Vanja Haberle
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CAGEr |
| Branch: master |
| Last Commit: d93551e |
| Last Changed Date: 2018-12-12 00:42:09 -0400 (Wed, 12 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:34:38 -0400 (Tue, 09 Apr 2019).
| Package 198/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CAGEr 1.25.1 Vanja Haberle
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: CAGEr |
| Version: 1.25.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CAGEr_1.25.1.tar.gz |
| StartedAt: 2019-04-08 23:10:18 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:17:49 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 450.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CAGEr_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.25.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CAGEr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
importPublicData 42.718 0.403 42.998
cumulativeCTSSdistribution 27.260 5.019 30.242
quantilePositions 24.599 0.330 24.952
aggregateTagClusters 13.220 0.123 10.400
clusterCTSS 12.077 0.397 9.760
plotReverseCumulatives 8.342 0.072 2.010
distclu-functions 7.763 0.585 6.129
CTSSnormalizedTpm 5.641 0.095 1.620
coverage-functions 4.919 0.504 5.426
consensusClusters 4.429 0.600 5.030
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘CAGEr’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CAGEr)
CAGEr.Rcheck/CAGEr-Ex.timings
| name | user | system | elapsed | |
| CAGEexp-class | 4.450 | 0.252 | 4.769 | |
| CAGEr_Multicore | 0.033 | 0.048 | 0.084 | |
| CAGEset-class | 0.000 | 0.004 | 0.004 | |
| CTSS-class | 0.048 | 0.000 | 0.048 | |
| CTSSclusteringMethod | 0.013 | 0.004 | 0.017 | |
| CTSScoordinates | 0.060 | 0.004 | 0.065 | |
| CTSSnormalizedTpm | 5.641 | 0.095 | 1.620 | |
| CTSStagCount | 0.272 | 0.008 | 0.280 | |
| CTSStagCountTable | 0.008 | 0.000 | 0.007 | |
| CTSStoGenes | 0.561 | 0.044 | 0.604 | |
| CustomConsensusClusters | 0.982 | 0.000 | 0.982 | |
| GeneExpDESeq2 | 1.818 | 0.032 | 1.855 | |
| GeneExpSE | 0.005 | 0.000 | 0.005 | |
| QuantileWidthFunctions | 0 | 0 | 0 | |
| aggregateTagClusters | 13.220 | 0.123 | 10.400 | |
| annotateCTSS | 1.102 | 0.004 | 1.106 | |
| byCtss | 0.204 | 0.000 | 0.039 | |
| clusterCTSS | 12.077 | 0.397 | 9.760 | |
| consensusClusterConvertors | 0.029 | 0.000 | 0.029 | |
| consensusClusters | 4.429 | 0.600 | 5.030 | |
| consensusClustersDESeq2 | 0.179 | 0.000 | 0.179 | |
| consensusClustersTpm | 0.006 | 0.000 | 0.006 | |
| coverage-functions | 4.919 | 0.504 | 5.426 | |
| cumulativeCTSSdistribution | 27.260 | 5.019 | 30.242 | |
| distclu-functions | 7.763 | 0.585 | 6.129 | |
| exampleCAGEexp | 0.000 | 0.000 | 0.001 | |
| exampleCAGEset | 0.018 | 0.000 | 0.018 | |
| exportCTSStoBedGraph | 2.032 | 0.014 | 2.047 | |
| exportToBed | 3.811 | 0.016 | 3.828 | |
| expressionClasses | 0.002 | 0.000 | 0.002 | |
| extractExpressionClass | 0.011 | 0.000 | 0.011 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 1.966 | 0.004 | 0.604 | |
| getExpressionProfiles | 0.25 | 0.00 | 0.25 | |
| getShiftingPromoters | 0.006 | 0.000 | 0.006 | |
| hanabi | 0.255 | 0.002 | 0.256 | |
| hanabiPlot | 0.374 | 0.020 | 0.394 | |
| import.CAGEscanMolecule | 0.001 | 0.000 | 0.000 | |
| import.CTSS | 0.051 | 0.000 | 0.051 | |
| import.bam | 0 | 0 | 0 | |
| import.bedCTSS | 0.000 | 0.000 | 0.001 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0.000 | 0.000 | 0.001 | |
| importPublicData | 42.718 | 0.403 | 42.998 | |
| inputFiles | 0 | 0 | 0 | |
| inputFilesType | 0 | 0 | 0 | |
| librarySizes | 0.001 | 0.000 | 0.000 | |
| mapStats | 0.307 | 0.003 | 0.311 | |
| mergeCAGEsets | 3.617 | 0.024 | 2.821 | |
| mergeSamples | 0.522 | 0.000 | 0.522 | |
| moleculesGR2CTSS | 0.124 | 0.000 | 0.124 | |
| normalizeTagCount | 4.041 | 0.023 | 1.272 | |
| parseCAGEscanBlocksToGrangeTSS | 0.009 | 0.000 | 0.009 | |
| plotAnnot | 2.74 | 0.00 | 2.74 | |
| plotCorrelation | 0.442 | 0.000 | 0.442 | |
| plotExpressionProfiles | 0.141 | 0.003 | 0.144 | |
| plotInterquantileWidth | 0.23 | 0.00 | 0.23 | |
| plotReverseCumulatives | 8.342 | 0.072 | 2.010 | |
| quantilePositions | 24.599 | 0.330 | 24.952 | |
| ranges2annot | 0.255 | 0.000 | 0.256 | |
| ranges2genes | 0.038 | 0.000 | 0.038 | |
| ranges2names | 0.038 | 0.000 | 0.037 | |
| sampleLabels | 0.001 | 0.000 | 0.000 | |
| scoreShift | 4.971 | 0.016 | 4.996 | |
| seqNameTotalsSE | 0.005 | 0.000 | 0.005 | |
| setColors | 0.44 | 0.00 | 0.44 | |
| strandInvaders | 1.049 | 0.041 | 0.960 | |
| summariseChrExpr | 0.581 | 0.004 | 0.586 | |
| tagClusterConvertors | 0.329 | 0.000 | 0.330 | |
| tagClusters | 0.047 | 0.003 | 0.049 | |