| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-18 11:41 -0400 (Mon, 18 Aug 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" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 822/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneStructureTools 1.28.0 (landing page) Beth Signal
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | 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 | | ||||||||
| kunpeng2 | 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: 1.28.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz |
| StartedAt: 2025-08-15 02:30:22 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 02:38:37 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 494.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* 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 '1.28.0'
* 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 29.25 2.11 31.44
whippetTranscriptChangeSummary 15.30 0.38 16.66
replaceJunction 4.83 0.05 5.59
* 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: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'GeneStructureTools' ... ** this is package 'GeneStructureTools' version '1.28.0' ** 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 | 3.25 | 0.15 | 3.44 | |
| addBroadTypes | 0.36 | 0.00 | 0.36 | |
| addIntronInTranscript | 3.72 | 0.05 | 4.81 | |
| alternativeIntronUsage | 4.55 | 0.08 | 4.63 | |
| annotateGeneModel | 1.20 | 0.00 | 1.22 | |
| attrChangeAltSpliced | 1.31 | 0.03 | 2.33 | |
| coordinates-methods | 0.03 | 0.00 | 3.06 | |
| diffSplicingResults-methods | 0.03 | 0.02 | 1.04 | |
| exonsToTranscripts | 0.47 | 0.00 | 0.47 | |
| filterGtfOverlap | 0.36 | 0.00 | 0.36 | |
| filterWhippetEvents | 0.08 | 0.03 | 1.05 | |
| findDEXexonType | 3.19 | 0.01 | 3.22 | |
| findExonContainingTranscripts | 0.58 | 0.03 | 1.61 | |
| findIntronContainingTranscripts | 0.86 | 0.04 | 1.89 | |
| findJunctionPairs | 1.78 | 0.01 | 2.74 | |
| formatWhippetEvents | 0.02 | 0.00 | 0.30 | |
| getOrfs | 1.08 | 0.02 | 1.09 | |
| getUOrfs | 0.86 | 0.04 | 0.91 | |
| junctions-methods | 0.07 | 0.03 | 1.10 | |
| leafcutterTranscriptChangeSummary | 29.25 | 2.11 | 31.44 | |
| makeGeneModel | 0.35 | 0.00 | 0.35 | |
| maxLocation | 0 | 0 | 0 | |
| orfDiff | 1.98 | 0.13 | 3.07 | |
| orfSimilarity | 0 | 0 | 0 | |
| overlapTypes | 4.44 | 0.01 | 4.45 | |
| readCounts-methods | 0.04 | 0.02 | 0.92 | |
| readWhippetDIFFfiles | 0.00 | 0.02 | 0.11 | |
| readWhippetDataSet | 0.03 | 0.01 | 1.05 | |
| readWhippetJNCfiles | 0.02 | 0.00 | 0.49 | |
| readWhippetPSIfiles | 0.0 | 0.0 | 0.4 | |
| removeDuplicateTranscripts | 0.56 | 0.00 | 0.56 | |
| removeSameExon | 0.5 | 0.0 | 0.5 | |
| removeVersion | 0 | 0 | 0 | |
| reorderExonNumbers | 0.42 | 0.03 | 0.46 | |
| replaceJunction | 4.83 | 0.05 | 5.59 | |
| skipExonInTranscript | 2.17 | 0.00 | 3.17 | |
| summariseExonTypes | 3.32 | 0.05 | 3.36 | |
| transcriptChangeSummary | 2.21 | 0.04 | 3.25 | |
| whippetTranscriptChangeSummary | 15.30 | 0.38 | 16.66 | |