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This page was generated on 2024-03-28 11:40:45 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 809/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.23.0  (landing page)
Beth Signal
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: devel
git_last_commit: def278e
git_last_commit_date: 2023-10-24 11:03:19 -0400 (Tue, 24 Oct 2023)
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  

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: 1.23.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings GeneStructureTools_1.23.0.tar.gz
StartedAt: 2024-03-28 05:36:52 -0000 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 05:46:32 -0000 (Thu, 28 Mar 2024)
EllapsedTime: 580.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings GeneStructureTools_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneStructureTools.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* 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 ‘1.23.0’
* 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 34.200  0.119  34.390
whippetTranscriptChangeSummary    20.459  0.211  20.715
alternativeIntronUsage             8.483  0.016   8.519
replaceJunction                    7.467  0.065   7.545
findDEXexonType                    6.240  0.040   6.296
summariseExonTypes                 5.947  0.004   5.961
UTR2UTR53                          5.611  0.232   5.864
overlapTypes                       5.556  0.020   5.585
addIntronInTranscript              5.012  0.093   5.123
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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
DEXSeqIdsToGeneIds0.0000.0030.004
UTR2UTR535.6110.2325.864
addBroadTypes2.6880.0242.717
addIntronInTranscript5.0120.0935.123
alternativeIntronUsage8.4830.0168.519
annotateGeneModel3.6140.0083.629
attrChangeAltSpliced4.1860.0444.237
coordinates-methods0.0900.0230.111
diffSplicingResults-methods0.0830.0260.108
exonsToTranscripts4.0120.0764.096
filterGtfOverlap2.7610.0282.795
filterWhippetEvents0.0950.0210.114
findDEXexonType6.2400.0406.296
findExonContainingTranscripts3.0050.0403.051
findIntronContainingTranscripts3.3530.0613.421
findJunctionPairs4.3430.0444.394
formatWhippetEvents0.0230.0000.023
getOrfs3.4610.0203.488
getUOrfs3.1660.0083.181
junctions-methods0.0850.0230.109
leafcutterTranscriptChangeSummary34.200 0.11934.390
makeGeneModel2.6030.0122.619
maxLocation0.0040.0000.003
orfDiff4.4350.0784.520
orfSimilarity0.0010.0000.001
overlapTypes5.5560.0205.585
readCounts-methods0.0760.0200.095
readWhippetDIFFfiles0.0070.0020.009
readWhippetDataSet0.0770.0220.098
readWhippetJNCfiles0.0410.0080.048
readWhippetPSIfiles0.0180.0110.028
removeDuplicateTranscripts2.7470.0162.768
removeSameExon2.6880.0042.698
removeVersion0.0000.0000.001
reorderExonNumbers2.6210.0002.626
replaceJunction7.4670.0657.545
skipExonInTranscript4.2190.0214.245
summariseExonTypes5.9470.0045.961
transcriptChangeSummary4.3310.0184.356
whippetTranscriptChangeSummary20.459 0.21120.715