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This page was generated on 2025-07-19 12:11 -0400 (Sat, 19 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4791
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4529
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4572
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4513
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4510
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 70/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.87.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-07-18 13:25 -0400 (Fri, 18 Jul 2025)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: devel
git_last_commit: 22204b6
git_last_commit_date: 2025-06-18 13:57:32 -0400 (Wed, 18 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for annotate on taishan

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: 1.87.0
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_1.87.0.tar.gz
StartedAt: 2025-07-18 04:18:58 -0000 (Fri, 18 Jul 2025)
EndedAt: 2025-07-18 04:23:26 -0000 (Fri, 18 Jul 2025)
EllapsedTime: 267.3 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_1.87.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/annotate.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.87.0’
* 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 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        14.795  0.634  15.499
pm.titles       1.697  0.185   7.230
pm.abstGrep     1.353  0.299   5.757
pm.getabst      1.290  0.330  10.107
accessionToUID  0.376  0.032   9.694
genbank         0.196  0.007   5.441
blastSequences  0.144  0.026  41.286
* 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-3.22-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-4.5.0/site-library’
* installing *source* package ‘annotate’ ...
** this is package ‘annotate’ version ‘1.87.0’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 18 04:23:20 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 
 10.561   0.437  11.015 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.7190.0361.758
GO2heatmap0.1490.0040.153
GOmnplot0.050.000.05
HTMLPage-class0.0000.0000.001
LL2homology000
PMIDAmat0.1110.0000.125
PWAmat2.1110.0392.156
UniGeneQuery0.0020.0000.002
accessionToUID0.3760.0329.694
annPkgName0.0010.0000.001
aqListGOIDs0.1580.0360.194
blastSequences 0.144 0.02641.286
buildChromLocation0.8920.1971.104
buildPubMedAbst0.0420.0161.414
chrCats14.795 0.63415.499
chromLocation-class0.7890.0500.841
compatibleVersions0.0380.0000.039
dropECode0.0510.0000.051
entrezGeneByID0.0010.0000.000
entrezGeneQuery0.0000.0000.001
filterGOByOntology0.0480.0120.061
findNeighbors0.0110.0120.030
genbank0.1960.0075.441
getAnnMap0.0270.0010.027
getEvidence0.0570.0030.061
getGOTerm0.2580.0120.272
getOntology0.0520.0000.051
getPMInfo0.4500.1312.051
getSYMBOL0.1460.0360.191
getSeq4Acc0.0210.0001.219
hasGOannote0.0260.0040.030
hgByChroms0.0170.0000.017
hgCLengths0.0010.0000.001
hgu95Achroloc0.0660.0000.066
hgu95Achrom0.0510.0000.051
hgu95All0.0570.0000.057
hgu95Asym0.0560.0020.059
homoData-class0.0030.0000.003
htmlpage0.0190.0080.028
isValidkey0.0010.0000.001
makeAnchor0.0010.0000.001
organism0.8750.0360.913
pm.abstGrep1.3530.2995.757
pm.getabst 1.290 0.33010.107
pm.titles1.6970.1857.230
pmAbst2HTML0.0620.0011.395
pmid2MIAME000
pmidQuery0.0000.0010.001
pubMedAbst-class0.0450.0031.398
pubmed0.0270.0041.833
readGEOAnn0.0010.0000.000
serializeEnv0.0020.0000.002
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.0700.0160.086