Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 61/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
annotate 1.70.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: annotate |
Version: 1.70.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotate_1.70.0.tar.gz |
StartedAt: 2021-10-14 16:15:14 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:18:41 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 207.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotate_1.70.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/annotate.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘annotate/DESCRIPTION’ ... OK * this is package ‘annotate’ version ‘1.70.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed chrCats 15.500 0.103 15.622 blastSequences 0.204 0.016 13.934 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/annotate.Rcheck/00check.log’ for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
annotate.Rcheck/tests/annotate_unit_tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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, 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 -- Thu Oct 14 16:18:33 2021 *********************************************** 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 8.614 0.599 9.199
annotate.Rcheck/annotate-Ex.timings
name | user | system | elapsed | |
ACCNUMStats | 2.147 | 0.034 | 2.183 | |
GO2heatmap | 0.187 | 0.007 | 0.195 | |
GOmnplot | 0.065 | 0.005 | 0.071 | |
HTMLPage-class | 0 | 0 | 0 | |
LL2homology | 0.000 | 0.000 | 0.001 | |
PMIDAmat | 0.099 | 0.003 | 0.104 | |
PWAmat | 2.415 | 0.045 | 2.463 | |
UniGeneQuery | 0.001 | 0.001 | 0.001 | |
accessionToUID | 0.389 | 0.042 | 3.710 | |
annPkgName | 0.001 | 0.001 | 0.001 | |
aqListGOIDs | 0.137 | 0.012 | 0.149 | |
blastSequences | 0.204 | 0.016 | 13.934 | |
buildChromLocation | 0.736 | 0.050 | 0.785 | |
buildPubMedAbst | 0.048 | 0.003 | 0.809 | |
chrCats | 15.500 | 0.103 | 15.622 | |
chromLocation-class | 0.766 | 0.064 | 0.829 | |
compatibleVersions | 0.054 | 0.003 | 0.057 | |
dropECode | 0.059 | 0.003 | 0.062 | |
entrezGeneByID | 0.000 | 0.001 | 0.001 | |
entrezGeneQuery | 0.001 | 0.001 | 0.002 | |
filterGOByOntology | 0.080 | 0.003 | 0.083 | |
findNeighbors | 0.025 | 0.003 | 0.030 | |
genbank | 0.237 | 0.020 | 1.173 | |
getAnnMap | 0.068 | 0.016 | 0.088 | |
getEvidence | 0.074 | 0.003 | 0.077 | |
getGOTerm | 0.245 | 0.010 | 0.261 | |
getOntology | 0.058 | 0.002 | 0.060 | |
getPMInfo | 0.539 | 0.005 | 1.095 | |
getSYMBOL | 0.171 | 0.019 | 0.192 | |
getSeq4Acc | 0.022 | 0.002 | 0.529 | |
hasGOannote | 0.029 | 0.001 | 0.030 | |
hgByChroms | 0.016 | 0.002 | 0.019 | |
hgCLengths | 0.002 | 0.002 | 0.004 | |
hgu95Achroloc | 0.083 | 0.005 | 0.089 | |
hgu95Achrom | 0.058 | 0.004 | 0.062 | |
hgu95All | 0.080 | 0.005 | 0.084 | |
hgu95Asym | 0.075 | 0.005 | 0.080 | |
homoData-class | 0.002 | 0.000 | 0.003 | |
htmlpage | 0.027 | 0.003 | 0.030 | |
isValidkey | 0 | 0 | 0 | |
makeAnchor | 0.001 | 0.000 | 0.001 | |
organism | 1.002 | 0.037 | 1.042 | |
p2LL | 0.000 | 0.001 | 0.001 | |
pm.abstGrep | 1.141 | 0.032 | 2.241 | |
pm.getabst | 1.017 | 0.032 | 2.925 | |
pm.titles | 1.197 | 0.032 | 2.358 | |
pmAbst2HTML | 0.069 | 0.005 | 0.819 | |
pmid2MIAME | 0 | 0 | 0 | |
pmidQuery | 0.001 | 0.000 | 0.001 | |
pubMedAbst-class | 0.055 | 0.003 | 0.587 | |
pubmed | 0.030 | 0.002 | 0.856 | |
readGEOAnn | 0 | 0 | 0 | |
serializeEnv | 0.002 | 0.001 | 0.002 | |
setRepository | 0.001 | 0.001 | 0.001 | |
updateSymbolsToValidKeys | 0 | 0 | 0 | |
usedChromGenes | 0.094 | 0.005 | 0.100 | |