| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:30 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 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 807/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneStructureTools 1.26.0 (landing page) Beth Signal
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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To the developers/maintainers of the GeneStructureTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneStructureTools.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: GeneStructureTools |
| Version: 1.26.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneStructureTools_1.26.0.tar.gz |
| StartedAt: 2025-04-01 01:50:42 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 01:59:06 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 503.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneStructureTools_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeneStructureTools.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneStructureTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneStructureTools' version '1.26.0'
* 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 whether package 'GeneStructureTools' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 31.59 1.88 33.49
whippetTranscriptChangeSummary 15.64 0.22 16.91
replaceJunction 4.69 0.02 5.68
* 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: OK
GeneStructureTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GeneStructureTools' ... ** using staged installation ** R ** 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 (GeneStructureTools)
GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings
| name | user | system | elapsed | |
| DEXSeqIdsToGeneIds | 0 | 0 | 0 | |
| UTR2UTR53 | 4.27 | 0.17 | 4.45 | |
| addBroadTypes | 0.26 | 0.00 | 0.26 | |
| addIntronInTranscript | 2.14 | 0.11 | 3.36 | |
| alternativeIntronUsage | 4.72 | 0.10 | 4.83 | |
| annotateGeneModel | 1.19 | 0.00 | 1.19 | |
| attrChangeAltSpliced | 1.47 | 0.01 | 2.47 | |
| coordinates-methods | 0.04 | 0.05 | 1.11 | |
| diffSplicingResults-methods | 0.05 | 0.03 | 1.08 | |
| exonsToTranscripts | 0.36 | 0.00 | 0.36 | |
| filterGtfOverlap | 0.31 | 0.03 | 0.34 | |
| filterWhippetEvents | 0.06 | 0.02 | 1.09 | |
| findDEXexonType | 4.77 | 0.03 | 4.83 | |
| findExonContainingTranscripts | 0.59 | 0.06 | 1.61 | |
| findIntronContainingTranscripts | 0.74 | 0.03 | 1.78 | |
| findJunctionPairs | 1.65 | 0.00 | 2.72 | |
| formatWhippetEvents | 0.02 | 0.00 | 0.13 | |
| getOrfs | 1.02 | 0.03 | 1.04 | |
| getUOrfs | 0.68 | 0.07 | 0.75 | |
| junctions-methods | 0.02 | 0.03 | 1.01 | |
| leafcutterTranscriptChangeSummary | 31.59 | 1.88 | 33.49 | |
| makeGeneModel | 0.30 | 0.01 | 0.31 | |
| maxLocation | 0 | 0 | 0 | |
| orfDiff | 2.08 | 0.03 | 3.23 | |
| orfSimilarity | 0 | 0 | 0 | |
| overlapTypes | 3.20 | 0.06 | 3.27 | |
| readCounts-methods | 0.05 | 0.05 | 1.09 | |
| readWhippetDIFFfiles | 0.00 | 0.02 | 0.11 | |
| readWhippetDataSet | 0.04 | 0.03 | 1.08 | |
| readWhippetJNCfiles | 0.02 | 0.01 | 0.48 | |
| readWhippetPSIfiles | 0.02 | 0.00 | 0.42 | |
| removeDuplicateTranscripts | 0.54 | 0.00 | 0.55 | |
| removeSameExon | 0.33 | 0.00 | 0.33 | |
| removeVersion | 0 | 0 | 0 | |
| reorderExonNumbers | 0.44 | 0.00 | 0.44 | |
| replaceJunction | 4.69 | 0.02 | 5.68 | |
| skipExonInTranscript | 1.75 | 0.06 | 2.80 | |
| summariseExonTypes | 3.48 | 0.02 | 3.50 | |
| transcriptChangeSummary | 2.02 | 0.03 | 3.09 | |
| whippetTranscriptChangeSummary | 15.64 | 0.22 | 16.91 | |