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This page was generated on 2024-05-04 11:40:34 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 817/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.24.0  (landing page)
Beth Signal
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_19
git_last_commit: a5cf135
git_last_commit_date: 2024-04-30 11:04:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for GeneStructureTools on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GeneStructureTools
Version: 1.24.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GeneStructureTools_1.24.0.tar.gz
StartedAt: 2024-05-04 07:47:45 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 07:56:20 -0000 (Sat, 04 May 2024)
EllapsedTime: 514.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GeneStructureTools_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneStructureTools’ version ‘1.24.0’
* 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 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 loading without being on the library search path ... 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 33.738  0.235  34.041
whippetTranscriptChangeSummary    16.834  0.088  16.953
alternativeIntronUsage             5.934  0.015   5.962
replaceJunction                    5.367  0.071   5.446
* 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


Installation output

GeneStructureTools.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)

Tests output


Example timings

GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds0.0040.0000.004
UTR2UTR533.1770.1233.317
addBroadTypes0.2480.0040.252
addIntronInTranscript2.4460.0682.527
alternativeIntronUsage5.9340.0155.962
annotateGeneModel1.1740.0041.180
attrChangeAltSpliced1.6460.0311.677
coordinates-methods0.0880.0100.098
diffSplicingResults-methods0.0840.0190.101
exonsToTranscripts0.4020.0190.422
filterGtfOverlap0.3400.0030.344
filterWhippetEvents0.1020.0080.110
findDEXexonType3.5700.0083.587
findExonContainingTranscripts0.5680.0280.595
findIntronContainingTranscripts0.8910.0310.923
findJunctionPairs1.8380.0331.872
formatWhippetEvents0.0190.0030.022
getOrfs0.9730.0080.983
getUOrfs0.7660.0040.774
junctions-methods0.0720.0300.101
leafcutterTranscriptChangeSummary33.738 0.23534.041
makeGeneModel0.2020.0000.202
maxLocation0.0030.0000.004
orfDiff2.1340.0512.188
orfSimilarity0.0010.0000.001
overlapTypes3.1800.0483.234
readCounts-methods0.0810.0210.103
readWhippetDIFFfiles0.0050.0030.009
readWhippetDataSet0.0870.0140.099
readWhippetJNCfiles0.0430.0080.051
readWhippetPSIfiles0.0240.0070.030
removeDuplicateTranscripts0.3540.0040.359
removeSameExon0.3090.0040.314
removeVersion0.0010.0000.001
reorderExonNumbers0.2180.0000.218
replaceJunction5.3670.0715.446
skipExonInTranscript1.9440.0311.977
summariseExonTypes3.4630.0043.473
transcriptChangeSummary1.9250.0802.007
whippetTranscriptChangeSummary16.834 0.08816.953