Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:05 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 759/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.19.0 (landing page) Beth Signal
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: GeneStructureTools |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GeneStructureTools_1.19.0.tar.gz |
StartedAt: 2023-02-07 02:18:03 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 02:28:23 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 620.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GeneStructureTools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GeneStructureTools_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneStructureTools.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.19.0’ * 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 for sufficient/correct file permissions ... 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 ... ERROR Running examples in ‘GeneStructureTools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: transcriptChangeSummary > ### Title: Compare open reading frames for two sets of paired transcripts > ### Aliases: transcriptChangeSummary > > ### ** Examples > > whippetFiles <- system.file("extdata","whippet/", + package = "GeneStructureTools") > wds <- readWhippetDataSet(whippetFiles) Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//01_v_21.diff.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//A01.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//A21.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//B01.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//B21.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//A01.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//A21.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//B01.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('zcat < /home/biocbuild/bbs-3.17-bioc/R/library/GeneStructureTools/extdata/whippet//B21.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. > wds <- filterWhippetEvents(wds) Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneStructureTools.Rcheck/00check.log’ for details.
GeneStructureTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 0.003 | 0.000 | 0.003 | |
UTR2UTR53 | 5.192 | 0.140 | 5.340 | |
addBroadTypes | 0.212 | 0.012 | 0.225 | |
addIntronInTranscript | 2.573 | 0.039 | 2.620 | |
alternativeIntronUsage | 5.988 | 0.008 | 6.000 | |
annotateGeneModel | 1.187 | 0.004 | 1.194 | |
attrChangeAltSpliced | 1.671 | 0.018 | 1.694 | |
coordinates-methods | 0.069 | 0.012 | 0.080 | |
diffSplicingResults-methods | 0.066 | 0.013 | 0.084 | |
exonsToTranscripts | 0.346 | 0.000 | 0.346 | |
filterGtfOverlap | 0.328 | 0.004 | 0.332 | |
filterWhippetEvents | 0.087 | 0.011 | 0.099 | |
findDEXexonType | 4.299 | 0.012 | 4.320 | |
findExonContainingTranscripts | 0.565 | 0.025 | 0.590 | |
findIntronContainingTranscripts | 0.870 | 0.015 | 0.886 | |
findJunctionPairs | 1.854 | 0.020 | 1.874 | |
formatWhippetEvents | 0.019 | 0.000 | 0.020 | |
getOrfs | 0.963 | 0.008 | 0.971 | |
getUOrfs | 0.746 | 0.016 | 0.762 | |
junctions-methods | 0.069 | 0.016 | 0.083 | |
leafcutterTranscriptChangeSummary | 32.697 | 0.256 | 33.090 | |
makeGeneModel | 0.186 | 0.015 | 0.204 | |
maxLocation | 0.003 | 0.000 | 0.004 | |
orfDiff | 3.190 | 0.061 | 3.296 | |
orfSimilarity | 0.001 | 0.000 | 0.001 | |
overlapTypes | 3.836 | 0.004 | 3.987 | |
readCounts-methods | 0.078 | 0.007 | 0.184 | |
readWhippetDIFFfiles | 0.008 | 0.000 | 0.036 | |
readWhippetDataSet | 0.075 | 0.005 | 0.153 | |
readWhippetJNCfiles | 0.033 | 0.005 | 0.040 | |
readWhippetPSIfiles | 0.017 | 0.002 | 0.020 | |
removeDuplicateTranscripts | 0.331 | 0.000 | 0.332 | |
removeSameExon | 0.272 | 0.008 | 0.279 | |
removeVersion | 0 | 0 | 0 | |
reorderExonNumbers | 0.216 | 0.000 | 0.216 | |
replaceJunction | 5.551 | 0.014 | 5.569 | |
skipExonInTranscript | 2.007 | 0.023 | 2.193 | |
summariseExonTypes | 4.224 | 0.043 | 4.922 | |