Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:19:57 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for annotate on nebbiolo1


To the developers/maintainers of the annotate package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 56/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.74.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_15
git_last_commit: 200c717
git_last_commit_date: 2022-04-26 10:54:23 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: annotate
Version: 1.74.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings annotate_1.74.0.tar.gz
StartedAt: 2022-10-18 18:32:35 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:35:24 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 168.7 seconds
RetCode: 0
Status:   OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings annotate_1.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/annotate.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.74.0’
* 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 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 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        8.472  0.208   8.680
blastSequences 0.168  0.040  29.025
* 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 in ‘inst/doc’ ... 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

annotate.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, sort, 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 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 -- Tue Oct 18 18:35:19 2022 
*********************************************** 
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 
  6.719   0.427   7.136 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.1380.0231.162
GO2heatmap0.1310.0040.135
GOmnplot0.0560.0000.056
HTMLPage-class0.0010.0000.000
LL2homology0.0010.0000.000
PMIDAmat0.1230.0000.124
PWAmat1.9510.0962.047
UniGeneQuery0.0010.0000.001
accessionToUID0.3780.0312.299
annPkgName0.0000.0020.002
aqListGOIDs0.1220.0290.151
blastSequences 0.168 0.04029.025
buildChromLocation0.6070.0400.647
buildPubMedAbst0.0520.0080.750
chrCats8.4720.2088.680
chromLocation-class0.5750.0600.634
compatibleVersions0.0360.0020.038
dropECode0.040.000.04
entrezGeneByID0.0000.0000.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0480.0040.052
findNeighbors0.0260.0000.030
genbank0.2710.0161.019
getAnnMap0.0470.0120.064
getEvidence0.0640.0000.064
getGOTerm0.1900.0000.193
getOntology0.0340.0000.035
getPMInfo0.3330.0240.699
getSYMBOL0.0980.0240.122
getSeq4Acc0.0160.0040.306
hasGOannote0.0170.0080.025
hgByChroms0.0120.0030.015
hgCLengths0.0000.0010.001
hgu95Achroloc0.0540.0060.060
hgu95Achrom0.0480.0000.048
hgu95All0.0500.0080.058
hgu95Asym0.0550.0040.059
homoData-class0.0030.0000.003
htmlpage0.0180.0000.018
isValidkey0.0010.0000.001
makeAnchor0.0010.0000.001
organism0.6830.0040.687
p2LL000
pm.abstGrep1.1870.1162.242
pm.getabst0.7860.0612.230
pm.titles0.7740.1161.744
pmAbst2HTML0.0550.0040.492
pmid2MIAME0.0010.0000.000
pmidQuery0.0010.0000.001
pubMedAbst-class0.0640.0000.621
pubmed0.0310.0040.405
readGEOAnn0.0000.0000.001
serializeEnv0.0020.0000.002
setRepository0.0010.0000.001
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0970.0040.101