Beth Signal
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/GeneStructureTools |
| git_branch: master |
| git_last_commit: f104af6 |
| git_last_commit_date: 2021-10-26 12:42:28 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:36 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the GeneStructureTools package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 738/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneStructureTools 1.15.0 (landing page) Beth Signal
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeneStructureTools |
| Version: 1.15.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneStructureTools_1.15.0.tar.gz |
| StartedAt: 2022-03-17 19:10:16 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:15:23 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 307.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneStructureTools_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GeneStructureTools.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneStructureTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneStructureTools' version '1.15.0'
* 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 R 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 20.60 1.21 21.81
whippetTranscriptChangeSummary 9.89 0.19 10.51
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
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###
### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GeneStructureTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneStructureTools'
finding HTML links ... done
DEXSeqIdsToGeneIds html
UTR2UTR53 html
addBroadTypes html
addIntronInTranscript html
addSets html
alternativeIntronUsage html
annotateGeneModel html
attrChangeAltSpliced html
coordinates-methods html
cumsumANDpad html
diffSplicingResults-methods html
exonsToTranscripts html
filterGtfOverlap html
filterWhippetEvents html
findDEXexonType html
findExonContainingTranscripts html
findIntronContainingTranscripts html
findJunctionPairs html
formatWhippetEvents html
getOrfs html
getUOrfs html
junctions-methods html
leafcutterTranscriptChangeSummary html
makeGeneModel html
maxLocation html
orfDiff html
orfSimilarity html
overlapTypes html
readCounts-methods html
readWhippetDIFFfiles html
readWhippetDataSet html
readWhippetJNCfiles html
readWhippetPSIfiles html
removeDuplicateTranscripts html
removeSameExon html
removeVersion html
reorderExonNumbers html
replaceJunction html
skipExonInTranscript html
summariseExonTypes html
transcriptChangeSummary html
whippetDataSet-class html
whippetTranscriptChangeSummary html
** 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)
Making 'packages.html' ... done
GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings
| name | user | system | elapsed | |
| DEXSeqIdsToGeneIds | 0 | 0 | 0 | |
| UTR2UTR53 | 2.34 | 0.16 | 2.50 | |
| addBroadTypes | 0.31 | 0.00 | 0.31 | |
| addIntronInTranscript | 1.30 | 0.06 | 2.06 | |
| alternativeIntronUsage | 2.93 | 0.03 | 2.97 | |
| annotateGeneModel | 0.65 | 0.00 | 0.64 | |
| attrChangeAltSpliced | 0.89 | 0.03 | 1.36 | |
| coordinates-methods | 0.03 | 0.02 | 0.44 | |
| diffSplicingResults-methods | 0.04 | 0.01 | 0.49 | |
| exonsToTranscripts | 0.25 | 0.00 | 0.25 | |
| filterGtfOverlap | 0.25 | 0.00 | 0.25 | |
| filterWhippetEvents | 0.05 | 0.00 | 0.39 | |
| findDEXexonType | 2.16 | 0.00 | 2.15 | |
| findExonContainingTranscripts | 0.51 | 0.04 | 0.96 | |
| findIntronContainingTranscripts | 0.57 | 0.01 | 1.09 | |
| findJunctionPairs | 1.25 | 0.03 | 1.75 | |
| formatWhippetEvents | 0.00 | 0.00 | 0.05 | |
| getOrfs | 0.62 | 0.02 | 0.64 | |
| getUOrfs | 0.41 | 0.03 | 0.44 | |
| junctions-methods | 0.04 | 0.02 | 0.51 | |
| leafcutterTranscriptChangeSummary | 20.60 | 1.21 | 21.81 | |
| makeGeneModel | 0.18 | 0.02 | 0.21 | |
| maxLocation | 0 | 0 | 0 | |
| orfDiff | 1.39 | 0.00 | 1.83 | |
| orfSimilarity | 0 | 0 | 0 | |
| overlapTypes | 2.66 | 0.00 | 2.66 | |
| readCounts-methods | 0.03 | 0.02 | 0.48 | |
| readWhippetDIFFfiles | 0.00 | 0.00 | 0.04 | |
| readWhippetDataSet | 0.04 | 0.01 | 0.49 | |
| readWhippetJNCfiles | 0.03 | 0.00 | 0.23 | |
| readWhippetPSIfiles | 0.00 | 0.02 | 0.14 | |
| removeDuplicateTranscripts | 0.23 | 0.00 | 0.24 | |
| removeSameExon | 0.22 | 0.01 | 0.23 | |
| removeVersion | 0 | 0 | 0 | |
| reorderExonNumbers | 0.19 | 0.00 | 0.19 | |
| replaceJunction | 3.28 | 0.02 | 3.75 | |
| skipExonInTranscript | 1.61 | 0.03 | 2.06 | |
| summariseExonTypes | 2.61 | 0.00 | 2.61 | |
| transcriptChangeSummary | 1.76 | 0.03 | 2.19 | |
| whippetTranscriptChangeSummary | 9.89 | 0.19 | 10.51 | |