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BioC 3.5: CHECK report for annotate on veracruz2

This page was generated on 2017-10-18 14:27:15 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz
StartedAt: 2017-10-18 00:24:46 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:27:29 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 163.3 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/annotate.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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        16.266  0.093  16.922
blastSequences  0.246  0.011  23.625
* 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
ACCNUMStats2.5620.0492.685
GO2heatmap0.2470.0090.261
GOmnplot0.0930.0070.107
HTMLPage-class0.0010.0000.001
LL2homology0.0010.0010.001
PMIDAmat0.1250.0030.142
PWAmat2.3810.0422.503
UniGeneQuery0.0020.0000.003
accessionToUID0.7090.0322.040
annPkgName0.0010.0000.002
aqListGOIDs0.3500.0200.373
blastSequences 0.246 0.01123.625
buildChromLocation0.6860.0220.720
buildPubMedAbst0.1050.0020.467
chrCats16.266 0.09316.922
chromLocation-class0.5270.0250.578
compatibleVersions0.0440.0020.046
dropECode0.0500.0010.051
entrezGeneByID0.0010.0000.002
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0920.0030.098
findNeighbors0.0200.0020.025
genbank0.1210.0130.594
getAnnMap0.0390.0100.052
getEvidence0.1350.0030.142
getGOTerm0.2540.0070.278
getOntology0.0840.0050.095
getPMInfo0.6130.0060.986
getSYMBOL0.1400.0110.163
getSeq4Acc0.0070.0010.257
hasGOannote0.0210.0010.023
hgByChroms0.0150.0050.019
hgCLengths0.0020.0010.003
hgu95Achroloc0.0520.0080.062
hgu95Achrom0.0460.0090.057
hgu95All0.0500.0070.059
hgu95Asym0.0590.0100.071
homoData-class0.0030.0000.004
htmlpage0.4320.0050.446
isValidkey0.0000.0000.001
makeAnchor0.0010.0000.000
organism0.4600.0080.477
p2LL000
pm.abstGrep0.6730.0221.556
pm.getabst0.9220.0201.934
pm.titles0.7610.0201.644
pmAbst2HTML0.1050.0030.479
pmid2MIAME0.0010.0000.001
pmidQuery0.0010.0000.002
pubMedAbst-class0.0320.0010.382
pubmed0.0190.0010.364
readGEOAnn0.0000.0000.001
serializeEnv0.0020.0000.003
setRepository0.0040.0010.004
updateSymbolsToValidKeys0.0010.0000.001
usedChromGenes0.0630.0060.069