Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:24 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 68/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.80.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_18
git_last_commit: 45a42c3
git_last_commit_date: 2023-10-24 09:31:23 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for annotate on kunpeng2


To the developers/maintainers of the annotate package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotate.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: annotate
Version: 1.80.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings annotate_1.80.0.tar.gz
StartedAt: 2023-11-02 08:19:09 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:26:31 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 441.9 seconds
RetCode: 137
Status:   ERROR  
CheckDir: annotate.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings annotate_1.80.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/annotate.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.80.0’
* 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 ‘annotate’ 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
checkRd: (-1) chrCats.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:14: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:53: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:60: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:69: Escaped LaTeX specials: \_ \_
checkRd: (-1) chrCats.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) htmlpage.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) htmlpage.Rd:57: Escaped LaTeX specials: \_
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples .../home/biocbuild/R/R-4.3.1/bin/check: line 10: 325140 Done                    echo 'tools:::.check_packages()'
     325141 Killed                  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --no-echo --args ${args}

Installation output

annotate.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘annotate’ ...
** using staged installation
** R
** data
** 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 (annotate)

Tests output


Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats2.1300.0322.167
GO2heatmap0.1300.0240.155
GOmnplot0.0430.0080.051
HTMLPage-class000
LL2homology000
PMIDAmat0.1020.0080.119
PWAmat1.9970.0802.081
UniGeneQuery0.0010.0000.001
accessionToUID 0.378 0.08710.780
annPkgName0.0010.0000.001
aqListGOIDs0.1460.0520.212
blastSequences158.604 9.214219.681
buildChromLocation1.3180.0681.466
buildPubMedAbst0.0420.0031.593
chrCats14.538 0.12414.721
chromLocation-class0.8410.0190.954
compatibleVersions0.0500.0050.058
dropECode0.0480.0040.058
entrezGeneByID0.0010.0000.000
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0520.0110.084
findNeighbors0.0240.0000.033
genbank0.2450.0203.262
getAnnMap0.0250.0080.034
getEvidence0.0730.0000.074
getGOTerm0.2370.1020.505
getOntology0.0420.0160.074
getPMInfo0.4790.4974.120
getSYMBOL0.1380.0240.196
getSeq4Acc0.0170.0001.515
hasGOannote0.0300.0000.031
hgByChroms0.0040.0120.017
hgCLengths0.0010.0000.002
hgu95Achroloc0.0590.0040.065
hgu95Achrom0.0540.0000.055
hgu95All0.0890.0040.095
hgu95Asym0.0560.0040.061
homoData-class0.0000.0030.003
htmlpage0.0230.0000.026
isValidkey0.0000.0000.001
makeAnchor0.0010.0000.001
organism0.9570.0201.049
p2LL000
pm.abstGrep1.2090.2414.364
pm.getabst1.2410.0324.243
pm.titles1.6760.1044.755
pmAbst2HTML0.0700.0071.589
pmid2MIAME0.0010.0000.000
pmidQuery0.0010.0000.000
pubMedAbst-class0.0410.0001.606
pubmed0.0180.0081.853
readGEOAnn000
serializeEnv0.0000.0010.002
setRepository0.0000.0010.001
updateSymbolsToValidKeys000
usedChromGenes0.0780.0020.081