Back to Multiple platform build/check report for BioC 3.19:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:40:15 -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 69/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.82.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_19
git_last_commit: 9710d81
git_last_commit_date: 2024-04-30 10:10:49 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.82.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings annotate_1.82.0.tar.gz
StartedAt: 2024-05-04 04:48:35 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 04:58:03 -0000 (Sat, 04 May 2024)
EllapsedTime: 568.1 seconds
RetCode: 0
Status:   OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings annotate_1.82.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/annotate.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 ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.82.0’
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
blastSequences 158.102  1.298 244.829
chrCats         14.726  0.239  14.999
pm.getabst       1.758  0.083   5.104
pm.titles        1.202  0.104  10.041
pm.abstGrep      1.198  0.036  26.050
accessionToUID   0.790  0.344  15.327
genbank          0.220  0.008   6.537
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/annotate.Rcheck/00check.log’
for details.


Installation output

annotate.Rcheck/00install.out

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


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

annotate.Rcheck/tests/annotate_unit_tests.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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: '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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 -- Sat May  4 04:57:59 2024 
*********************************************** 
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 
 12.092   0.539  12.644 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.7640.0321.800
GO2heatmap0.1620.0000.164
GOmnplot0.0560.0000.055
HTMLPage-class000
LL2homology000
PMIDAmat0.1140.0040.124
PWAmat2.4520.0642.521
UniGeneQuery0.0020.0000.002
accessionToUID 0.790 0.34415.327
annPkgName000
aqListGOIDs0.1540.0320.186
blastSequences158.102 1.298244.829
buildChromLocation0.8200.0640.886
buildPubMedAbst0.0500.0161.567
chrCats14.726 0.23914.999
chromLocation-class0.8830.0100.894
compatibleVersions0.0420.0000.043
dropECode0.0520.0040.057
entrezGeneByID0.0010.0000.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0540.0040.058
findNeighbors0.0220.0040.035
genbank0.2200.0086.537
getAnnMap0.0360.0040.041
getEvidence0.0740.0000.075
getGOTerm0.2700.0120.289
getOntology0.0570.0040.061
getPMInfo0.5330.0242.372
getSYMBOL0.1500.0040.159
getSeq4Acc0.0150.0001.351
hasGOannote0.0280.0030.031
hgByChroms0.0150.0000.015
hgCLengths0.0010.0000.001
hgu95Achroloc0.0670.0000.066
hgu95Achrom0.0550.0080.063
hgu95All0.0600.0040.064
hgu95Asym0.0590.0040.064
homoData-class0.0000.0030.003
htmlpage0.0180.0080.026
isValidkey000
makeAnchor0.0000.0000.001
organism1.0090.0281.040
p2LL000
pm.abstGrep 1.198 0.03626.050
pm.getabst1.7580.0835.104
pm.titles 1.202 0.10410.041
pmAbst2HTML0.0530.0362.256
pmid2MIAME000
pmidQuery0.0010.0000.001
pubMedAbst-class0.0430.0082.557
pubmed0.0250.0041.823
readGEOAnn0.0000.0000.001
serializeEnv0.0020.0000.003
setRepository0.0010.0000.001
updateSymbolsToValidKeys0.0000.0010.000
usedChromGenes0.0730.0230.096