Charles Plessy
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CAGEr |
| git_branch: master |
| git_last_commit: 5a58b26 |
| git_last_commit_date: 2021-11-17 15:27:06 -0400 (Wed, 17 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:06 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CAGEr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 235/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.1.3 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CAGEr |
| Version: 2.1.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CAGEr_2.1.3.tar.gz |
| StartedAt: 2022-03-17 18:37:40 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:43:49 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 368.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CAGEr_2.1.3.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CAGEr.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '2.1.3'
* 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cumulativeCTSSdistribution 16.97 12.35 29.31
clusterCTSS 23.51 0.64 24.16
exportToTrack 19.25 0.10 19.35
quantilePositions 16.92 0.06 16.98
aggregateTagClusters 5.73 0.03 5.77
CAGEexp-class 4.18 1.19 5.38
* 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
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CAGEr
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'CAGEr'
finding HTML links ... done
CAGEexp-class html
finding level-2 HTML links ... done
CAGEr-class html
CAGEr-package html
CAGEr_Multicore html
CTSS-class html
CTSSclusteringMethod html
CTSScoordinates html
CTSScumulativesTagClusters html
CTSSnormalizedTpm html
CTSStagCount html
CTSStoGenes html
ConsensusClusters-class html
CustomConsensusClusters html
FANTOM5humanSamples html
FANTOM5mouseSamples html
GeneExpDESeq2 html
GeneExpSE html
QuantileWidthFunctions html
TagClusters-class html
aggregateTagClusters html
annotateCTSS html
bam2CTSS html
byCtss html
clusterAggregateAndSum html
clusterCTSS html
coerceInBSgenome html
consensusClusterConvertors html
consensusClusters-set html
consensusClusters html
consensusClustersDESeq2 html
consensusClustersQuantile html
consensusClustersTpm html
coverage-functions html
cumulativeCTSSdistribution html
distclu-functions html
exampleCAGEexp html
exampleZv9_annot html
exportToTrack html
expressionClasses html
genomeName html
getCTSS html
getExpressionProfiles html
getShiftingPromoters html
hanabi-class html
hanabi html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CAGEr/00new/CAGEr/help/hanabi+2Clist-method.html
hanabiPlot html
import.CAGEscanMolecule html
import.CTSS html
import.bam html
import.bam.ctss html
import.bedCTSS html
import.bedScore html
import.bedmolecule html
inputFiles html
inputFilesType html
librarySizes html
loadFileIntoGPos html
mapStats html
mapStatsScopes html
mergeCAGEsets html
mergeSamples html
moleculesGR2CTSS html
normalizeTagCount html
parseCAGEscanBlocksToGrangeTSS html
plot.hanabi html
plotAnnot html
plotCorrelation html
plotExpressionProfiles html
plotInterquantileWidth html
plotReverseCumulatives html
powerLaw html
quantilePositions html
ranges2annot html
ranges2genes html
ranges2names html
sampleLabels html
scoreShift html
seqNameTotalsSE html
setColors html
strandInvaders html
summariseChrExpr html
tagClusters html
** 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)
Making 'packages.html' ... done
CAGEr.Rcheck/CAGEr-Ex.timings
| name | user | system | elapsed | |
| CAGEexp-class | 4.18 | 1.19 | 5.38 | |
| CAGEr_Multicore | 0.05 | 0.03 | 0.07 | |
| CTSS-class | 0.39 | 0.04 | 0.44 | |
| CTSSclusteringMethod | 0 | 0 | 0 | |
| CTSScoordinates | 0.07 | 0.00 | 0.07 | |
| CTSSnormalizedTpm | 0.75 | 0.00 | 0.75 | |
| CTSStagCount | 0.83 | 0.00 | 0.83 | |
| CTSStoGenes | 0.33 | 0.00 | 0.33 | |
| CustomConsensusClusters | 0.66 | 0.04 | 0.69 | |
| GeneExpDESeq2 | 0.87 | 0.01 | 0.89 | |
| GeneExpSE | 0 | 0 | 0 | |
| QuantileWidthFunctions | 0.10 | 0.00 | 0.09 | |
| aggregateTagClusters | 5.73 | 0.03 | 5.77 | |
| annotateCTSS | 1.11 | 0.02 | 1.12 | |
| byCtss | 0 | 0 | 0 | |
| clusterCTSS | 23.51 | 0.64 | 24.16 | |
| consensusClusters | 0.10 | 0.00 | 0.09 | |
| consensusClustersDESeq2 | 0.12 | 0.00 | 0.13 | |
| consensusClustersTpm | 0 | 0 | 0 | |
| coverage-functions | 2.46 | 0.76 | 3.22 | |
| cumulativeCTSSdistribution | 16.97 | 12.35 | 29.31 | |
| distclu-functions | 2.71 | 0.95 | 3.67 | |
| exampleCAGEexp | 0 | 0 | 0 | |
| exportToTrack | 19.25 | 0.10 | 19.35 | |
| expressionClasses | 0 | 0 | 0 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 0.88 | 0.03 | 0.90 | |
| getExpressionProfiles | 1.95 | 0.00 | 1.95 | |
| getShiftingPromoters | 0 | 0 | 0 | |
| hanabi | 0.21 | 0.01 | 0.22 | |
| hanabiPlot | 0.23 | 0.06 | 0.30 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.11 | 0.00 | 0.11 | |
| import.bam | 0 | 0 | 0 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0 | 0 | 0 | |
| inputFiles | 0 | 0 | 0 | |
| inputFilesType | 0 | 0 | 0 | |
| librarySizes | 0 | 0 | 0 | |
| mapStats | 0.06 | 0.00 | 0.06 | |
| mergeCAGEsets | 2.74 | 0.05 | 2.78 | |
| mergeSamples | 0.53 | 0.00 | 0.53 | |
| moleculesGR2CTSS | 0.19 | 0.00 | 0.19 | |
| normalizeTagCount | 0.63 | 0.02 | 0.64 | |
| parseCAGEscanBlocksToGrangeTSS | 0.03 | 0.00 | 0.03 | |
| plotAnnot | 1.90 | 0.01 | 1.92 | |
| plotCorrelation | 0.21 | 0.00 | 0.20 | |
| plotExpressionProfiles | 3.79 | 0.36 | 4.16 | |
| plotInterquantileWidth | 2.44 | 0.02 | 2.45 | |
| plotReverseCumulatives | 0.28 | 0.00 | 0.29 | |
| quantilePositions | 16.92 | 0.06 | 16.98 | |
| ranges2annot | 0.33 | 0.00 | 0.33 | |
| ranges2genes | 0.06 | 0.00 | 0.06 | |
| ranges2names | 0.07 | 0.00 | 0.06 | |
| sampleLabels | 0.01 | 0.00 | 0.02 | |
| scoreShift | 0 | 0 | 0 | |
| seqNameTotalsSE | 0 | 0 | 0 | |
| setColors | 0.46 | 0.00 | 0.45 | |
| strandInvaders | 0.81 | 0.13 | 0.92 | |
| summariseChrExpr | 0.69 | 0.01 | 0.71 | |
| tagClusters | 0.06 | 0.00 | 0.06 | |