Vanja Haberle
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CAGEr |
| Branch: RELEASE_3_8 |
| Last Commit: 420fec4 |
| Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:55 -0400 (Tue, 16 Apr 2019).
| Package 191/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CAGEr 1.24.0 Vanja Haberle
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CAGEr |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CAGEr_1.24.0.tar.gz |
| StartedAt: 2019-04-15 22:37:09 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:44:24 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 434.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CAGEr_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CAGEr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.24.0’
* 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 37.560 0.468 37.290
cumulativeCTSSdistribution 29.372 4.608 31.684
quantilePositions 24.384 0.544 24.977
clusterCTSS 13.464 0.392 10.891
aggregateTagClusters 13.676 0.032 10.749
plotReverseCumulatives 9.856 0.028 2.291
distclu-functions 8.840 0.612 6.870
CTSSnormalizedTpm 5.876 0.060 1.674
scoreShift 5.512 0.012 5.530
consensusClusters 4.808 0.532 5.352
CAGEexp-class 4.196 0.160 6.102
* 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-3.8-bioc/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘CAGEr’ ... ** 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 * DONE (CAGEr)
CAGEr.Rcheck/CAGEr-Ex.timings
| name | user | system | elapsed | |
| CAGEexp-class | 4.196 | 0.160 | 6.102 | |
| CAGEr_Multicore | 0.032 | 0.048 | 0.083 | |
| CAGEset-class | 0.004 | 0.000 | 0.004 | |
| CTSS-class | 0.044 | 0.004 | 0.052 | |
| CTSSclusteringMethod | 0.012 | 0.004 | 0.015 | |
| CTSScoordinates | 0.076 | 0.000 | 0.075 | |
| CTSSnormalizedTpm | 5.876 | 0.060 | 1.674 | |
| CTSStagCount | 0.272 | 0.020 | 0.293 | |
| CTSStagCountTable | 0.012 | 0.000 | 0.011 | |
| CTSStoGenes | 0.580 | 0.004 | 0.582 | |
| CustomConsensusClusters | 1.000 | 0.016 | 1.018 | |
| GeneExpDESeq2 | 1.672 | 0.016 | 1.690 | |
| GeneExpSE | 0.004 | 0.000 | 0.004 | |
| QuantileWidthFunctions | 0 | 0 | 0 | |
| aggregateTagClusters | 13.676 | 0.032 | 10.749 | |
| annotateCTSS | 1.996 | 0.004 | 2.002 | |
| byCtss | 0.064 | 0.000 | 0.012 | |
| clusterCTSS | 13.464 | 0.392 | 10.891 | |
| consensusClusterConvertors | 0.036 | 0.000 | 0.035 | |
| consensusClusters | 4.808 | 0.532 | 5.352 | |
| consensusClustersDESeq2 | 0.168 | 0.004 | 0.169 | |
| consensusClustersTpm | 0.008 | 0.000 | 0.007 | |
| coverage-functions | 4.484 | 0.492 | 4.986 | |
| cumulativeCTSSdistribution | 29.372 | 4.608 | 31.684 | |
| distclu-functions | 8.840 | 0.612 | 6.870 | |
| exampleCAGEexp | 0.004 | 0.000 | 0.001 | |
| exampleCAGEset | 0.02 | 0.00 | 0.02 | |
| exportCTSStoBedGraph | 1.876 | 0.000 | 1.879 | |
| exportToBed | 4.220 | 0.008 | 4.239 | |
| expressionClasses | 0.000 | 0.000 | 0.002 | |
| extractExpressionClass | 0.008 | 0.000 | 0.007 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 2.240 | 0.000 | 0.734 | |
| getExpressionProfiles | 0.260 | 0.004 | 0.265 | |
| getShiftingPromoters | 0.004 | 0.000 | 0.003 | |
| hanabi | 0.252 | 0.020 | 0.271 | |
| hanabiPlot | 0.304 | 0.032 | 0.336 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.036 | 0.000 | 0.038 | |
| import.bam | 0 | 0 | 0 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0 | 0 | 0 | |
| importPublicData | 37.560 | 0.468 | 37.290 | |
| inputFiles | 0 | 0 | 0 | |
| inputFilesType | 0 | 0 | 0 | |
| librarySizes | 0 | 0 | 0 | |
| mapStats | 0.276 | 0.000 | 0.277 | |
| mergeCAGEsets | 2.836 | 0.000 | 1.923 | |
| mergeSamples | 0.3 | 0.0 | 0.3 | |
| moleculesGR2CTSS | 0.092 | 0.000 | 0.092 | |
| normalizeTagCount | 4.892 | 0.028 | 1.556 | |
| parseCAGEscanBlocksToGrangeTSS | 0.016 | 0.000 | 0.018 | |
| plotAnnot | 3.588 | 0.008 | 3.601 | |
| plotCorrelation | 0.668 | 0.000 | 0.668 | |
| plotExpressionProfiles | 0.216 | 0.004 | 0.220 | |
| plotInterquantileWidth | 0.384 | 0.000 | 0.383 | |
| plotReverseCumulatives | 9.856 | 0.028 | 2.291 | |
| quantilePositions | 24.384 | 0.544 | 24.977 | |
| ranges2annot | 0.436 | 0.000 | 0.438 | |
| ranges2genes | 0.072 | 0.000 | 0.072 | |
| ranges2names | 0.068 | 0.004 | 0.071 | |
| sampleLabels | 0 | 0 | 0 | |
| scoreShift | 5.512 | 0.012 | 5.530 | |
| seqNameTotalsSE | 0.004 | 0.000 | 0.004 | |
| setColors | 0.408 | 0.000 | 0.405 | |
| strandInvaders | 1.084 | 0.048 | 1.019 | |
| summariseChrExpr | 0.684 | 0.000 | 0.686 | |
| tagClusterConvertors | 0.360 | 0.000 | 0.359 | |
| tagClusters | 0.048 | 0.004 | 0.051 | |