Vanja Haberle
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/CAGEr |
| Branch: RELEASE_3_10 |
| Last Commit: de5899e |
| Last Changed Date: 2019-10-29 13:08:37 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:07:30 -0400 (Wed, 15 Apr 2020).
| Package 214/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CAGEr 1.28.0 Vanja Haberle
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CAGEr |
| Version: 1.28.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAGEr_1.28.0.tar.gz |
| StartedAt: 2020-04-15 01:37:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:45:55 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 506.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAGEr_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CAGEr.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.28.0’
* 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
cumulativeCTSSdistribution 34.296 4.800 37.053
importPublicData 38.336 0.472 43.187
quantilePositions 25.268 0.704 26.009
aggregateTagClusters 18.020 0.052 15.159
clusterCTSS 13.844 0.376 11.573
distclu-functions 11.004 0.656 9.087
plotReverseCumulatives 9.384 0.048 2.330
scoreShift 6.296 0.064 6.397
CTSSnormalizedTpm 5.956 0.076 2.014
coverage-functions 5.172 0.476 5.668
normalizeTagCount 5.460 0.032 2.116
mergeCAGEsets 5.360 0.016 4.444
CAGEexp-class 4.864 0.172 5.276
* 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-3.10-bioc/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 | 4.864 | 0.172 | 5.276 | |
| CAGEr_Multicore | 0.920 | 0.192 | 1.118 | |
| CAGEset-class | 0.004 | 0.000 | 0.004 | |
| CTSS-class | 0.060 | 0.004 | 0.061 | |
| CTSSclusteringMethod | 0.012 | 0.000 | 0.013 | |
| CTSScoordinates | 0.192 | 0.004 | 0.193 | |
| CTSSnormalizedTpm | 5.956 | 0.076 | 2.014 | |
| CTSStagCount | 0.392 | 0.020 | 0.415 | |
| CTSStagCountTable | 0.004 | 0.000 | 0.007 | |
| CTSStoGenes | 0.604 | 0.048 | 0.654 | |
| CustomConsensusClusters | 1.588 | 0.000 | 1.595 | |
| GeneExpDESeq2 | 1.828 | 0.016 | 1.847 | |
| GeneExpSE | 0.004 | 0.000 | 0.004 | |
| QuantileWidthFunctions | 0 | 0 | 0 | |
| aggregateTagClusters | 18.020 | 0.052 | 15.159 | |
| annotateCTSS | 1.804 | 0.000 | 1.806 | |
| byCtss | 0.288 | 0.004 | 0.108 | |
| clusterCTSS | 13.844 | 0.376 | 11.573 | |
| consensusClusterConvertors | 0.052 | 0.000 | 0.058 | |
| consensusClusters | 3.848 | 0.532 | 4.410 | |
| consensusClustersDESeq2 | 0.140 | 0.000 | 0.141 | |
| consensusClustersTpm | 0.012 | 0.000 | 0.012 | |
| coverage-functions | 5.172 | 0.476 | 5.668 | |
| cumulativeCTSSdistribution | 34.296 | 4.800 | 37.053 | |
| distclu-functions | 11.004 | 0.656 | 9.087 | |
| exampleCAGEexp | 0 | 0 | 0 | |
| exampleCAGEset | 0.016 | 0.000 | 0.017 | |
| exportCTSStoBedGraph | 3.468 | 0.012 | 3.489 | |
| exportToBed | 4.620 | 0.008 | 4.662 | |
| expressionClasses | 0.004 | 0.000 | 0.002 | |
| extractExpressionClass | 0.004 | 0.000 | 0.006 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 2.132 | 0.016 | 0.675 | |
| getExpressionProfiles | 0.148 | 0.004 | 0.154 | |
| getShiftingPromoters | 0.000 | 0.000 | 0.004 | |
| hanabi | 0.264 | 0.024 | 0.291 | |
| hanabiPlot | 0.320 | 0.020 | 0.336 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.136 | 0.000 | 0.133 | |
| import.bam | 0.000 | 0.000 | 0.001 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0 | 0 | 0 | |
| importPublicData | 38.336 | 0.472 | 43.187 | |
| inputFiles | 0 | 0 | 0 | |
| inputFilesType | 0 | 0 | 0 | |
| librarySizes | 0 | 0 | 0 | |
| mapStats | 0.080 | 0.000 | 0.079 | |
| mergeCAGEsets | 5.360 | 0.016 | 4.444 | |
| mergeSamples | 0.684 | 0.000 | 0.685 | |
| moleculesGR2CTSS | 0.224 | 0.000 | 0.228 | |
| normalizeTagCount | 5.460 | 0.032 | 2.116 | |
| parseCAGEscanBlocksToGrangeTSS | 0.036 | 0.000 | 0.035 | |
| plotAnnot | 3.284 | 0.004 | 3.294 | |
| plotCorrelation | 0.472 | 0.000 | 0.472 | |
| plotExpressionProfiles | 0.156 | 0.000 | 0.156 | |
| plotInterquantileWidth | 0.352 | 0.000 | 0.352 | |
| plotReverseCumulatives | 9.384 | 0.048 | 2.330 | |
| quantilePositions | 25.268 | 0.704 | 26.009 | |
| ranges2annot | 0.452 | 0.000 | 0.452 | |
| ranges2genes | 0.088 | 0.000 | 0.086 | |
| ranges2names | 0.084 | 0.000 | 0.087 | |
| sampleLabels | 0 | 0 | 0 | |
| scoreShift | 6.296 | 0.064 | 6.397 | |
| seqNameTotalsSE | 0.004 | 0.000 | 0.004 | |
| setColors | 0.380 | 0.000 | 0.381 | |
| strandInvaders | 1.272 | 0.036 | 1.212 | |
| summariseChrExpr | 0.964 | 0.000 | 0.964 | |
| tagClusterConvertors | 0.524 | 0.004 | 0.530 | |
| tagClusters | 0.072 | 0.000 | 0.074 | |