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Package 25/444 | Hostname | OS / Arch | BUILD | CHECK | BUILD BIN | ||||
annotate 1.29.3 Biocore Team c/o BioC user list
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |||||
liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK | |||||
gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK | |||||
pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK | |||||
petty | Mac OS X Snow Leopard (10.6.6) / i386 | OK | [ OK ] | OK |
Package: annotate |
Version: 1.29.3 |
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.29.3.tar.gz |
StartedAt: 2011-03-17 15:29:40 -0700 (Thu, 17 Mar 2011) |
EndedAt: 2011-03-17 15:33:47 -0700 (Thu, 17 Mar 2011) |
EllapsedTime: 247.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/annotate.Rcheck' * using R version 2.13.0 Under development (unstable) (2011-03-06 r54683) * using platform: i386-apple-darwin9.8.0 (32-bit) * using session charset: ASCII * using option '--no-vignettes' * checking for file 'annotate/DESCRIPTION' ... OK * this is package 'annotate' version '1.29.3' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'annotate' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level 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 name space can be loaded with stated dependencies ... OK * checking whether the name space can be unloaded cleanly ... OK * checking for unstated 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 ... NOTE 'library' or 'require' calls not declared from: hsahomology humanCHRLOC * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... SKIPPED * checking PDF version of manual ... OK
annotate.Rcheck/00install.out:
* installing *source* package 'annotate' ... ** R ** data ** inst ** preparing package for lazy loading Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (annotate)
annotate.Rcheck/annotate-Ex.timings:
name | user | system | elapsed | |
ACCNUMStats | 2.842 | 0.024 | 2.867 | |
GO2heatmap | 0.288 | 0.012 | 0.299 | |
GOmnplot | 0.191 | 0.004 | 0.196 | |
HTMLPage-class | 0.001 | 0.000 | 0.001 | |
LL2homology | 0.002 | 0.001 | 0.003 | |
PMIDAmat | 0.279 | 0.006 | 0.340 | |
PWAmat | 4.041 | 0.083 | 4.123 | |
UniGeneQuery | 0.002 | 0.000 | 0.002 | |
accessionToUID | 0.438 | 0.025 | 7.819 | |
annPkgName | 0.001 | 0.000 | 0.000 | |
aqListGOIDs | 0.623 | 0.047 | 0.671 | |
blastSequences | 3.943 | 0.029 | 83.921 | |
buildChromLocation | 1.876 | 0.051 | 1.926 | |
buildPubMedAbst | 0.108 | 0.004 | 1.033 | |
chrCats | 5.562 | 0.051 | 5.830 | |
chromLocation-class | 1.487 | 0.016 | 1.502 | |
compatibleVersions | 0.099 | 0.004 | 0.105 | |
dropECode | 0.085 | 0.003 | 0.088 | |
entrezGeneByID | 0.000 | 0.001 | 0.001 | |
entrezGeneQuery | 0 | 0 | 0 | |
filterGOByOntology | 0.170 | 0.003 | 0.173 | |
findNeighbors | 0.018 | 0.001 | 0.018 | |
genbank | 0.089 | 0.005 | 1.130 | |
genelocator | 0 | 0 | 0 | |
getAnnMap | 0.145 | 0.019 | 0.437 | |
getEvidence | 0.089 | 0.004 | 0.092 | |
getGOTerm | 0.127 | 0.004 | 0.162 | |
getOntology | 0.087 | 0.005 | 0.092 | |
getPMInfo | 1.200 | 0.015 | 3.799 | |
getSYMBOL | 0.187 | 0.011 | 1.367 | |
getSeq4Acc | 0.000 | 0.001 | 0.185 | |
hasGOannote | 0.055 | 0.003 | 0.058 | |
hgByChroms | 0.012 | 0.001 | 0.012 | |
hgCLengths | 0.003 | 0.000 | 0.003 | |
hgu95Achroloc | 0.076 | 0.001 | 0.078 | |
hgu95Achrom | 0.069 | 0.001 | 0.070 | |
hgu95All | 0.066 | 0.003 | 0.069 | |
hgu95Asym | 0.072 | 0.001 | 0.073 | |
homoData-class | 0.002 | 0.001 | 0.003 | |
htmlpage | 0.048 | 0.002 | 0.053 | |
isValidkey | 0.000 | 0.000 | 0.001 | |
makeAnchor | 0 | 0 | 0 | |
neighborGeneFinder | 0.000 | 0.000 | 0.001 | |
organism | 1.522 | 0.022 | 1.544 | |
p2LL | 0 | 0 | 0 | |
pm.abstGrep | 15.005 | 0.078 | 17.677 | |
pm.getabst | 15.125 | 0.167 | 19.330 | |
pm.titles | 13.544 | 0.174 | 16.530 | |
pmAbst2HTML | 0.212 | 0.011 | 0.849 | |
pmid2MIAME | 0.001 | 0.000 | 0.000 | |
pmidQuery | 0.001 | 0.000 | 0.000 | |
probesByLL | 2.070 | 0.006 | 2.076 | |
pubMedAbst-class | 0.112 | 0.002 | 0.741 | |
pubmed | 0.055 | 0.002 | 0.780 | |
readGEOAnn | 0 | 0 | 0 | |
serializeEnv | 0.002 | 0.000 | 0.002 | |
setRepository | 0.001 | 0.000 | 0.002 | |
updateSymbolsToValidKeys | 0.000 | 0.000 | 0.001 | |
usedChromGenes | 0.095 | 0.001 | 0.096 | |