Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:30:58 -0400 (Thu, 12 Apr 2018).
Package 49/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
annotate 1.56.2 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: annotate |
Version: 1.56.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz |
StartedAt: 2018-04-12 00:22:08 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:24:44 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 156.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/annotate.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.56.2’ * 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 12.699 0.071 12.902 blastSequences 0.227 0.011 20.343 * 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/tests/annotate_unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, 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:base': expand.grid Loading required package: org.Hs.eg.db 'select()' returned 1:many mapping between keys and columns RUNIT TEST PROTOCOL -- Thu Apr 12 00:24:39 2018 *********************************************** 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 5.347 0.249 5.653
annotate.Rcheck/annotate-Ex.timings
name | user | system | elapsed | |
ACCNUMStats | 2.491 | 0.037 | 2.586 | |
GO2heatmap | 0.221 | 0.007 | 0.228 | |
GOmnplot | 0.078 | 0.006 | 0.085 | |
HTMLPage-class | 0.001 | 0.001 | 0.001 | |
LL2homology | 0.000 | 0.000 | 0.001 | |
PMIDAmat | 0.118 | 0.004 | 0.127 | |
PWAmat | 2.097 | 0.041 | 2.159 | |
UniGeneQuery | 0.003 | 0.000 | 0.003 | |
accessionToUID | 0.759 | 0.036 | 2.136 | |
annPkgName | 0.001 | 0.000 | 0.001 | |
aqListGOIDs | 0.347 | 0.022 | 0.381 | |
blastSequences | 0.227 | 0.011 | 20.343 | |
buildChromLocation | 0.639 | 0.029 | 0.675 | |
buildPubMedAbst | 0.089 | 0.002 | 0.403 | |
chrCats | 12.699 | 0.071 | 12.902 | |
chromLocation-class | 0.458 | 0.017 | 0.478 | |
compatibleVersions | 0.040 | 0.001 | 0.042 | |
dropECode | 0.047 | 0.001 | 0.048 | |
entrezGeneByID | 0.001 | 0.000 | 0.001 | |
entrezGeneQuery | 0.001 | 0.000 | 0.001 | |
filterGOByOntology | 0.084 | 0.005 | 0.089 | |
findNeighbors | 0.017 | 0.002 | 0.021 | |
genbank | 0.125 | 0.013 | 1.220 | |
getAnnMap | 0.034 | 0.009 | 0.057 | |
getEvidence | 0.096 | 0.004 | 0.101 | |
getGOTerm | 0.258 | 0.011 | 0.277 | |
getOntology | 0.031 | 0.002 | 0.035 | |
getPMInfo | 0.417 | 0.004 | 1.044 | |
getSYMBOL | 0.120 | 0.008 | 0.130 | |
getSeq4Acc | 0.007 | 0.001 | 0.269 | |
hasGOannote | 0.021 | 0.001 | 0.021 | |
hgByChroms | 0.011 | 0.001 | 0.012 | |
hgCLengths | 0.001 | 0.000 | 0.002 | |
hgu95Achroloc | 0.047 | 0.003 | 0.050 | |
hgu95Achrom | 0.040 | 0.004 | 0.045 | |
hgu95All | 0.046 | 0.004 | 0.049 | |
hgu95Asym | 0.044 | 0.003 | 0.048 | |
homoData-class | 0.002 | 0.000 | 0.002 | |
htmlpage | 0.415 | 0.003 | 0.424 | |
isValidkey | 0.001 | 0.000 | 0.001 | |
makeAnchor | 0.001 | 0.000 | 0.001 | |
organism | 0.418 | 0.015 | 0.435 | |
p2LL | 0.000 | 0.000 | 0.001 | |
pm.abstGrep | 0.781 | 0.035 | 1.813 | |
pm.getabst | 0.932 | 0.023 | 1.961 | |
pm.titles | 0.967 | 0.031 | 1.880 | |
pmAbst2HTML | 0.081 | 0.002 | 0.414 | |
pmid2MIAME | 0.000 | 0.001 | 0.001 | |
pmidQuery | 0.001 | 0.000 | 0.002 | |
pubMedAbst-class | 0.032 | 0.002 | 0.350 | |
pubmed | 0.016 | 0.002 | 1.370 | |
readGEOAnn | 0.001 | 0.000 | 0.000 | |
serializeEnv | 0.002 | 0.000 | 0.002 | |
setRepository | 0.003 | 0.001 | 0.003 | |
updateSymbolsToValidKeys | 0 | 0 | 0 | |
usedChromGenes | 0.067 | 0.005 | 0.072 | |