Charles Plessy
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/CAGEr |
| git_branch: RELEASE_3_21 |
| git_last_commit: 446e1ca |
| git_last_commit_date: 2025-04-15 10:18:00 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 268/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.14.0 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / 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. |
| Package: CAGEr |
| Version: 2.14.0 |
| 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_2.14.0.tar.gz |
| StartedAt: 2025-10-14 15:01:27 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 15:12:52 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 685.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEr.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_2.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
CAGEexp-class.Rd: MultiAssayExperiment, DataFrame, Rle
CAGEr-class.Rd: MultiAssayExperiment
CTSStagCount.Rd: DataFrame, Rle, RangedSummarizedExperiment
CTSStoGenes.Rd: SummarizedExperiment
CustomConsensusClusters.Rd: GRanges, RangedSummarizedExperiment
TSSlogo.Rd: BSgenome
aggregateTagClusters.Rd: RangedSummarizedExperiment
annotateCTSS.Rd: GRanges, TxDb
bam2CTSS.Rd: GRanges
byCtss.Rd: data.table
consensusClusters.Rd: GRanges, SummarizedExperiment
distclu.Rd: GRangesList
dot-ctss_summary_for_clusters.Rd: GRanges
expressionClasses.Rd: Rle
flagLowExpCTSS.Rd: Rle
getCTSS.Rd: RangedSummarizedExperiment
import.CAGEscanMolecule.Rd: GRanges
import.CTSS.Rd: GPos
loadFileIntoGPos.Rd: GPos
moleculesGR2CTSS.Rd: GRanges
paraclu.Rd: RangedSummarizedExperiment, GRangesList
plotCorrelation.Rd: SummarizedExperiment, DataFrame
quantilePositions.Rd: RangedSummarizedExperiment
ranges2annot.Rd: rowRanges, Rle
ranges2names.Rd: Rle
strandInvaders.Rd: Rle
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
paraclu 41.681 0.158 42.371
exportToTrack 36.495 0.188 37.086
aggregateTagClusters 20.863 0.165 21.334
scoreShift 17.248 0.121 17.458
annotateCTSS 12.246 0.055 12.417
quantilePositions 12.122 0.095 12.312
distclu 9.311 0.042 9.416
plotExpressionProfiles 9.011 0.238 9.303
CAGEexp-class 5.620 0.785 6.514
getExpressionProfiles 5.370 0.040 5.445
CustomConsensusClusters 4.835 0.101 5.007
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/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/4.5-arm64/Resources/library’ * installing *source* package ‘CAGEr’ ... ** this is package ‘CAGEr’ version ‘2.14.0’ ** 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 | 5.620 | 0.785 | 6.514 | |
| CAGEr_Multicore | 4.631 | 0.071 | 4.804 | |
| CTSS-class | 0.283 | 0.003 | 0.298 | |
| CTSScoordinates | 0.088 | 0.004 | 0.095 | |
| CTSSnormalizedTpm | 0.786 | 0.008 | 0.814 | |
| CTSStagCount | 0.748 | 0.052 | 0.817 | |
| CTSStoGenes | 0.517 | 0.040 | 0.567 | |
| CustomConsensusClusters | 4.835 | 0.101 | 5.007 | |
| GeneExpDESeq2 | 0.528 | 0.013 | 0.542 | |
| GeneExpSE | 0.004 | 0.000 | 0.004 | |
| QuantileWidthFunctions | 0.156 | 0.002 | 0.160 | |
| TSSlogo | 2.750 | 0.048 | 2.818 | |
| aggregateTagClusters | 20.863 | 0.165 | 21.334 | |
| annotateCTSS | 12.246 | 0.055 | 12.417 | |
| byCtss | 0.021 | 0.001 | 0.023 | |
| consensusClusters | 0.184 | 0.003 | 0.188 | |
| consensusClustersDESeq2 | 1.961 | 0.008 | 1.995 | |
| consensusClustersTpm | 0.006 | 0.001 | 0.007 | |
| cumulativeCTSSdistribution | 4.257 | 0.087 | 4.393 | |
| distclu | 9.311 | 0.042 | 9.416 | |
| dot-ctss_summary_for_clusters | 0.942 | 0.006 | 0.952 | |
| exampleCAGEexp | 0.000 | 0.000 | 0.001 | |
| exportToTrack | 36.495 | 0.188 | 37.086 | |
| expressionClasses | 1.764 | 0.005 | 1.775 | |
| filteredCTSSidx | 0.011 | 0.000 | 0.011 | |
| flagLowExpCTSS | 0.068 | 0.001 | 0.069 | |
| genomeName | 0.000 | 0.000 | 0.001 | |
| getCTSS | 1.240 | 0.022 | 1.277 | |
| getExpressionProfiles | 5.370 | 0.040 | 5.445 | |
| getShiftingPromoters | 1.891 | 0.009 | 1.921 | |
| hanabi | 0.259 | 0.013 | 0.274 | |
| hanabiPlot | 0.308 | 0.027 | 0.340 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.087 | 0.002 | 0.093 | |
| import.bam | 0.000 | 0.001 | 0.000 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0 | 0 | 0 | |
| import.bedmolecule | 0.000 | 0.000 | 0.001 | |
| importPublicData | 0.000 | 0.000 | 0.001 | |
| inputFiles | 0.002 | 0.000 | 0.002 | |
| inputFilesType | 0.001 | 0.000 | 0.001 | |
| librarySizes | 0.001 | 0.001 | 0.001 | |
| mapStats | 0.055 | 0.003 | 0.060 | |
| mergeCAGEsets | 2.642 | 0.058 | 2.751 | |
| mergeSamples | 0.775 | 0.010 | 0.803 | |
| moleculesGR2CTSS | 0.145 | 0.001 | 0.148 | |
| normalizeTagCount | 0.632 | 0.009 | 0.651 | |
| paraclu | 41.681 | 0.158 | 42.371 | |
| parseCAGEscanBlocksToGrangeTSS | 0.025 | 0.001 | 0.025 | |
| plotAnnot | 3.560 | 0.029 | 3.657 | |
| plotCorrelation | 0.256 | 0.003 | 0.262 | |
| plotExpressionProfiles | 9.011 | 0.238 | 9.303 | |
| plotInterquantileWidth | 4.246 | 0.066 | 4.347 | |
| plotReverseCumulatives | 2.776 | 0.032 | 2.833 | |
| quantilePositions | 12.122 | 0.095 | 12.312 | |
| quickEnhancers | 0.000 | 0.001 | 0.000 | |
| ranges2annot | 0.383 | 0.005 | 0.392 | |
| ranges2genes | 0.064 | 0.002 | 0.066 | |
| ranges2names | 0.085 | 0.003 | 0.088 | |
| resetCAGEexp | 0.372 | 0.003 | 0.380 | |
| rowSums.RleDataFrame | 0.028 | 0.001 | 0.028 | |
| rowsum.RleDataFrame | 0.032 | 0.001 | 0.033 | |
| sampleLabels | 0.005 | 0.000 | 0.005 | |
| scoreShift | 17.248 | 0.121 | 17.458 | |
| seqNameTotalsSE | 0.003 | 0.000 | 0.004 | |
| setColors | 0.443 | 0.006 | 0.449 | |
| strandInvaders | 0.850 | 0.081 | 0.933 | |
| summariseChrExpr | 0.582 | 0.019 | 0.601 | |
| tagClusters | 0.446 | 0.031 | 0.480 | |