R453Plus1Toolbox 1.12.0
Hans-Ulrich Klein
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/R453Plus1Toolbox | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Scanning files .
adding: CITATION (188 bytes security) (deflated 40%)
adding: data/ (256 bytes security) (stored 0%)
adding: data/avaSetExample.RData (188 bytes security) (deflated 3%)
adding: data/avaSetFiltered.RData (188 bytes security) (deflated 3%)
adding: data/avaSetFiltered_annot.RData (188 bytes security) (stored 0%)
adding: data/breakpoints.RData (188 bytes security) (stored 0%)
adding: data/captureArray.RData (188 bytes security) (stored 0%)
adding: data/mapperSetExample.RData (188 bytes security) (deflated 1%)
adding: data/plotVariantsExample.RData (188 bytes security) (stored 0%)
adding: DESCRIPTION (188 bytes security) (deflated 43%)
adding: doc/ (256 bytes security) (stored 0%)
adding: doc/index.html (188 bytes security) (deflated 57%)
adding: doc/vignette.pdf (188 bytes security) (deflated 20%)
adding: doc/vignette.R (188 bytes security) (deflated 82%)
adding: doc/vignette.Rnw (188 bytes security) (deflated 71%)
adding: extdata/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/ProjectDef/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/ProjectDef/ampliconsProject.txt (188 bytes security) (deflated 73%)
adding: extdata/AVASet/Amplicons/Results/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I36/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I36/I116_vs_I36.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I37/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I37/I116_vs_I37.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I40/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I40/I116_vs_I40.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I42/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I116/I42/I116_vs_I42.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I36/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I36/I117_vs_I36.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I37/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I37/I117_vs_I37.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I40/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I40/I117_vs_I40.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I42/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I117/I42/I117_vs_I42.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I36/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I36/I118_vs_I36.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I37/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I37/I118_vs_I37.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I40/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I40/I118_vs_I40.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I42/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I118/I42/I118_vs_I42.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I36/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I36/I9644_vs_I36.ampIds.txt (188 bytes security) (deflated 6%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I37/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I37/I9644_vs_I37.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I40/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I40/I9644_vs_I40.ampIds.txt (188 bytes security) (deflated 6%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I42/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9644/I42/I9644_vs_I42.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I36/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I36/I9645_vs_I36.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I37/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I37/I9645_vs_I37.ampIds.txt (188 bytes security) (deflated 6%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I40/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I40/I9645_vs_I40.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I42/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9645/I42/I9645_vs_I42.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I36/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I36/I9646_vs_I36.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I37/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.readAlign.txt (188 bytes security) (deflated 97%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I40/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I40/I9646_vs_I40.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I42/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Align/I9646/I42/I9646_vs_I42.ampIds.txt (188 bytes security) (deflated 4%)
adding: extdata/AVASet/Amplicons/Results/Variants/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/currentVariantDefs.txt (188 bytes security) (deflated 77%)
adding: extdata/AVASet/Amplicons/Results/Variants/I116/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/I116/I116xI36detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I116/I116xI37detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I116/I116xI40detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I116/I116xI42detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I117/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/I117/I117xI36detectedVariants.txt (188 bytes security) (deflated 84%)
adding: extdata/AVASet/Amplicons/Results/Variants/I117/I117xI37detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I117/I117xI40detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I117/I117xI42detectedVariants.txt (188 bytes security) (deflated 82%)
adding: extdata/AVASet/Amplicons/Results/Variants/I118/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/I118/I118xI36detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I118/I118xI37detectedVariants.txt (188 bytes security) (deflated 83%)
adding: extdata/AVASet/Amplicons/Results/Variants/I118/I118xI40detectedVariants.txt (188 bytes security) (deflated 82%)
adding: extdata/AVASet/Amplicons/Results/Variants/I118/I118xI42detectedVariants.txt (188 bytes security) (deflated 82%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9644/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI36detectedVariants.txt (188 bytes security) (deflated 86%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI37detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI40detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI42detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9645/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI36detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI37detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI40detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI42detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9646/ (256 bytes security) (stored 0%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI36detectedVariants.txt (188 bytes security) (deflated 86%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI37detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI40detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI42detectedVariants.txt (188 bytes security) (deflated 85%)
adding: extdata/AVASet_doAmplicon/ (256 bytes security) (stored 0%)
adding: extdata/AVASet_doAmplicon/amp.csv (188 bytes security) (deflated 42%)
adding: extdata/AVASet_doAmplicon/reference.csv (188 bytes security) (deflated 63%)
adding: extdata/AVASet_doAmplicon/sample.csv (188 bytes security) (deflated 58%)
adding: extdata/AVASet_doAmplicon/variant.csv (188 bytes security) (deflated 82%)
adding: extdata/AVASet_doAmplicon/variantHits.csv (188 bytes security) (deflated 92%)
adding: extdata/AVAVarFreqExport/ (256 bytes security) (stored 0%)
adding: extdata/AVAVarFreqExport/AVAVarFreqExport.xls (188 bytes security) (deflated 81%)
adding: extdata/MapperSet/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N01/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N01/mapping/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N01/mapping/454HCDiffs.txt (188 bytes security) (deflated 85%)
adding: extdata/MapperSet/N01/mapping/454NewblerMetrics.txt (188 bytes security) (deflated 77%)
adding: extdata/MapperSet/N03/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N03/mapping/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N03/mapping/454HCDiffs.txt (188 bytes security) (deflated 85%)
adding: extdata/MapperSet/N03/mapping/454NewblerMetrics.txt (188 bytes security) (deflated 77%)
adding: extdata/MapperSet/N04/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N04/mapping/ (256 bytes security) (stored 0%)
adding: extdata/MapperSet/N04/mapping/454HCDiffs.txt (188 bytes security) (deflated 85%)
adding: extdata/MapperSet/N04/mapping/454NewblerMetrics.txt (188 bytes security) (deflated 77%)
adding: extdata/qualityReport.Rnw (188 bytes security) (deflated 79%)
adding: extdata/SFF/ (256 bytes security) (stored 0%)
adding: extdata/SFF/example.sff (188 bytes security) (deflated 70%)
adding: extdata/SVDetection/ (256 bytes security) (stored 0%)
adding: extdata/SVDetection/bam/ (256 bytes security) (stored 0%)
adding: extdata/SVDetection/bam/N01.bam (188 bytes security) (deflated 0%)
adding: extdata/SVDetection/chip/ (256 bytes security) (stored 0%)
adding: extdata/SVDetection/chip/CaptureArray_hg19.bed (188 bytes security) (deflated 67%)
adding: extdata/SVDetection/R_2009_07_30/ (256 bytes security) (stored 0%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/ (256 bytes security) (stored 0%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.fna (188 bytes security) (deflated 69%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.qual (188 bytes security) (deflated 82%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.fna (188 bytes security) (deflated 69%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.qual (188 bytes security) (deflated 83%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.fna (188 bytes security) (deflated 69%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.qual (188 bytes security) (deflated 81%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.fna (188 bytes security) (deflated 69%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.qual (188 bytes security) (deflated 82%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.csv (188 bytes security) (deflated 53%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.txt (188 bytes security) (deflated 82%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454DataProcessingDir.xml (188 bytes security) (deflated 35%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.csv (188 bytes security) (deflated 58%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.txt (188 bytes security) (deflated 71%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.csv (188 bytes security) (deflated 69%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.txt (188 bytes security) (deflated 81%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/dataRunParams.xml (188 bytes security) (deflated 81%)
adding: extdata/SVDetection/R_2009_07_30/D_2009_07_31/gsRunProcessor.log (188 bytes security) (deflated 89%)
adding: help/ (256 bytes security) (stored 0%)
adding: help/aliases.rds (188 bytes security) (stored 0%)
adding: help/AnIndex (188 bytes security) (deflated 86%)
adding: help/paths.rds (188 bytes security) (stored 0%)
adding: help/R453Plus1Toolbox.rdb (188 bytes security) (deflated 1%)
adding: help/R453Plus1Toolbox.rdx (188 bytes security) (stored 0%)
adding: html/ (256 bytes security) (stored 0%)
adding: html/00Index.html (188 bytes security) (deflated 89%)
adding: html/R.css (188 bytes security) (deflated 70%)
adding: INDEX (188 bytes security) (deflated 66%)
adding: javascript/ (256 bytes security) (stored 0%)
adding: javascript/sorttable.js (188 bytes security) (deflated 70%)
adding: libs/ (256 bytes security) (stored 0%)
adding: libs/i386/ (256 bytes security) (stored 0%)
adding: libs/i386/R453Plus1Toolbox.dll (188 bytes security) (deflated 56%)
adding: libs/x64/ (256 bytes security) (stored 0%)
adding: libs/x64/R453Plus1Toolbox.dll (188 bytes security) (deflated 58%)
adding: MD5 (188 bytes security) (deflated 65%)
adding: Meta/ (256 bytes security) (stored 0%)
adding: Meta/data.rds (188 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 64%)
adding: NEWS.Rd (188 bytes security) (deflated 57%)
adding: R/ (256 bytes security) (stored 0%)
adding: R/R453Plus1Toolbox (188 bytes security) (deflated 41%)
adding: R/R453Plus1Toolbox.rdb (188 bytes security) (deflated 40%)
adding: R/R453Plus1Toolbox.rdx (188 bytes security) (deflated 6%)