Charles Plessy
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/CAGEr |
| git_branch: RELEASE_3_19 |
| git_last_commit: 6c8b145 |
| git_last_commit_date: 2024-04-30 10:30:39 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:34:56 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 | ||||
| Package 264/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.10.0 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the CAGEr package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CAGEr |
| Version: 2.10.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEr_2.10.0.tar.gz |
| StartedAt: 2024-05-29 20:46:35 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 21:02:39 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 964.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEr_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.10.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) inputFiles.Rd:28: Lost braces
28 | code{\link{CAGEexp}} objects.
| ^
checkRd: (-1) inputFilesType.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:53-55: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
S3 methods shown with full name in Rd file 'rowsum.RleDataFrame.Rd':
'rowsum.RleDataFrame'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
aggregateTagClusters 30.791 3.512 34.304
exportToTrack 29.215 0.527 29.743
clusterCTSS 27.572 0.536 28.098
cumulativeCTSSdistribution 19.976 4.488 24.478
annotateCTSS 20.932 2.556 23.490
scoreShift 20.348 1.484 21.831
quantilePositions 17.964 2.076 20.040
CustomConsensusClusters 10.687 1.252 11.940
getExpressionProfiles 8.299 0.792 9.092
plotExpressionProfiles 8.071 0.472 8.544
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck/00check.log’
for details.
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 2.771 | 0.040 | 2.815 | |
| CAGEr_Multicore | 3.224 | 0.140 | 3.364 | |
| CTSS-class | 0.249 | 0.000 | 0.249 | |
| CTSSclusteringMethod | 0.001 | 0.000 | 0.001 | |
| CTSScoordinates | 0.065 | 0.000 | 0.065 | |
| CTSSnormalizedTpm | 0.638 | 0.080 | 0.718 | |
| CTSStagCount | 0.765 | 0.112 | 0.877 | |
| CTSStoGenes | 0.313 | 0.068 | 0.380 | |
| CustomConsensusClusters | 10.687 | 1.252 | 11.940 | |
| GeneExpDESeq2 | 0.432 | 0.020 | 0.452 | |
| GeneExpSE | 0.004 | 0.000 | 0.003 | |
| QuantileWidthFunctions | 0.128 | 0.000 | 0.128 | |
| aggregateTagClusters | 30.791 | 3.512 | 34.304 | |
| annotateCTSS | 20.932 | 2.556 | 23.490 | |
| byCtss | 0.013 | 0.003 | 0.017 | |
| clusterCTSS | 27.572 | 0.536 | 28.098 | |
| consensusClusters | 0.137 | 0.000 | 0.137 | |
| consensusClustersDESeq2 | 3.393 | 0.452 | 3.846 | |
| consensusClustersTpm | 0.006 | 0.000 | 0.005 | |
| coverage-functions | 1.567 | 0.408 | 1.974 | |
| cumulativeCTSSdistribution | 19.976 | 4.488 | 24.478 | |
| distclu-functions | 3.436 | 0.700 | 4.084 | |
| exampleCAGEexp | 0.000 | 0.001 | 0.001 | |
| exportToTrack | 29.215 | 0.527 | 29.743 | |
| expressionClasses | 3.279 | 0.483 | 3.762 | |
| genomeName | 0.001 | 0.000 | 0.000 | |
| getCTSS | 0.950 | 0.016 | 0.965 | |
| getExpressionProfiles | 8.299 | 0.792 | 9.092 | |
| getShiftingPromoters | 3.143 | 0.404 | 3.547 | |
| hanabi | 0.223 | 0.000 | 0.224 | |
| hanabiPlot | 0.258 | 0.024 | 0.283 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.071 | 0.004 | 0.074 | |
| import.bam | 0.001 | 0.000 | 0.000 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0.000 | 0.000 | 0.001 | |
| import.bedmolecule | 0 | 0 | 0 | |
| inputFiles | 0.001 | 0.000 | 0.001 | |
| inputFilesType | 0.001 | 0.000 | 0.001 | |
| librarySizes | 0.000 | 0.001 | 0.001 | |
| mapStats | 0.046 | 0.007 | 0.052 | |
| mergeCAGEsets | 1.862 | 0.004 | 1.866 | |
| mergeSamples | 0.432 | 0.000 | 0.431 | |
| moleculesGR2CTSS | 0.11 | 0.00 | 0.11 | |
| normalizeTagCount | 0.439 | 0.004 | 0.414 | |
| parseCAGEscanBlocksToGrangeTSS | 0.023 | 0.000 | 0.022 | |
| plotAnnot | 2.116 | 0.008 | 2.123 | |
| plotCorrelation | 0.222 | 0.007 | 0.230 | |
| plotExpressionProfiles | 8.071 | 0.472 | 8.544 | |
| plotInterquantileWidth | 1.688 | 0.004 | 1.693 | |
| plotReverseCumulatives | 0.313 | 0.005 | 0.273 | |
| quantilePositions | 17.964 | 2.076 | 20.040 | |
| quickEnhancers | 0 | 0 | 0 | |
| ranges2annot | 0.337 | 0.000 | 0.337 | |
| ranges2genes | 0.049 | 0.003 | 0.052 | |
| ranges2names | 0.052 | 0.000 | 0.052 | |
| resetCAGEexp | 0.300 | 0.004 | 0.304 | |
| rowSums.RleDataFrame | 0.018 | 0.004 | 0.022 | |
| rowsum.RleDataFrame | 0.019 | 0.004 | 0.023 | |
| sampleLabels | 0.004 | 0.000 | 0.004 | |
| scoreShift | 20.348 | 1.484 | 21.831 | |
| seqNameTotalsSE | 0.004 | 0.000 | 0.004 | |
| setColors | 0.308 | 0.000 | 0.307 | |
| strandInvaders | 0.739 | 0.063 | 0.776 | |
| summariseChrExpr | 0.362 | 0.000 | 0.362 | |
| tagClusters | 0.203 | 0.003 | 0.207 | |