Charles Plessy
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/CAGEr |
| git_branch: RELEASE_3_16 |
| git_last_commit: 4ce371f |
| git_last_commit_date: 2022-11-01 11:07:54 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:27 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 246/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.4.0 (landing page) Charles Plessy
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CAGEr |
| Version: 2.4.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CAGEr_2.4.0.tar.gz |
| StartedAt: 2023-04-10 23:36:12 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:43:47 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 455.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CAGEr_2.4.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CAGEr.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '2.4.0'
* 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 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 38.49 2.13 40.62
clusterCTSS 34.03 0.54 34.57
exportToTrack 29.58 0.24 29.82
quantilePositions 18.03 0.36 18.39
aggregateTagClusters 7.63 0.11 7.74
CAGEexp-class 5.27 1.46 6.87
plotExpressionProfiles 5.33 0.17 5.50
* 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: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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 | 5.27 | 1.46 | 6.87 | |
| CAGEr_Multicore | 0.06 | 0.00 | 0.07 | |
| CTSS-class | 0.29 | 0.05 | 0.35 | |
| CTSSclusteringMethod | 0.02 | 0.00 | 0.01 | |
| CTSScoordinates | 0.06 | 0.00 | 0.06 | |
| CTSSnormalizedTpm | 0.67 | 0.02 | 0.69 | |
| CTSStagCount | 1.00 | 0.01 | 1.02 | |
| CTSStoGenes | 0.40 | 0.00 | 0.39 | |
| CustomConsensusClusters | 1.33 | 0.00 | 1.33 | |
| GeneExpDESeq2 | 1.25 | 0.06 | 1.41 | |
| GeneExpSE | 0 | 0 | 0 | |
| QuantileWidthFunctions | 0.12 | 0.00 | 0.12 | |
| aggregateTagClusters | 7.63 | 0.11 | 7.74 | |
| annotateCTSS | 1.94 | 0.04 | 1.97 | |
| byCtss | 0 | 0 | 0 | |
| clusterCTSS | 34.03 | 0.54 | 34.57 | |
| consensusClusters | 0.11 | 0.00 | 0.11 | |
| consensusClustersDESeq2 | 0.14 | 0.00 | 0.14 | |
| consensusClustersTpm | 0 | 0 | 0 | |
| coverage-functions | 4.19 | 0.08 | 4.27 | |
| cumulativeCTSSdistribution | 38.49 | 2.13 | 40.62 | |
| distclu-functions | 3.89 | 0.15 | 4.05 | |
| exampleCAGEexp | 0 | 0 | 0 | |
| exportToTrack | 29.58 | 0.24 | 29.82 | |
| expressionClasses | 0.02 | 0.00 | 0.01 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 1.26 | 0.01 | 1.28 | |
| getExpressionProfiles | 2.27 | 0.03 | 2.30 | |
| getShiftingPromoters | 0 | 0 | 0 | |
| hanabi | 0.32 | 0.02 | 0.34 | |
| hanabiPlot | 0.43 | 0.05 | 0.47 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.10 | 0.00 | 0.09 | |
| 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 | 0.04 | 0.00 | 0.04 | |
| mergeCAGEsets | 2.55 | 0.05 | 2.60 | |
| mergeSamples | 1.58 | 0.00 | 1.58 | |
| moleculesGR2CTSS | 0.12 | 0.00 | 0.12 | |
| normalizeTagCount | 0.42 | 0.01 | 0.44 | |
| parseCAGEscanBlocksToGrangeTSS | 0.02 | 0.00 | 0.01 | |
| plotAnnot | 2.87 | 0.07 | 2.97 | |
| plotCorrelation | 0.30 | 0.01 | 0.31 | |
| plotExpressionProfiles | 5.33 | 0.17 | 5.50 | |
| plotInterquantileWidth | 2.37 | 0.02 | 2.39 | |
| plotReverseCumulatives | 0.3 | 0.0 | 0.3 | |
| quantilePositions | 18.03 | 0.36 | 18.39 | |
| ranges2annot | 0.39 | 0.00 | 0.39 | |
| ranges2genes | 0.06 | 0.00 | 0.07 | |
| ranges2names | 0.05 | 0.00 | 0.04 | |
| sampleLabels | 0 | 0 | 0 | |
| scoreShift | 0 | 0 | 0 | |
| seqNameTotalsSE | 0.01 | 0.00 | 0.02 | |
| setColors | 0.40 | 0.00 | 0.39 | |
| strandInvaders | 0.82 | 0.14 | 1.02 | |
| summariseChrExpr | 0.62 | 0.00 | 0.63 | |
| tagClusters | 0.10 | 0.00 | 0.09 | |