Vanja Haberle
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CAGEr |
| Branch: RELEASE_3_7 |
| Last Commit: 5a42f82 |
| Last Changed Date: 2018-06-25 03:38:36 -0400 (Mon, 25 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:51:17 -0400 (Wed, 17 Oct 2018).
| Package 179/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CAGEr 1.22.3 Vanja Haberle
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CAGEr |
| Version: 1.22.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.22.3.tar.gz |
| StartedAt: 2018-10-16 20:13:37 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:22:05 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 508.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.22.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.22.3’
* 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 ... NOTE
clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for '<<-'
assignment to ‘idx’
clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for global
variable ‘idx’
clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for '<<-'
assignment to ‘idx’
clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for global
variable ‘idx’
clusterCTSS,CAGEset: no visible binding for global variable ‘idx’
Undefined global functions or variables:
idx
* 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 40.848 2.591 43.139
cumulativeCTSSdistribution 26.378 7.205 31.480
quantilePositions 28.744 0.854 29.634
aggregateTagClusters 13.438 4.341 11.493
clusterCTSS 10.064 0.405 8.746
distclu-functions 8.699 1.343 7.335
coverage-functions 5.018 0.616 5.674
scoreShift 5.184 0.095 5.307
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck/00check.log’
for details.
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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 | 4.347 | 0.299 | 4.681 | |
| CAGEr_Multicore | 0.032 | 0.006 | 0.038 | |
| CAGEset-class | 0.004 | 0.001 | 0.004 | |
| CTSS-class | 0.042 | 0.002 | 0.044 | |
| CTSSclusteringMethod | 0.011 | 0.001 | 0.012 | |
| CTSScoordinates | 0.069 | 0.000 | 0.071 | |
| CTSSnormalizedTpm | 1.528 | 0.091 | 1.275 | |
| CTSStagCount | 0.280 | 0.006 | 0.287 | |
| CTSStagCountTable | 0.010 | 0.000 | 0.011 | |
| CTSStoGenes | 0.589 | 0.004 | 0.597 | |
| CustomConsensusClusters | 1.087 | 0.010 | 1.099 | |
| GeneExpDESeq2 | 1.701 | 0.051 | 1.757 | |
| GeneExpSE | 0.007 | 0.000 | 0.008 | |
| QuantileWidthFunctions | 0.002 | 0.000 | 0.001 | |
| aggregateTagClusters | 13.438 | 4.341 | 11.493 | |
| annotateCTSS | 1.592 | 0.018 | 1.618 | |
| byCtss | 0.009 | 0.000 | 0.010 | |
| clusterCTSS | 10.064 | 0.405 | 8.746 | |
| consensusClusterConvertors | 0.156 | 0.014 | 0.045 | |
| consensusClusters | 3.544 | 0.411 | 3.962 | |
| consensusClustersDESeq2 | 0.131 | 0.001 | 0.132 | |
| consensusClustersTpm | 0.006 | 0.000 | 0.007 | |
| coverage-functions | 5.018 | 0.616 | 5.674 | |
| cumulativeCTSSdistribution | 26.378 | 7.205 | 31.480 | |
| distclu-functions | 8.699 | 1.343 | 7.335 | |
| exampleCAGEexp | 0.012 | 0.001 | 0.003 | |
| exampleCAGEset | 0.088 | 0.005 | 0.024 | |
| exportCTSStoBedGraph | 2.103 | 0.014 | 2.115 | |
| exportToBed | 4.277 | 0.050 | 4.341 | |
| expressionClasses | 0.005 | 0.000 | 0.006 | |
| extractExpressionClass | 0.009 | 0.000 | 0.010 | |
| genomeName | 0.002 | 0.000 | 0.002 | |
| getCTSS | 0.666 | 0.162 | 0.396 | |
| getExpressionProfiles | 0.898 | 0.109 | 0.514 | |
| getShiftingPromoters | 0.005 | 0.000 | 0.006 | |
| hanabi | 0.250 | 0.008 | 0.260 | |
| hanabiPlot | 0.347 | 0.025 | 0.375 | |
| import.CAGEscanMolecule | 0.001 | 0.000 | 0.000 | |
| import.CTSS | 0.069 | 0.002 | 0.071 | |
| import.bam | 0.000 | 0.000 | 0.001 | |
| import.bedCTSS | 0.001 | 0.000 | 0.001 | |
| import.bedScore | 0.001 | 0.000 | 0.001 | |
| import.bedmolecule | 0.001 | 0.000 | 0.001 | |
| importPublicData | 40.848 | 2.591 | 43.139 | |
| inputFiles | 0.008 | 0.001 | 0.002 | |
| inputFilesType | 0.008 | 0.001 | 0.002 | |
| librarySizes | 0.007 | 0.002 | 0.002 | |
| mapStats | 0.474 | 0.036 | 0.292 | |
| mergeCAGEsets | 3.449 | 0.064 | 2.754 | |
| mergeSamples | 0.523 | 0.005 | 0.534 | |
| moleculesGR2CTSS | 0.121 | 0.000 | 0.122 | |
| normalizeTagCount | 0.607 | 0.014 | 0.464 | |
| parseCAGEscanBlocksToGrangeTSS | 0.037 | 0.002 | 0.039 | |
| plotAnnot | 2.761 | 0.010 | 2.797 | |
| plotCorrelation | 0.585 | 0.002 | 0.592 | |
| plotExpressionProfiles | 0.153 | 0.003 | 0.155 | |
| plotInterquantileWidth | 0.443 | 0.006 | 0.461 | |
| plotReverseCumulatives | 1.254 | 0.030 | 0.917 | |
| quantilePositions | 28.744 | 0.854 | 29.634 | |
| ranges2annot | 0.120 | 0.000 | 0.121 | |
| ranges2genes | 0.066 | 0.000 | 0.068 | |
| ranges2names | 0.065 | 0.000 | 0.066 | |
| sampleLabels | 0.001 | 0.000 | 0.002 | |
| scoreShift | 5.184 | 0.095 | 5.307 | |
| seqNameTotalsSE | 0.004 | 0.000 | 0.005 | |
| setColors | 0.297 | 0.005 | 0.302 | |
| strandInvaders | 1.814 | 2.723 | 1.159 | |
| summariseChrExpr | 0.571 | 0.010 | 0.589 | |
| tagClusterConvertors | 0.253 | 0.003 | 0.256 | |
| tagClusters | 0.056 | 0.002 | 0.058 | |