Charles Plessy
| Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/CAGEr |
| git_branch: devel |
| git_last_commit: cdfe2b1 |
| git_last_commit_date: 2024-10-29 09:44:43 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-28 11:47 -0500 (Tue, 28 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| 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 262/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.13.0 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 2.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEr_2.13.0.tar.gz |
| StartedAt: 2025-01-28 08:53:03 -0000 (Tue, 28 Jan 2025) |
| EndedAt: 2025-01-28 09:06:43 -0000 (Tue, 28 Jan 2025) |
| EllapsedTime: 820.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CAGEr.Rcheck |
| Warnings: 6 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEr_2.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.13.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
* 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 71.948 0.299 72.418
exportToTrack 56.695 0.251 57.070
aggregateTagClusters 32.224 0.527 32.829
scoreShift 26.650 0.196 26.907
quantilePositions 20.215 0.127 20.392
annotateCTSS 19.190 0.163 19.400
distclu 14.527 0.036 14.593
plotExpressionProfiles 10.950 0.080 11.054
CustomConsensusClusters 7.446 0.255 7.719
getExpressionProfiles 7.581 0.100 7.700
cumulativeCTSSdistribution 5.460 0.144 5.618
* 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: 6 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck/00check.log’
for details.
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (CAGEr)
CAGEr.Rcheck/CAGEr-Ex.timings
| name | user | system | elapsed | |
| CAGEexp-class | 2.606 | 0.120 | 2.758 | |
| CAGEr_Multicore | 4.267 | 0.299 | 4.577 | |
| CTSS-class | 0.367 | 0.001 | 0.368 | |
| CTSScoordinates | 0.117 | 0.000 | 0.117 | |
| CTSSnormalizedTpm | 1.000 | 0.059 | 1.062 | |
| CTSStagCount | 0.918 | 0.096 | 1.015 | |
| CTSStoGenes | 0.517 | 0.064 | 0.582 | |
| CustomConsensusClusters | 7.446 | 0.255 | 7.719 | |
| GeneExpDESeq2 | 0.707 | 0.028 | 0.737 | |
| GeneExpSE | 0.006 | 0.000 | 0.006 | |
| QuantileWidthFunctions | 0.198 | 0.000 | 0.199 | |
| TSSlogo | 3.965 | 0.112 | 4.103 | |
| aggregateTagClusters | 32.224 | 0.527 | 32.829 | |
| annotateCTSS | 19.190 | 0.163 | 19.400 | |
| byCtss | 0.023 | 0.000 | 0.023 | |
| consensusClusters | 0.215 | 0.016 | 0.231 | |
| consensusClustersDESeq2 | 3.218 | 0.016 | 3.242 | |
| consensusClustersTpm | 0.007 | 0.000 | 0.007 | |
| cumulativeCTSSdistribution | 5.460 | 0.144 | 5.618 | |
| distclu | 14.527 | 0.036 | 14.593 | |
| dot-ctss_summary_for_clusters | 1.210 | 0.004 | 1.217 | |
| exampleCAGEexp | 0 | 0 | 0 | |
| exportToTrack | 56.695 | 0.251 | 57.070 | |
| expressionClasses | 2.919 | 0.008 | 2.935 | |
| filteredCTSSidx | 0.012 | 0.000 | 0.012 | |
| flagLowExpCTSS | 0.046 | 0.000 | 0.046 | |
| genomeName | 0 | 0 | 0 | |
| getCTSS | 1.316 | 0.008 | 1.327 | |
| getExpressionProfiles | 7.581 | 0.100 | 7.700 | |
| getShiftingPromoters | 3.120 | 0.052 | 3.179 | |
| hanabi | 0.329 | 0.008 | 0.338 | |
| hanabiPlot | 0.403 | 0.020 | 0.424 | |
| import.CAGEscanMolecule | 0 | 0 | 0 | |
| import.CTSS | 0.118 | 0.000 | 0.118 | |
| import.bam | 0 | 0 | 0 | |
| import.bedCTSS | 0 | 0 | 0 | |
| import.bedScore | 0.001 | 0.000 | 0.000 | |
| import.bedmolecule | 0 | 0 | 0 | |
| importPublicData | 0 | 0 | 0 | |
| inputFiles | 0.000 | 0.002 | 0.001 | |
| inputFilesType | 0.001 | 0.000 | 0.001 | |
| librarySizes | 0.001 | 0.000 | 0.001 | |
| mapStats | 0.071 | 0.000 | 0.071 | |
| mergeCAGEsets | 2.942 | 0.016 | 2.967 | |
| mergeSamples | 0.658 | 0.000 | 0.659 | |
| moleculesGR2CTSS | 0.186 | 0.000 | 0.186 | |
| normalizeTagCount | 0.683 | 0.000 | 0.680 | |
| paraclu | 71.948 | 0.299 | 72.418 | |
| parseCAGEscanBlocksToGrangeTSS | 0.034 | 0.000 | 0.034 | |
| plotAnnot | 3.318 | 0.016 | 3.342 | |
| plotCorrelation | 0.359 | 0.004 | 0.364 | |
| plotExpressionProfiles | 10.950 | 0.080 | 11.054 | |
| plotInterquantileWidth | 3.014 | 0.044 | 3.064 | |
| plotReverseCumulatives | 3.333 | 0.020 | 3.349 | |
| quantilePositions | 20.215 | 0.127 | 20.392 | |
| quickEnhancers | 0 | 0 | 0 | |
| ranges2annot | 0.482 | 0.004 | 0.488 | |
| ranges2genes | 0.080 | 0.000 | 0.081 | |
| ranges2names | 0.079 | 0.000 | 0.079 | |
| resetCAGEexp | 0.432 | 0.000 | 0.432 | |
| rowSums.RleDataFrame | 0.028 | 0.000 | 0.028 | |
| rowsum.RleDataFrame | 0.024 | 0.008 | 0.031 | |
| sampleLabels | 0.005 | 0.000 | 0.005 | |
| scoreShift | 26.650 | 0.196 | 26.907 | |
| seqNameTotalsSE | 0.005 | 0.000 | 0.005 | |
| setColors | 0.457 | 0.000 | 0.459 | |
| strandInvaders | 0.845 | 0.028 | 0.872 | |
| summariseChrExpr | 0.559 | 0.000 | 0.561 | |
| tagClusters | 0.572 | 0.000 | 0.574 | |