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 08:24:57 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CAGEr_1.22.3.tar.gz |
| StartedAt: 2018-10-15 22:56:39 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:02:42 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 362.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CAGEr_1.22.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.22.3’
* 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 25.096 0.340 31.920
cumulativeCTSSdistribution 18.864 3.792 22.711
quantilePositions 20.688 0.368 21.078
aggregateTagClusters 7.684 0.060 7.749
clusterCTSS 7.084 0.272 7.362
CAGEexp-class 4.408 0.444 35.258
* 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
‘/home/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck/00check.log’
for details.
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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 | 4.408 | 0.444 | 35.258 | |
| CAGEr_Multicore | 0.024 | 0.020 | 0.053 | |
| CAGEset-class | 0.004 | 0.000 | 0.002 | |
| CTSS-class | 0.028 | 0.004 | 0.032 | |
| CTSSclusteringMethod | 0.024 | 0.008 | 0.034 | |
| CTSScoordinates | 0.044 | 0.008 | 0.051 | |
| CTSSnormalizedTpm | 0.732 | 0.044 | 0.779 | |
| CTSStagCount | 0.228 | 0.012 | 0.240 | |
| CTSStagCountTable | 0.004 | 0.000 | 0.008 | |
| CTSStoGenes | 0.392 | 0.004 | 0.397 | |
| CustomConsensusClusters | 0.736 | 0.004 | 0.742 | |
| GeneExpDESeq2 | 1.164 | 0.028 | 1.260 | |
| GeneExpSE | 0.004 | 0.000 | 0.005 | |
| QuantileWidthFunctions | 0.000 | 0.000 | 0.001 | |
| aggregateTagClusters | 7.684 | 0.060 | 7.749 | |
| annotateCTSS | 1.092 | 0.012 | 1.102 | |
| byCtss | 0.004 | 0.000 | 0.005 | |
| clusterCTSS | 7.084 | 0.272 | 7.362 | |
| consensusClusterConvertors | 0.028 | 0.000 | 0.026 | |
| consensusClusters | 2.996 | 0.392 | 3.393 | |
| consensusClustersDESeq2 | 0.092 | 0.000 | 0.091 | |
| consensusClustersTpm | 0.004 | 0.000 | 0.004 | |
| coverage-functions | 4.160 | 0.424 | 4.590 | |
| cumulativeCTSSdistribution | 18.864 | 3.792 | 22.711 | |
| distclu-functions | 4.328 | 0.556 | 4.896 | |
| exampleCAGEexp | 0.000 | 0.000 | 0.001 | |
| exampleCAGEset | 0.012 | 0.000 | 0.012 | |
| exportCTSStoBedGraph | 1.468 | 0.016 | 1.488 | |
| exportToBed | 2.784 | 0.000 | 2.784 | |
| expressionClasses | 0.004 | 0.000 | 0.002 | |
| extractExpressionClass | 0.008 | 0.000 | 0.007 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 0.228 | 0.000 | 0.228 | |
| getExpressionProfiles | 0.212 | 0.000 | 0.211 | |
| getShiftingPromoters | 0.004 | 0.000 | 0.004 | |
| hanabi | 0.172 | 0.004 | 0.179 | |
| hanabiPlot | 0.244 | 0.024 | 0.270 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.036 | 0.004 | 0.042 | |
| import.bam | 0.000 | 0.000 | 0.001 | |
| import.bedCTSS | 0.000 | 0.000 | 0.001 | |
| import.bedScore | 0.000 | 0.000 | 0.001 | |
| import.bedmolecule | 0 | 0 | 0 | |
| importPublicData | 25.096 | 0.340 | 31.920 | |
| inputFiles | 0.000 | 0.000 | 0.001 | |
| inputFilesType | 0.004 | 0.000 | 0.001 | |
| librarySizes | 0 | 0 | 0 | |
| mapStats | 0.240 | 0.000 | 0.238 | |
| mergeCAGEsets | 1.820 | 0.016 | 1.835 | |
| mergeSamples | 0.372 | 0.000 | 0.375 | |
| moleculesGR2CTSS | 0.080 | 0.000 | 0.081 | |
| normalizeTagCount | 0.292 | 0.000 | 0.294 | |
| parseCAGEscanBlocksToGrangeTSS | 0.012 | 0.000 | 0.012 | |
| plotAnnot | 1.828 | 0.004 | 1.832 | |
| plotCorrelation | 0.464 | 0.000 | 0.465 | |
| plotExpressionProfiles | 0.148 | 0.000 | 0.145 | |
| plotInterquantileWidth | 0.308 | 0.008 | 0.316 | |
| plotReverseCumulatives | 0.616 | 0.000 | 0.618 | |
| quantilePositions | 20.688 | 0.368 | 21.078 | |
| ranges2annot | 0.1 | 0.0 | 0.1 | |
| ranges2genes | 0.040 | 0.000 | 0.042 | |
| ranges2names | 0.060 | 0.000 | 0.056 | |
| sampleLabels | 0.000 | 0.000 | 0.001 | |
| scoreShift | 4.332 | 0.016 | 4.348 | |
| seqNameTotalsSE | 0.004 | 0.000 | 0.004 | |
| setColors | 0.220 | 0.000 | 0.221 | |
| strandInvaders | 0.880 | 0.024 | 0.726 | |
| summariseChrExpr | 0.456 | 0.000 | 0.455 | |
| tagClusterConvertors | 0.236 | 0.000 | 0.237 | |
| tagClusters | 0.044 | 0.000 | 0.040 | |