Vanja Haberle
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CAGEr |
| Branch: RELEASE_3_9 |
| Last Commit: 7b90ab5 |
| Last Changed Date: 2019-05-02 11:53:41 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:02:23 -0400 (Wed, 16 Oct 2019).
| Package 201/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CAGEr 1.26.0 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 | |
| Package: CAGEr |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2019-10-16 00:14:09 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:21:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 448.2 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_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CAGEr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.26.0’
* 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 37.683 0.517 38.169
cumulativeCTSSdistribution 27.558 5.287 30.935
quantilePositions 20.297 0.543 21.214
clusterCTSS 12.405 0.391 10.081
aggregateTagClusters 10.350 0.027 8.000
distclu-functions 9.193 0.684 7.657
plotReverseCumulatives 8.305 0.063 2.058
coverage-functions 5.310 0.516 5.827
CTSSnormalizedTpm 5.479 0.012 1.313
consensusClusters 4.719 0.599 5.319
* 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 | 4.578 | 0.228 | 4.922 | |
| CAGEr_Multicore | 0.785 | 0.174 | 0.975 | |
| CAGEset-class | 0.004 | 0.000 | 0.004 | |
| CTSS-class | 0.038 | 0.000 | 0.038 | |
| CTSSclusteringMethod | 0.009 | 0.004 | 0.013 | |
| CTSScoordinates | 0.048 | 0.000 | 0.048 | |
| CTSSnormalizedTpm | 5.479 | 0.012 | 1.313 | |
| CTSStagCount | 0.300 | 0.036 | 0.335 | |
| CTSStagCountTable | 0.011 | 0.000 | 0.011 | |
| CTSStoGenes | 0.556 | 0.008 | 0.564 | |
| CustomConsensusClusters | 1.13 | 0.00 | 1.13 | |
| GeneExpDESeq2 | 1.292 | 0.016 | 1.308 | |
| GeneExpSE | 0.003 | 0.000 | 0.003 | |
| QuantileWidthFunctions | 0 | 0 | 0 | |
| aggregateTagClusters | 10.350 | 0.027 | 8.000 | |
| annotateCTSS | 1.150 | 0.008 | 1.157 | |
| byCtss | 0.230 | 0.000 | 0.036 | |
| clusterCTSS | 12.405 | 0.391 | 10.081 | |
| consensusClusterConvertors | 0.021 | 0.003 | 0.024 | |
| consensusClusters | 4.719 | 0.599 | 5.319 | |
| consensusClustersDESeq2 | 0.169 | 0.000 | 0.169 | |
| consensusClustersTpm | 0.007 | 0.000 | 0.007 | |
| coverage-functions | 5.310 | 0.516 | 5.827 | |
| cumulativeCTSSdistribution | 27.558 | 5.287 | 30.935 | |
| distclu-functions | 9.193 | 0.684 | 7.657 | |
| exampleCAGEexp | 0 | 0 | 0 | |
| exampleCAGEset | 0.018 | 0.000 | 0.017 | |
| exportCTSStoBedGraph | 1.606 | 0.012 | 1.624 | |
| exportToBed | 3.379 | 0.019 | 3.494 | |
| expressionClasses | 0.001 | 0.000 | 0.001 | |
| extractExpressionClass | 0.007 | 0.000 | 0.006 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 1.979 | 0.016 | 0.653 | |
| getExpressionProfiles | 0.241 | 0.003 | 0.244 | |
| getShiftingPromoters | 0.007 | 0.001 | 0.006 | |
| hanabi | 0.278 | 0.004 | 0.282 | |
| hanabiPlot | 0.353 | 0.016 | 0.369 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.055 | 0.000 | 0.055 | |
| import.bam | 0 | 0 | 0 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0 | 0 | 0 | |
| importPublicData | 37.683 | 0.517 | 38.169 | |
| inputFiles | 0.001 | 0.000 | 0.000 | |
| inputFilesType | 0.001 | 0.000 | 0.000 | |
| librarySizes | 0.001 | 0.000 | 0.000 | |
| mapStats | 0.364 | 0.004 | 0.367 | |
| mergeCAGEsets | 3.515 | 0.004 | 2.664 | |
| mergeSamples | 0.404 | 0.000 | 0.404 | |
| moleculesGR2CTSS | 0.08 | 0.00 | 0.08 | |
| normalizeTagCount | 4.244 | 0.017 | 1.070 | |
| parseCAGEscanBlocksToGrangeTSS | 0.009 | 0.000 | 0.008 | |
| plotAnnot | 2.468 | 0.004 | 2.477 | |
| plotCorrelation | 0.712 | 0.000 | 0.833 | |
| plotExpressionProfiles | 0.222 | 0.000 | 0.221 | |
| plotInterquantileWidth | 0.311 | 0.000 | 0.311 | |
| plotReverseCumulatives | 8.305 | 0.063 | 2.058 | |
| quantilePositions | 20.297 | 0.543 | 21.214 | |
| ranges2annot | 0.255 | 0.000 | 0.254 | |
| ranges2genes | 0.039 | 0.000 | 0.039 | |
| ranges2names | 0.04 | 0.00 | 0.04 | |
| sampleLabels | 0.000 | 0.000 | 0.001 | |
| scoreShift | 4.828 | 0.015 | 4.850 | |
| seqNameTotalsSE | 0.004 | 0.000 | 0.003 | |
| setColors | 0.333 | 0.000 | 0.332 | |
| strandInvaders | 1.068 | 0.048 | 0.991 | |
| summariseChrExpr | 0.583 | 0.000 | 0.582 | |
| tagClusterConvertors | 0.349 | 0.004 | 0.353 | |
| tagClusters | 0.043 | 0.003 | 0.047 | |