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This page was generated on 2025-07-28 11:47 -0400 (Mon, 28 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 71/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.86.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-07-24 13:40 -0400 (Thu, 24 Jul 2025)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_21
git_last_commit: fc6937c
git_last_commit_date: 2025-06-18 14:09:36 -0400 (Wed, 18 Jun 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.86.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings annotate_1.86.1.tar.gz
StartedAt: 2025-07-25 05:52:02 -0000 (Fri, 25 Jul 2025)
EndedAt: 2025-07-25 05:57:23 -0000 (Fri, 25 Jul 2025)
EllapsedTime: 320.6 seconds
RetCode: 0
Status:   OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings annotate_1.86.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.86.1’
* 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 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 whether 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 ... 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
chrCats        14.869  0.410  15.598
pm.getabst      1.323  0.097  14.319
pm.titles       1.316  0.040   5.302
pm.abstGrep     1.284  0.049   9.998
accessionToUID  0.376  0.040  11.627
genbank         0.215  0.035  24.618
blastSequences  0.129  0.016  37.826
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/annotate.Rcheck/00check.log’
for details.


Installation output

annotate.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘annotate’ ...
** this is package ‘annotate’ version ‘1.86.1’
** 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

annotate.Rcheck/tests/annotate_unit_tests.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("annotate")

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Fri Jul 25 05:57:15 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
annotate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 12.282   0.490  13.641 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.7560.0361.863
GO2heatmap0.1710.0080.322
GOmnplot0.0530.0040.063
HTMLPage-class000
LL2homology000
PMIDAmat0.1330.0000.219
PWAmat2.0630.0442.133
UniGeneQuery0.0020.0000.002
accessionToUID 0.376 0.04011.627
annPkgName0.0010.0000.001
aqListGOIDs0.1660.0090.206
blastSequences 0.129 0.01637.826
buildChromLocation0.8710.0640.958
buildPubMedAbst0.050.001.78
chrCats14.869 0.41015.598
chromLocation-class0.8360.0350.873
compatibleVersions0.0360.0080.044
dropECode0.0500.0020.052
entrezGeneByID0.0010.0000.001
entrezGeneQuery0.0010.0000.000
filterGOByOntology0.0650.0040.069
findNeighbors0.0220.0040.035
genbank 0.215 0.03524.618
getAnnMap0.0290.0040.035
getEvidence0.0710.0000.076
getGOTerm0.2400.0080.424
getOntology0.0520.0010.105
getPMInfo0.4740.0232.140
getSYMBOL0.1170.0280.204
getSeq4Acc0.0110.0123.685
hasGOannote0.0310.0000.063
hgByChroms0.0150.0000.031
hgCLengths0.0010.0000.001
hgu95Achroloc0.0630.0010.129
hgu95Achrom0.0540.0000.107
hgu95All0.0570.0000.057
hgu95Asym0.0550.0040.060
homoData-class0.0030.0000.003
htmlpage0.0190.0040.022
isValidkey000
makeAnchor0.0010.0000.000
organism0.8310.0200.852
p2LL000
pm.abstGrep1.2840.0499.998
pm.getabst 1.323 0.09714.319
pm.titles1.3160.0405.302
pmAbst2HTML0.1760.0041.456
pmid2MIAME000
pmidQuery000
pubMedAbst-class0.0420.0041.306
pubmed0.0300.0002.568
readGEOAnn000
serializeEnv0.0020.0000.006
setRepository0.0010.0000.001
updateSymbolsToValidKeys000
usedChromGenes0.0790.0000.160