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BioC 3.5: CHECK report for annotate on malbec2

This page was generated on 2017-10-18 14:12:13 -0400 (Wed, 18 Oct 2017).

Package 47/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.54.0
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/annotate
Branch: RELEASE_3_5
Last Commit: 860cc5b
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotate
Version: 1.54.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz
StartedAt: 2017-10-17 21:09:48 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:12:25 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 156.9 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/annotate.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.54.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        14.688  0.008  14.803
blastSequences  0.944  0.092  25.825
* 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

annotate.Rcheck/00install.out:

* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotate)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats1.8160.0161.831
GO2heatmap0.200.000.21
GOmnplot0.0640.0040.067
HTMLPage-class000
LL2homology0.0040.0000.000
PMIDAmat0.1000.0000.206
PWAmat2.2080.0082.221
UniGeneQuery0.0040.0000.003
accessionToUID1.3600.0523.104
annPkgName0.0000.0000.002
aqListGOIDs0.3800.0080.389
blastSequences 0.944 0.09225.825
buildChromLocation0.7480.0000.747
buildPubMedAbst0.1720.0040.731
chrCats14.688 0.00814.803
chromLocation-class0.4520.0040.455
compatibleVersions0.0360.0000.035
dropECode0.0360.0040.038
entrezGeneByID0.0000.0000.001
entrezGeneQuery000
filterGOByOntology0.0760.0000.076
findNeighbors0.0240.0000.067
genbank0.1840.0080.612
getAnnMap0.0360.0080.943
getEvidence0.0880.0080.098
getGOTerm0.3360.0000.679
getOntology0.0600.0000.063
getPMInfo0.8760.0121.303
getSYMBOL0.2160.0040.331
getSeq4Acc0.1000.0000.419
hasGOannote0.0400.0000.038
hgByChroms0.0120.0200.036
hgCLengths0.0040.0000.001
hgu95Achroloc0.0760.0200.095
hgu95Achrom0.0880.0160.104
hgu95All0.0600.0160.075
hgu95Asym0.060.020.08
homoData-class0.0040.0000.003
htmlpage0.4880.0000.488
isValidkey0.0040.0000.001
makeAnchor0.0000.0000.001
organism0.5920.0000.590
p2LL000
pm.abstGrep0.9040.0081.758
pm.getabst1.1600.0082.131
pm.titles0.8120.0042.487
pmAbst2HTML0.3840.0000.781
pmid2MIAME000
pmidQuery0.0000.0000.001
pubMedAbst-class0.1040.0120.640
pubmed0.0720.0080.485
readGEOAnn000
serializeEnv0.0040.0000.002
setRepository0.0000.0000.001
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0640.0240.090