ShortRead 1.31.1
Bioconductor Package Maintainer
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead | | Last Changed Rev: 119243 / Revision: 121152 | | Last Changed Date: 2016-07-10 01:46:24 -0700 (Sun, 10 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | [ OK ] | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### cd ShortRead.buildbin-libdir/ShortRead && zip -r ../../ShortRead_1.31.1.zip . & cd ../..
###
##############################################################################
##############################################################################
adding: CITATION (188 bytes security) (deflated 60%)
adding: DESCRIPTION (188 bytes security) (deflated 44%)
adding: doc/ (208 bytes security) (stored 0%)
adding: doc/index.html (188 bytes security) (deflated 58%)
adding: doc/Overview.pdf (188 bytes security) (deflated 11%)
adding: doc/Overview.R (188 bytes security) (deflated 77%)
adding: doc/Overview.Rnw (188 bytes security) (deflated 62%)
adding: extdata/ (208 bytes security) (stored 0%)
adding: extdata/bowtie/ (208 bytes security) (stored 0%)
adding: extdata/bowtie/s_1_aligned_bowtie.txt (188 bytes security) (deflated 73%)
adding: extdata/Data/ (208 bytes security) (stored 0%)
adding: extdata/Data/C1-36Firecrest/ (208 bytes security) (stored 0%)
adding: extdata/Data/C1-36Firecrest/Bustard/ (208 bytes security) (stored 0%)
adding: extdata/Data/C1-36Firecrest/Bustard/GERALD/ (208 bytes security) (stored 0%)
adding: extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt (188 bytes security) (deflated 72%)
adding: extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt (188 bytes security) (deflated 71%)
adding: extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt (188 bytes security) (deflated 76%)
adding: extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt (188 bytes security) (deflated 94%)
adding: extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt (188 bytes security) (deflated 65%)
adding: extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt (188 bytes security) (deflated 66%)
adding: extdata/Data/C1-36Firecrest/s_1_0001_int.txt (188 bytes security) (deflated 58%)
adding: extdata/Data/C1-36Firecrest/s_1_0001_nse.txt (188 bytes security) (deflated 94%)
adding: extdata/E-MTAB-1147/ (208 bytes security) (stored 0%)
adding: extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz (188 bytes security) (deflated 0%)
adding: extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz (188 bytes security) (deflated 0%)
adding: extdata/maq/ (208 bytes security) (stored 0%)
adding: extdata/maq/out.aln.1.txt (188 bytes security) (deflated 93%)
adding: extdata/maq/out.aln.2.txt (188 bytes security) (deflated 94%)
adding: help/ (208 bytes security) (stored 0%)
adding: help/aliases.rds (188 bytes security) (stored 0%)
adding: help/AnIndex (188 bytes security) (deflated 85%)
adding: help/paths.rds (188 bytes security) (stored 0%)
adding: help/ShortRead.rdb (188 bytes security) (deflated 1%)
adding: help/ShortRead.rdx (188 bytes security) (stored 0%)
adding: html/ (208 bytes security) (stored 0%)
adding: html/00Index.html (188 bytes security) (deflated 92%)
adding: html/R.css (188 bytes security) (deflated 75%)
adding: INDEX (188 bytes security) (deflated 72%)
adding: libs/ (208 bytes security) (stored 0%)
adding: libs/i386/ (208 bytes security) (stored 0%)
adding: libs/i386/ShortRead.dll (188 bytes security) (deflated 65%)
adding: libs/x64/ (208 bytes security) (stored 0%)
adding: libs/x64/ShortRead.dll (188 bytes security) (deflated 67%)
adding: MD5 (188 bytes security) (deflated 53%)
adding: Meta/ (208 bytes security) (stored 0%)
adding: Meta/hsearch.rds (188 bytes security) (deflated 0%)
adding: Meta/links.rds (188 bytes security) (stored 0%)
adding: Meta/nsInfo.rds (188 bytes security) (stored 0%)
adding: Meta/package.rds (188 bytes security) (stored 0%)
adding: Meta/Rd.rds (188 bytes security) (stored 0%)
adding: Meta/vignette.rds (188 bytes security) (stored 0%)
adding: NAMESPACE (188 bytes security) (deflated 50%)
adding: NEWS (188 bytes security) (deflated 63%)
adding: R/ (208 bytes security) (stored 0%)
adding: R/ShortRead (188 bytes security) (deflated 41%)
adding: R/ShortRead.rdb (188 bytes security) (deflated 27%)
adding: R/ShortRead.rdx (188 bytes security) (deflated 4%)
adding: script/ (208 bytes security) (stored 0%)
adding: script/qa-test.R (188 bytes security) (deflated 28%)
adding: template/ (208 bytes security) (stored 0%)
adding: template/0000-Header.html (188 bytes security) (deflated 40%)
adding: template/1000-Overview.html (188 bytes security) (deflated 41%)
adding: template/1100-Overview-SolexaRealign.html (188 bytes security) (deflated 27%)
adding: template/2000-RunSummary.html (188 bytes security) (deflated 46%)
adding: template/3000-ReadDistribution.html (188 bytes security) (deflated 57%)
adding: template/4000-CycleSpecific.html (188 bytes security) (deflated 46%)
adding: template/5000-PerTile.html (188 bytes security) (deflated 56%)
adding: template/6000-Alignment.html (188 bytes security) (deflated 29%)
adding: template/7000-MultipleAlignment.html (188 bytes security) (deflated 26%)
adding: template/8000-DepthOfCoverage.html (188 bytes security) (deflated 22%)
adding: template/9000-AdapterContamination.html (188 bytes security) (deflated 40%)
adding: template/9999-Footer.html (188 bytes security) (deflated 7%)
adding: template/image/ (208 bytes security) (stored 0%)
adding: template/image/bioclogo-small.gif (188 bytes security) (deflated 1%)
adding: template/QA.css (188 bytes security) (deflated 56%)
adding: template/QAAdapterContamination.html (188 bytes security) (deflated 39%)
adding: template/QAFiltered.html (188 bytes security) (deflated 15%)
adding: template/QAFlagged.html (188 bytes security) (deflated 14%)
adding: template/QAFooter.html (188 bytes security) (deflated 7%)
adding: template/QAFrequentSequence.html (188 bytes security) (deflated 30%)
adding: template/QAHeader.html (188 bytes security) (deflated 40%)
adding: template/QANucleotideByCycle.html (188 bytes security) (deflated 27%)
adding: template/QANucleotideUse.html (188 bytes security) (deflated 28%)
adding: template/QAQualityByCycle.html (188 bytes security) (deflated 40%)
adding: template/QAQualityUse.html (188 bytes security) (deflated 26%)
adding: template/QAReadQuality.html (188 bytes security) (deflated 28%)
adding: template/QASequenceUse.html (188 bytes security) (deflated 52%)
adding: template/QASources.html (188 bytes security) (deflated 18%)
adding: template/qa_solexa.Rnw (188 bytes security) (deflated 59%)
adding: unitTests/ (208 bytes security) (stored 0%)
adding: unitTests/cases/ (208 bytes security) (stored 0%)
adding: unitTests/cases/PE_export.txt.gz (188 bytes security) (stored 0%)
adding: unitTests/cases/sanger.fastq (188 bytes security) (deflated 29%)
adding: unitTests/cases/soap.txt (188 bytes security) (deflated 76%)
adding: unitTests/cases/solexa.fastq (188 bytes security) (deflated 28%)
adding: unitTests/cases/s_1_0001_int_head.txt.p (188 bytes security) (deflated 52%)
adding: unitTests/cases/s_1_0001_nse_head.txt.p (188 bytes security) (deflated 61%)
adding: unitTests/cases/s_1_0001_pos_head.txt (188 bytes security) (deflated 34%)
adding: unitTests/cases/s_1_results_head.txt (188 bytes security) (deflated 74%)
adding: unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt (188 bytes security) (deflated 50%)
adding: unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt (188 bytes security) (deflated 50%)
adding: unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt (188 bytes security) (deflated 50%)
adding: unitTests/cases/s_1_sequence.9_lines.txt (188 bytes security) (deflated 52%)
adding: unitTests/cases/s_1_sequence.txt (188 bytes security) (deflated 72%)
adding: unitTests/cases/s_2_0001_realign_3col_head.txt (188 bytes security) (deflated 58%)
adding: unitTests/cases/s_2_0001_realign_head.txt (188 bytes security) (deflated 68%)
adding: unitTests/cases/s_2_export_run_as_factor.txt (188 bytes security) (deflated 57%)
adding: unitTests/cases/s_2_export_toIUPAC.txt (188 bytes security) (deflated 54%)
adding: unitTests/test_AlignedRead.R (188 bytes security) (deflated 77%)
adding: unitTests/test_AllClasses.R (188 bytes security) (deflated 46%)
adding: unitTests/test_append.R (188 bytes security) (deflated 67%)
adding: unitTests/test_coverage.R (188 bytes security) (deflated 75%)
adding: unitTests/test_FastqFile.R (188 bytes security) (deflated 62%)
adding: unitTests/test_filterFastq.R (188 bytes security) (deflated 59%)
adding: unitTests/test_functions.R (188 bytes security) (deflated 73%)
adding: unitTests/test_Intensity.R (188 bytes security) (deflated 69%)
adding: unitTests/test_qa.R (188 bytes security) (deflated 63%)
adding: unitTests/test_readPrb.R (188 bytes security) (deflated 70%)
adding: unitTests/test_readQseq.R (188 bytes security) (deflated 63%)
adding: unitTests/test_readXStringColumns.R (188 bytes security) (deflated 69%)
adding: unitTests/test_renew.R (188 bytes security) (deflated 57%)
adding: unitTests/test_ShortRead.R (188 bytes security) (deflated 67%)
adding: unitTests/test_ShortReadQ.R (188 bytes security) (deflated 78%)
adding: unitTests/test_SolexaIntensity.R (188 bytes security) (deflated 73%)
adding: unitTests/test_SRError.R (188 bytes security) (deflated 77%)
adding: unitTests/test_SRFilter.R (188 bytes security) (deflated 80%)
adding: unitTests/test_SRFilterResult.R (188 bytes security) (deflated 80%)
adding: unitTests/test_SRList.R (188 bytes security) (deflated 76%)
adding: unitTests/test_SRVector.R (188 bytes security) (deflated 59%)
adding: unitTests/test_trimEnds.R (188 bytes security) (deflated 64%)
adding: unitTests/test_trimTails.R (188 bytes security) (deflated 77%)
adding: unitTests/test_writeFastq.R (188 bytes security) (deflated 63%)