Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 54/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
annotate 1.77.0 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: annotate |
Version: 1.77.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings annotate_1.77.0.tar.gz |
StartedAt: 2023-02-27 20:17:41 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 20:24:35 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 413.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings annotate_1.77.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/annotate.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘annotate/DESCRIPTION’ ... OK * this is package ‘annotate’ version ‘1.77.0’ * 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 ... NOTE Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator. * 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 ... NOTE checkRd: (-1) chrCats.Rd:13: Escaped LaTeX specials: \_ checkRd: (-1) chrCats.Rd:14: Escaped LaTeX specials: \_ checkRd: (-1) chrCats.Rd:47: Escaped LaTeX specials: \_ checkRd: (-1) chrCats.Rd:53: Escaped LaTeX specials: \_ checkRd: (-1) chrCats.Rd:60: Escaped LaTeX specials: \_ checkRd: (-1) chrCats.Rd:69: Escaped LaTeX specials: \_ \_ checkRd: (-1) chrCats.Rd:77: Escaped LaTeX specials: \_ checkRd: (-1) htmlpage.Rd:56: Escaped LaTeX specials: \_ checkRd: (-1) htmlpage.Rd:57: Escaped LaTeX specials: \_ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed chrCats 14.008 0.404 14.414 accessionToUID 0.675 0.037 9.758 blastSequences 0.324 0.040 29.938 * 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 ... ‘GOusage.Rnw’... OK ‘annotate.Rnw’... OK ‘chromLoc.Rnw’... OK ‘prettyOutput.Rnw’... OK ‘query.Rnw’... OK ‘useDataPkgs.Rnw’... OK ‘useProbeInfo.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/annotate.Rcheck/00check.log’ for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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 -- Mon Feb 27 20:21:21 2023 *********************************************** 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 9.412 0.464 9.862
annotate.Rcheck/annotate-Ex.timings
name | user | system | elapsed | |
ACCNUMStats | 1.547 | 0.016 | 1.564 | |
GO2heatmap | 0.150 | 0.009 | 0.160 | |
GOmnplot | 0.041 | 0.008 | 0.050 | |
HTMLPage-class | 0 | 0 | 0 | |
LL2homology | 0.000 | 0.000 | 0.001 | |
PMIDAmat | 0.101 | 0.003 | 0.108 | |
PWAmat | 2.234 | 0.079 | 2.315 | |
UniGeneQuery | 0.001 | 0.000 | 0.001 | |
accessionToUID | 0.675 | 0.037 | 9.758 | |
annPkgName | 0.000 | 0.000 | 0.001 | |
aqListGOIDs | 0.157 | 0.012 | 0.168 | |
blastSequences | 0.324 | 0.040 | 29.938 | |
buildChromLocation | 0.863 | 0.024 | 0.887 | |
buildPubMedAbst | 0.186 | 0.004 | 1.768 | |
chrCats | 14.008 | 0.404 | 14.414 | |
chromLocation-class | 0.854 | 0.008 | 0.861 | |
compatibleVersions | 0.033 | 0.008 | 0.042 | |
dropECode | 0.047 | 0.000 | 0.048 | |
entrezGeneByID | 0.001 | 0.000 | 0.000 | |
entrezGeneQuery | 0.001 | 0.000 | 0.001 | |
filterGOByOntology | 0.058 | 0.008 | 0.065 | |
findNeighbors | 0.023 | 0.000 | 0.030 | |
genbank | 0.362 | 0.016 | 2.942 | |
getAnnMap | 0.040 | 0.016 | 0.077 | |
getEvidence | 0.066 | 0.004 | 0.071 | |
getGOTerm | 0.271 | 0.008 | 0.284 | |
getOntology | 0.043 | 0.004 | 0.047 | |
getPMInfo | 0.581 | 0.024 | 2.375 | |
getSYMBOL | 0.119 | 0.016 | 0.138 | |
getSeq4Acc | 0.134 | 0.024 | 1.619 | |
hasGOannote | 0.025 | 0.003 | 0.028 | |
hgByChroms | 0.017 | 0.000 | 0.016 | |
hgCLengths | 0.001 | 0.000 | 0.002 | |
hgu95Achroloc | 0.061 | 0.004 | 0.065 | |
hgu95Achrom | 0.050 | 0.004 | 0.053 | |
hgu95All | 0.123 | 0.024 | 0.146 | |
hgu95Asym | 0.059 | 0.000 | 0.060 | |
homoData-class | 0.003 | 0.000 | 0.003 | |
htmlpage | 0.024 | 0.000 | 0.024 | |
isValidkey | 0.001 | 0.000 | 0.000 | |
makeAnchor | 0.001 | 0.000 | 0.000 | |
organism | 1.260 | 0.092 | 1.352 | |
p2LL | 0 | 0 | 0 | |
pm.abstGrep | 1.167 | 0.068 | 4.405 | |
pm.getabst | 1.174 | 0.028 | 4.514 | |
pm.titles | 1.179 | 0.063 | 4.650 | |
pmAbst2HTML | 0.183 | 0.000 | 1.662 | |
pmid2MIAME | 0 | 0 | 0 | |
pmidQuery | 0.000 | 0.000 | 0.001 | |
pubMedAbst-class | 0.169 | 0.000 | 1.696 | |
pubmed | 0.154 | 0.000 | 2.005 | |
readGEOAnn | 0 | 0 | 0 | |
serializeEnv | 0.002 | 0.000 | 0.001 | |
setRepository | 0.001 | 0.001 | 0.001 | |
updateSymbolsToValidKeys | 0 | 0 | 0 | |
usedChromGenes | 0.070 | 0.006 | 0.077 | |