PureCN 1.2.3
Markus Riester
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/PureCN | | Last Changed Rev: 123130 / Revision: 128728 | | Last Changed Date: 2016-10-27 18:26:46 -0400 (Thu, 27 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / 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_1.2.3.zip . & cd ../..
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adding: CITATION (284 bytes security) (deflated 60%)
adding: data/ (324 bytes security) (stored 0%)
adding: data/centromeres.rda (284 bytes security) (stored 0%)
adding: data/purecn.example.output.rda (284 bytes security) (deflated 0%)
adding: DESCRIPTION (284 bytes security) (deflated 42%)
adding: doc/ (324 bytes security) (stored 0%)
adding: doc/index.html (284 bytes security) (deflated 58%)
adding: doc/PureCN.pdf (284 bytes security) (deflated 21%)
adding: doc/PureCN.R (284 bytes security) (deflated 73%)
adding: doc/PureCN.Rnw (284 bytes security) (deflated 68%)
adding: extdata/ (324 bytes security) (stored 0%)
adding: extdata/Coverage.R (284 bytes security) (deflated 61%)
adding: extdata/downloadCentromeres.R (284 bytes security) (deflated 55%)
adding: extdata/ex1.bam (284 bytes security) (deflated 0%)
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adding: extdata/ex2_reference.fa (284 bytes security) (deflated 63%)
adding: extdata/ex2_reference.fa.fai (284 bytes security) (deflated 22%)
adding: extdata/example_cosmic.vcf.gz (284 bytes security) (stored 0%)
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adding: extdata/example_gc.gene.file.txt (284 bytes security) (deflated 70%)
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adding: extdata/example_vcf.vcf (284 bytes security) (deflated 74%)
adding: extdata/NormalDB.R (284 bytes security) (deflated 63%)
adding: extdata/PureCN.R (284 bytes security) (deflated 70%)
adding: extdata/test_coverage_overlapping_intervals.txt (284 bytes security) (deflated 55%)
adding: help/ (324 bytes security) (stored 0%)
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adding: help/AnIndex (284 bytes security) (deflated 67%)
adding: help/paths.rds (284 bytes security) (stored 0%)
adding: help/PureCN.rdb (284 bytes security) (deflated 1%)
adding: help/PureCN.rdx (284 bytes security) (stored 0%)
adding: html/ (324 bytes security) (stored 0%)
adding: html/00Index.html (284 bytes security) (deflated 74%)
adding: html/R.css (284 bytes security) (deflated 75%)
adding: INDEX (284 bytes security) (deflated 63%)
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adding: NAMESPACE (284 bytes security) (deflated 60%)
adding: NEWS (284 bytes security) (deflated 53%)
adding: R/ (324 bytes security) (stored 0%)
adding: R/PureCN (284 bytes security) (deflated 41%)
adding: R/PureCN.rdb (284 bytes security) (deflated 1%)
adding: R/PureCN.rdx (284 bytes security) (stored 0%)
adding: unitTests/ (324 bytes security) (stored 0%)
adding: unitTests/test_autoCurateResults.R (284 bytes security) (deflated 58%)
adding: unitTests/test_bootstrapResults.R (284 bytes security) (deflated 66%)
adding: unitTests/test_calculateBamCoverageByInterval.R (284 bytes security) (deflated 60%)
adding: unitTests/test_calculateGCContentByInterval.R (284 bytes security) (deflated 58%)
adding: unitTests/test_calculatePowerDetectSomatic.R (284 bytes security) (deflated 73%)
adding: unitTests/test_callAlterations.R (284 bytes security) (deflated 54%)
adding: unitTests/test_callAlterationsFromSegmentation.R (284 bytes security) (deflated 54%)
adding: unitTests/test_callLOH.R (284 bytes security) (deflated 34%)
adding: unitTests/test_correctCoverageBias.R (284 bytes security) (deflated 63%)
adding: unitTests/test_createCurationFile.R (284 bytes security) (deflated 80%)
adding: unitTests/test_createNormalDatabase.R (284 bytes security) (deflated 71%)
adding: unitTests/test_createSNPBlacklist.R (284 bytes security) (deflated 57%)
adding: unitTests/test_filterVcf.R (284 bytes security) (deflated 67%)
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adding: unitTests/test_getSexFromCoverage.R (284 bytes security) (deflated 70%)
adding: unitTests/test_getSexFromVcf.R (284 bytes security) (deflated 31%)
adding: unitTests/test_poolCoverage.R (284 bytes security) (deflated 65%)
adding: unitTests/test_predictSomatic.R (284 bytes security) (deflated 56%)
adding: unitTests/test_readCoverageGatk.R (284 bytes security) (deflated 55%)
adding: unitTests/test_runAbsoluteCN.R (284 bytes security) (deflated 80%)
adding: unitTests/test_setMappingBiasVcf.R (284 bytes security) (deflated 52%)
adding: unitTests/test_setPriorVcf.R (284 bytes security) (deflated 44%)