Charles Plessy
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 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 Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the CAGEr package: - 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.10.0.tar.gz |
| StartedAt: 2024-05-06 20:08:22 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 20:12:27 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 245.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CAGEr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 12.405 0.652 13.059
quantilePositions 10.531 0.451 10.982
exportToTrack 9.371 0.132 9.502
scoreShift 8.469 0.312 8.781
clusterCTSS 8.090 0.067 8.156
cumulativeCTSSdistribution 7.080 0.906 7.989
annotateCTSS 6.475 0.549 7.023
* 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
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CAGEr.Rcheck/00check.log’
for details.
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 1.119 | 0.226 | 1.352 | |
| CAGEr_Multicore | 1.660 | 0.004 | 1.665 | |
| CTSS-class | 0.081 | 0.001 | 0.081 | |
| CTSSclusteringMethod | 0 | 0 | 0 | |
| CTSScoordinates | 0.019 | 0.000 | 0.020 | |
| CTSSnormalizedTpm | 0.201 | 0.005 | 0.205 | |
| CTSStagCount | 0.260 | 0.006 | 0.267 | |
| CTSStoGenes | 0.133 | 0.001 | 0.134 | |
| CustomConsensusClusters | 4.546 | 0.169 | 4.715 | |
| GeneExpDESeq2 | 0.160 | 0.003 | 0.164 | |
| GeneExpSE | 0.001 | 0.000 | 0.001 | |
| QuantileWidthFunctions | 0.041 | 0.000 | 0.041 | |
| aggregateTagClusters | 12.405 | 0.652 | 13.059 | |
| annotateCTSS | 6.475 | 0.549 | 7.023 | |
| byCtss | 0.006 | 0.000 | 0.006 | |
| clusterCTSS | 8.090 | 0.067 | 8.156 | |
| consensusClusters | 0.032 | 0.001 | 0.032 | |
| consensusClustersDESeq2 | 1.504 | 0.113 | 1.617 | |
| consensusClustersTpm | 0.001 | 0.000 | 0.002 | |
| coverage-functions | 1.029 | 0.074 | 1.103 | |
| cumulativeCTSSdistribution | 7.080 | 0.906 | 7.989 | |
| distclu-functions | 1.195 | 0.120 | 1.315 | |
| exampleCAGEexp | 0.001 | 0.000 | 0.001 | |
| exportToTrack | 9.371 | 0.132 | 9.502 | |
| expressionClasses | 1.440 | 0.082 | 1.523 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 0.289 | 0.007 | 0.296 | |
| getExpressionProfiles | 4.439 | 0.214 | 4.657 | |
| getShiftingPromoters | 1.472 | 0.084 | 1.557 | |
| hanabi | 0.073 | 0.001 | 0.074 | |
| hanabiPlot | 0.089 | 0.006 | 0.094 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.023 | 0.000 | 0.024 | |
| 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 | 0.001 | |
| inputFilesType | 0.000 | 0.001 | 0.000 | |
| librarySizes | 0 | 0 | 0 | |
| mapStats | 0.015 | 0.001 | 0.018 | |
| mergeCAGEsets | 0.679 | 0.020 | 0.700 | |
| mergeSamples | 0.152 | 0.002 | 0.153 | |
| moleculesGR2CTSS | 0.033 | 0.000 | 0.033 | |
| normalizeTagCount | 0.154 | 0.002 | 0.156 | |
| parseCAGEscanBlocksToGrangeTSS | 0.006 | 0.001 | 0.006 | |
| plotAnnot | 0.635 | 0.008 | 0.643 | |
| plotCorrelation | 0.069 | 0.001 | 0.070 | |
| plotExpressionProfiles | 3.646 | 0.160 | 3.808 | |
| plotInterquantileWidth | 0.521 | 0.003 | 0.523 | |
| plotReverseCumulatives | 0.093 | 0.002 | 0.095 | |
| quantilePositions | 10.531 | 0.451 | 10.982 | |
| quickEnhancers | 0 | 0 | 0 | |
| ranges2annot | 0.098 | 0.001 | 0.099 | |
| ranges2genes | 0.016 | 0.001 | 0.017 | |
| ranges2names | 0.017 | 0.000 | 0.016 | |
| resetCAGEexp | 0.088 | 0.001 | 0.089 | |
| rowSums.RleDataFrame | 0.007 | 0.000 | 0.006 | |
| rowsum.RleDataFrame | 0.006 | 0.000 | 0.007 | |
| sampleLabels | 0.001 | 0.001 | 0.001 | |
| scoreShift | 8.469 | 0.312 | 8.781 | |
| seqNameTotalsSE | 0.001 | 0.000 | 0.001 | |
| setColors | 0.128 | 0.002 | 0.129 | |
| strandInvaders | 0.257 | 0.033 | 0.292 | |
| summariseChrExpr | 0.157 | 0.014 | 0.171 | |
| tagClusters | 0.064 | 0.006 | 0.070 | |