 60%)
adding: include/samtools/faidx.h (332 bytes security) (deflated 62%)
adding: include/samtools/kaln.h (332 bytes security) (deflated 49%)
adding: include/samtools/khash.h (332 bytes security) (deflated 75%)
adding: include/samtools/knetfile.h (332 bytes security) (deflated 56%)
adding: include/samtools/kprobaln.h (332 bytes security) (deflated 44%)
adding: include/samtools/kseq.h (332 bytes security) (deflated 66%)
adding: include/samtools/ksort.h (332 bytes security) (deflated 67%)
adding: include/samtools/kstring.h (332 bytes security) (deflated 63%)
adding: include/samtools/razf.h (332 bytes security) (deflated 53%)
adding: include/samtools/sam.h (332 bytes security) (deflated 58%)
adding: include/samtools/sam_header.h (332 bytes security) (deflated 62%)
adding: include/tabix/ (548 bytes security) (stored 0%)
adding: include/tabix/bgzf.h (332 bytes security) (deflated 60%)
adding: include/tabix/knetfile.h (332 bytes security) (deflated 56%)
adding: include/tabix/kstring.h (332 bytes security) (deflated 63%)
adding: include/tabix/tabix.h (332 bytes security) (deflated 59%)
adding: INDEX (332 bytes security) (deflated 66%)
adding: libs/ (372 bytes security) (stored 0%)
adding: libs/i386/ (372 bytes security) (stored 0%)
adding: libs/i386/Rsamtools.dll (332 bytes security) (deflated 62%)
adding: libs/x64/ (372 bytes security) (stored 0%)
adding: libs/x64/Rsamtools.dll (332 bytes security) (deflated 62%)
adding: LICENSE (332 bytes security) (deflated 41%)
adding: MD5 (332 bytes security) (deflated 53%)
adding: Meta/ (372 bytes security) (stored 0%)
adding: Meta/features.rds (332 bytes security) (stored 0%)
adding: Meta/hsearch.rds (332 bytes security) (stored 0%)
adding: Meta/links.rds (332 bytes security) (stored 0%)
adding: Meta/nsInfo.rds (332 bytes security) (stored 0%)
adding: Meta/package.rds (332 bytes security) (stored 0%)
adding: Meta/Rd.rds (332 bytes security) (stored 0%)
adding: Meta/vignette.rds (332 bytes security) (stored 0%)
adding: NAMESPACE (332 bytes security) (deflated 61%)
adding: NEWS (332 bytes security) (deflated 64%)
adding: R/ (372 bytes security) (stored 0%)
adding: R/Rsamtools (332 bytes security) (deflated 41%)
adding: R/Rsamtools.rdb (332 bytes security) (deflated 37%)
adding: R/Rsamtools.rdx (332 bytes security) (deflated 2%)
adding: scripts/ (372 bytes security) (stored 0%)
adding: scripts/BamViews-1000g.R (332 bytes security) (deflated 53%)
adding: scripts/features.R (332 bytes security) (deflated 52%)
adding: scripts/remote_test.R (332 bytes security) (deflated 56%)
adding: scripts/update-samtools.sh (332 bytes security) (deflated 66%)
adding: unitTests/ (372 bytes security) (stored 0%)
adding: unitTests/cases/ (372 bytes security) (stored 0%)
adding: unitTests/cases/ex1.sam.gz (332 bytes security) (deflated 0%)
adding: unitTests/cases/ex1_noindex.bam (332 bytes security) (deflated 0%)
adding: unitTests/cases/ex1_shuf1000.bam (332 bytes security) (deflated 0%)
adding: unitTests/cases/ex1_shuf1000.bam.bai (332 bytes security) (deflated 56%)
adding: unitTests/cases/ex1_unsort.bam (332 bytes security) (deflated 0%)
adding: unitTests/cases/ex1_zero_index.bam.bai (332 bytes security) (stored 0%)
adding: unitTests/cases/no_header_line.vcf (332 bytes security) (deflated 56%)
adding: unitTests/cases/no_SAMPLE_header.vcf (332 bytes security) (deflated 49%)
adding: unitTests/cases/pileup-no-stars.txt (332 bytes security) (deflated 40%)
adding: unitTests/cases/plp_refskip.bam (332 bytes security) (deflated 12%)
adding: unitTests/cases/plp_refskip.bam.bai (332 bytes security) (deflated 59%)
adding: unitTests/test_applyPileups.R (332 bytes security) (deflated 82%)
adding: unitTests/test_asBam.R (332 bytes security) (deflated 48%)
adding: unitTests/test_bam.R (332 bytes security) (deflated 77%)
adding: unitTests/test_BamFile.R (332 bytes security) (deflated 80%)
adding: unitTests/test_BamViews.R (332 bytes security) (deflated 75%)
adding: unitTests/test_bam_count.R (332 bytes security) (deflated 69%)
adding: unitTests/test_bam_header.R (332 bytes security) (deflated 28%)
adding: unitTests/test_BcfFile.R (332 bytes security) (deflated 69%)
adding: unitTests/test_compression.R (332 bytes security) (deflated 65%)
adding: unitTests/test_FaFile.R (332 bytes security) (deflated 73%)
adding: unitTests/test_mapqfilter.R (332 bytes security) (deflated 61%)
adding: unitTests/test_phred2ASCIIOffset.R (332 bytes security) (deflated 72%)
adding: unitTests/test_pileup_nowhich.R (332 bytes security) (deflated 75%)
adding: unitTests/test_pileup_querybins.R (332 bytes security) (deflated 86%)
adding: unitTests/test_pileup_revbins.R (332 bytes security) (deflated 87%)
adding: unitTests/test_pileup_single_range.R (332 bytes security) (deflated 89%)
adding: unitTests/test_readPileup.R (332 bytes security) (deflated 63%)
adding: unitTests/test_RsamtoolsFile.R (332 bytes security) (deflated 76%)
adding: unitTests/test_scanBamFlag.R (332 bytes security) (deflated 43%)
adding: unitTests/test_sortBam_test.R (332 bytes security) (deflated 55%)
adding: unitTests/test_TabixFile.R (332 bytes security) (deflated 65%)
adding: unitTests/test_tagfilter.R (332 bytes security) (deflated 74%)
adding: unitTests/test_testPairedEndBam.R (332 bytes security) (deflated 31%)
adding: unitTests/test_utilities.R (332 bytes security) (deflated 51%)
adding: usretc/ (548 bytes security) (stored 0%)
adding: usretc/i386/ (548 bytes security) (stored 0%)
adding: usretc/i386/Rsamtools.mk (332 bytes security) (deflated 58%)
adding: usretc/x64/ (548 bytes security) (stored 0%)
adding: usretc/x64/Rsamtools.mk (332 bytes security) (deflated 58%)
adding: usrlib/ (548 bytes security) (stored 0%)
adding: usrlib/i386/ (548 bytes security) (stored 0%)
adding: usrlib/i386/libbam.a (332 bytes security) (deflated 58%)
adding: usrlib/i386/libbcf.a (332 bytes security) (deflated 59%)
adding: usrlib/i386/libtabix.a (332 bytes security) (deflated 55%)
adding: usrlib/x64/ (548 bytes security) (stored 0%)
adding: usrlib/x64/libbam.a (332 bytes security) (deflated 56%)
adding: usrlib/x64/libbcf.a (332 bytes security) (deflated 58%)
adding: usrlib/x64/libtabix.a (332 bytes security) (deflated 54%)