Charles Plessy
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/CAGEr |
| git_branch: devel |
| git_last_commit: 18d7295 |
| git_last_commit_date: 2023-10-24 09:52:59 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:24 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 262/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.9.0 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: CAGEr |
| Version: 2.9.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings CAGEr_2.9.0.tar.gz |
| StartedAt: 2024-03-28 03:31:10 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:46:17 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 906.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings CAGEr_2.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.9.0’
* 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
exportToTrack 49.071 0.351 49.520
clusterCTSS 47.119 0.395 47.601
aggregateTagClusters 45.804 1.338 47.235
scoreShift 38.913 0.431 39.422
quantilePositions 36.271 0.682 37.023
cumulativeCTSSdistribution 35.407 1.214 36.695
annotateCTSS 34.806 0.842 35.714
CustomConsensusClusters 17.287 0.456 17.778
getExpressionProfiles 15.682 0.223 15.938
plotExpressionProfiles 13.394 0.112 13.532
consensusClustersDESeq2 7.475 0.192 7.680
expressionClasses 7.082 0.104 7.201
distclu-functions 6.503 0.208 6.720
getShiftingPromoters 5.714 0.088 5.815
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 | 3.821 | 0.184 | 4.033 | |
| CAGEr_Multicore | 4.103 | 0.080 | 4.189 | |
| CTSS-class | 0.39 | 0.00 | 0.39 | |
| CTSSclusteringMethod | 0.001 | 0.000 | 0.001 | |
| CTSScoordinates | 0.102 | 0.000 | 0.103 | |
| CTSSnormalizedTpm | 0.995 | 0.040 | 1.036 | |
| CTSStagCount | 1.201 | 0.076 | 1.279 | |
| CTSStoGenes | 0.490 | 0.031 | 0.523 | |
| CustomConsensusClusters | 17.287 | 0.456 | 17.778 | |
| GeneExpDESeq2 | 0.652 | 0.019 | 0.673 | |
| GeneExpSE | 0.005 | 0.001 | 0.005 | |
| QuantileWidthFunctions | 0.172 | 0.007 | 0.180 | |
| aggregateTagClusters | 45.804 | 1.338 | 47.235 | |
| annotateCTSS | 34.806 | 0.842 | 35.714 | |
| byCtss | 0.019 | 0.000 | 0.019 | |
| clusterCTSS | 47.119 | 0.395 | 47.601 | |
| consensusClusters | 0.190 | 0.004 | 0.194 | |
| consensusClustersDESeq2 | 7.475 | 0.192 | 7.680 | |
| consensusClustersTpm | 0.008 | 0.000 | 0.008 | |
| coverage-functions | 4.433 | 0.127 | 4.569 | |
| cumulativeCTSSdistribution | 35.407 | 1.214 | 36.695 | |
| distclu-functions | 6.503 | 0.208 | 6.720 | |
| exampleCAGEexp | 0 | 0 | 0 | |
| exportToTrack | 49.071 | 0.351 | 49.520 | |
| expressionClasses | 7.082 | 0.104 | 7.201 | |
| genomeName | 0.001 | 0.000 | 0.001 | |
| getCTSS | 1.286 | 0.028 | 1.316 | |
| getExpressionProfiles | 15.682 | 0.223 | 15.938 | |
| getShiftingPromoters | 5.714 | 0.088 | 5.815 | |
| hanabi | 0.322 | 0.016 | 0.339 | |
| hanabiPlot | 0.399 | 0.012 | 0.413 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.108 | 0.000 | 0.108 | |
| import.bam | 0 | 0 | 0 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0 | 0 | 0 | |
| inputFiles | 0.001 | 0.000 | 0.002 | |
| inputFilesType | 0.001 | 0.000 | 0.001 | |
| librarySizes | 0.001 | 0.000 | 0.001 | |
| mapStats | 0.066 | 0.004 | 0.070 | |
| mergeCAGEsets | 2.802 | 0.008 | 2.816 | |
| mergeSamples | 0.626 | 0.000 | 0.628 | |
| moleculesGR2CTSS | 0.177 | 0.000 | 0.178 | |
| normalizeTagCount | 0.671 | 0.000 | 0.669 | |
| parseCAGEscanBlocksToGrangeTSS | 0.031 | 0.000 | 0.031 | |
| plotAnnot | 3.184 | 0.004 | 3.195 | |
| plotCorrelation | 0.353 | 0.000 | 0.353 | |
| plotExpressionProfiles | 13.394 | 0.112 | 13.532 | |
| plotInterquantileWidth | 2.605 | 0.004 | 2.614 | |
| plotReverseCumulatives | 0.428 | 0.000 | 0.418 | |
| quantilePositions | 36.271 | 0.682 | 37.023 | |
| quickEnhancers | 0 | 0 | 0 | |
| ranges2annot | 0.528 | 0.000 | 0.529 | |
| ranges2genes | 0.083 | 0.000 | 0.084 | |
| ranges2names | 0.082 | 0.000 | 0.083 | |
| resetCAGEexp | 0.455 | 0.004 | 0.461 | |
| rowSums.RleDataFrame | 0.029 | 0.000 | 0.029 | |
| rowsum.RleDataFrame | 0.033 | 0.000 | 0.034 | |
| sampleLabels | 0.006 | 0.000 | 0.006 | |
| scoreShift | 38.913 | 0.431 | 39.422 | |
| seqNameTotalsSE | 0.005 | 0.000 | 0.004 | |
| setColors | 0.437 | 0.000 | 0.438 | |
| strandInvaders | 0.939 | 0.036 | 0.985 | |
| summariseChrExpr | 0.537 | 0.000 | 0.538 | |
| tagClusters | 0.315 | 0.000 | 0.315 | |