PureCN 1.1.50
Markus Riester
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN | | Last Changed Rev: 121142 / Revision: 121152 | | Last Changed Date: 2016-09-19 09:27:55 -0700 (Mon, 19 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | [ OK ] | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### cd PureCN.buildbin-libdir/PureCN && zip -r ../../PureCN_1.1.50.zip . & cd ../..
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adding: CITATION (188 bytes security) (deflated 60%)
adding: data/ (208 bytes security) (stored 0%)
adding: data/centromeres.rda (188 bytes security) (stored 0%)
adding: data/purecn.example.output.rda (188 bytes security) (deflated 0%)
adding: DESCRIPTION (188 bytes security) (deflated 42%)
adding: doc/ (208 bytes security) (stored 0%)
adding: doc/index.html (188 bytes security) (deflated 58%)
adding: doc/PureCN.pdf (188 bytes security) (deflated 21%)
adding: doc/PureCN.R (188 bytes security) (deflated 73%)
adding: doc/PureCN.Rnw (188 bytes security) (deflated 68%)
adding: extdata/ (208 bytes security) (stored 0%)
adding: extdata/Coverage.R (188 bytes security) (deflated 61%)
adding: extdata/downloadCentromeres.R (188 bytes security) (deflated 55%)
adding: extdata/ex1.bam (188 bytes security) (deflated 0%)
adding: extdata/ex1.bam.bai (188 bytes security) (deflated 63%)
adding: extdata/ex1_intervals.txt (188 bytes security) (deflated 37%)
adding: extdata/ex2_intervals.txt (188 bytes security) (deflated 34%)
adding: extdata/ex2_reference.fa (188 bytes security) (deflated 63%)
adding: extdata/ex2_reference.fa.fai (188 bytes security) (deflated 22%)
adding: extdata/example_cosmic.vcf.gz (188 bytes security) (stored 0%)
adding: extdata/example_cosmic.vcf.gz.tbi (188 bytes security) (deflated 39%)
adding: extdata/example_gc.gene.file.txt (188 bytes security) (deflated 70%)
adding: extdata/example_normal.txt (188 bytes security) (deflated 57%)
adding: extdata/example_normal2.txt (188 bytes security) (deflated 57%)
adding: extdata/example_seg.txt (188 bytes security) (deflated 58%)
adding: extdata/example_tumor.txt (188 bytes security) (deflated 56%)
adding: extdata/example_vcf.vcf (188 bytes security) (deflated 74%)
adding: extdata/NormalDB.R (188 bytes security) (deflated 63%)
adding: extdata/PureCN.R (188 bytes security) (deflated 69%)
adding: help/ (208 bytes security) (stored 0%)
adding: help/aliases.rds (188 bytes security) (stored 0%)
adding: help/AnIndex (188 bytes security) (deflated 66%)
adding: help/paths.rds (188 bytes security) (stored 0%)
adding: help/PureCN.rdb (188 bytes security) (deflated 1%)
adding: help/PureCN.rdx (188 bytes security) (stored 0%)
adding: html/ (208 bytes security) (stored 0%)
adding: html/00Index.html (188 bytes security) (deflated 74%)
adding: html/R.css (188 bytes security) (deflated 75%)
adding: INDEX (188 bytes security) (deflated 62%)
adding: MD5 (188 bytes security) (deflated 48%)
adding: Meta/ (208 bytes security) (stored 0%)
adding: Meta/data.rds (188 bytes security) (stored 0%)
adding: Meta/hsearch.rds (188 bytes security) (stored 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 60%)
adding: NEWS (188 bytes security) (deflated 56%)
adding: R/ (208 bytes security) (stored 0%)
adding: R/PureCN (188 bytes security) (deflated 41%)
adding: R/PureCN.rdb (188 bytes security) (deflated 1%)
adding: R/PureCN.rdx (188 bytes security) (stored 0%)
adding: unitTests/ (208 bytes security) (stored 0%)
adding: unitTests/test_autoCurateResults.R (188 bytes security) (deflated 58%)
adding: unitTests/test_bootstrapResults.R (188 bytes security) (deflated 66%)
adding: unitTests/test_calculateBamCoverageByInterval.R (188 bytes security) (deflated 60%)
adding: unitTests/test_calculateGCContentByInterval.R (188 bytes security) (deflated 58%)
adding: unitTests/test_calculatePowerDetectSomatic.R (188 bytes security) (deflated 73%)
adding: unitTests/test_callAlterations.R (188 bytes security) (deflated 54%)
adding: unitTests/test_callLOH.R (188 bytes security) (deflated 34%)
adding: unitTests/test_correctCoverageBias.R (188 bytes security) (deflated 63%)
adding: unitTests/test_createCurationFile.R (188 bytes security) (deflated 80%)
adding: unitTests/test_createNormalDatabase.R (188 bytes security) (deflated 71%)
adding: unitTests/test_createSNPBlacklist.R (188 bytes security) (deflated 57%)
adding: unitTests/test_filterVcf.R (188 bytes security) (deflated 67%)
adding: unitTests/test_findFocal.R (188 bytes security) (deflated 48%)
adding: unitTests/test_getDiploid.R (188 bytes security) (deflated 52%)
adding: unitTests/test_getSexFromCoverage.R (188 bytes security) (deflated 70%)
adding: unitTests/test_getSexFromVcf.R (188 bytes security) (deflated 31%)
adding: unitTests/test_poolCoverage.R (188 bytes security) (deflated 65%)
adding: unitTests/test_predictSomatic.R (188 bytes security) (deflated 56%)
adding: unitTests/test_readCoverageGatk.R (188 bytes security) (deflated 36%)
adding: unitTests/test_runAbsoluteCN.R (188 bytes security) (deflated 81%)
adding: unitTests/test_setMappingBiasVcf.R (188 bytes security) (deflated 52%)
adding: unitTests/test_setPriorVcf.R (188 bytes security) (deflated 44%)