Beth Signal
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/GeneStructureTools |
| git_branch: devel |
| git_last_commit: 001986b |
| git_last_commit_date: 2024-10-29 10:26:11 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:38 -0500 (Sat, 25 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" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 803/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneStructureTools 1.27.0 (landing page) Beth Signal
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.27.0 |
| 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_1.27.0.tar.gz |
| StartedAt: 2025-01-25 01:53:28 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 02:01:37 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 488.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 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 '1.27.0'
* 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 30.63 1.74 32.38
whippetTranscriptChangeSummary 16.11 0.53 17.64
replaceJunction 5.93 0.00 6.78
* 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 '1.27.0' ** 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 | 2.86 | 0.15 | 3.02 | |
| addBroadTypes | 0.25 | 0.01 | 0.27 | |
| addIntronInTranscript | 3.53 | 0.00 | 4.65 | |
| alternativeIntronUsage | 4.89 | 0.09 | 4.99 | |
| annotateGeneModel | 1.36 | 0.00 | 1.36 | |
| attrChangeAltSpliced | 1.33 | 0.04 | 2.30 | |
| coordinates-methods | 0.03 | 0.00 | 1.03 | |
| diffSplicingResults-methods | 0.03 | 0.01 | 1.00 | |
| exonsToTranscripts | 0.42 | 0.02 | 0.43 | |
| filterGtfOverlap | 0.36 | 0.00 | 0.36 | |
| filterWhippetEvents | 0.05 | 0.03 | 0.97 | |
| findDEXexonType | 3.31 | 0.01 | 3.38 | |
| findExonContainingTranscripts | 0.72 | 0.05 | 2.03 | |
| findIntronContainingTranscripts | 0.97 | 0.00 | 2.00 | |
| findJunctionPairs | 1.87 | 0.02 | 2.86 | |
| formatWhippetEvents | 0.02 | 0.00 | 0.12 | |
| getOrfs | 0.98 | 0.01 | 1.00 | |
| getUOrfs | 0.97 | 0.05 | 1.02 | |
| junctions-methods | 0.06 | 0.01 | 1.06 | |
| leafcutterTranscriptChangeSummary | 30.63 | 1.74 | 32.38 | |
| makeGeneModel | 0.25 | 0.01 | 0.27 | |
| maxLocation | 0 | 0 | 0 | |
| orfDiff | 2.00 | 0.07 | 3.08 | |
| orfSimilarity | 0 | 0 | 0 | |
| overlapTypes | 2.82 | 0.06 | 2.87 | |
| readCounts-methods | 0.03 | 0.00 | 1.04 | |
| readWhippetDIFFfiles | 0.00 | 0.00 | 0.14 | |
| readWhippetDataSet | 0.07 | 0.03 | 2.00 | |
| readWhippetJNCfiles | 0.01 | 0.00 | 0.53 | |
| readWhippetPSIfiles | 0.02 | 0.00 | 0.44 | |
| removeDuplicateTranscripts | 0.48 | 0.00 | 0.49 | |
| removeSameExon | 0.47 | 0.00 | 0.47 | |
| removeVersion | 0.02 | 0.00 | 0.01 | |
| reorderExonNumbers | 0.36 | 0.03 | 0.39 | |
| replaceJunction | 5.93 | 0.00 | 6.78 | |
| skipExonInTranscript | 1.78 | 0.02 | 2.83 | |
| summariseExonTypes | 3.11 | 0.03 | 3.14 | |
| transcriptChangeSummary | 1.85 | 0.08 | 3.03 | |
| whippetTranscriptChangeSummary | 16.11 | 0.53 | 17.64 | |