Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 70/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
annotate 1.84.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the annotate package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: annotate |
Version: 1.84.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotate_1.84.0.tar.gz |
StartedAt: 2024-12-19 23:40:59 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:46:56 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 356.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotate_1.84.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/annotate.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘annotate/DESCRIPTION’ ... OK * this is package ‘annotate’ version ‘1.84.0’ * 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 code 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 whether startup messages can be suppressed ... 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 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 25.822 0.176 26.691 accessionToUID 0.566 0.050 6.185 blastSequences 0.228 0.021 31.690 * 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/annotate.Rcheck/00check.log’ for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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, saveRDS, setdiff, 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 object is masked from 'package:utils': findMatches 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 Dec 19 23:46:38 2024 *********************************************** 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 18.095 1.521 21.051
annotate.Rcheck/annotate-Ex.timings
name | user | system | elapsed | |
ACCNUMStats | 3.672 | 0.091 | 3.799 | |
GO2heatmap | 0.258 | 0.013 | 0.273 | |
GOmnplot | 0.085 | 0.009 | 0.096 | |
HTMLPage-class | 0.000 | 0.000 | 0.001 | |
LL2homology | 0.000 | 0.001 | 0.001 | |
PMIDAmat | 0.186 | 0.006 | 0.196 | |
PWAmat | 3.154 | 0.065 | 3.257 | |
UniGeneQuery | 0.003 | 0.001 | 0.003 | |
accessionToUID | 0.566 | 0.050 | 6.185 | |
annPkgName | 0.000 | 0.000 | 0.001 | |
aqListGOIDs | 0.241 | 0.025 | 0.270 | |
blastSequences | 0.228 | 0.021 | 31.690 | |
buildChromLocation | 1.708 | 0.081 | 1.913 | |
buildPubMedAbst | 0.068 | 0.004 | 0.544 | |
chrCats | 25.822 | 0.176 | 26.691 | |
chromLocation-class | 1.534 | 0.100 | 1.666 | |
compatibleVersions | 0.067 | 0.005 | 0.071 | |
dropECode | 0.082 | 0.004 | 0.087 | |
entrezGeneByID | 0.001 | 0.000 | 0.002 | |
entrezGeneQuery | 0.002 | 0.001 | 0.002 | |
filterGOByOntology | 0.089 | 0.004 | 0.095 | |
findNeighbors | 0.035 | 0.006 | 0.044 | |
genbank | 0.340 | 0.021 | 0.835 | |
getAnnMap | 0.064 | 0.015 | 0.085 | |
getEvidence | 0.104 | 0.004 | 0.109 | |
getGOTerm | 0.396 | 0.011 | 0.420 | |
getOntology | 0.067 | 0.004 | 0.070 | |
getPMInfo | 0.783 | 0.008 | 1.337 | |
getSYMBOL | 0.209 | 0.037 | 0.249 | |
getSeq4Acc | 0.021 | 0.003 | 0.274 | |
hasGOannote | 0.039 | 0.002 | 0.042 | |
hgByChroms | 0.021 | 0.002 | 0.023 | |
hgCLengths | 0.001 | 0.004 | 0.005 | |
hgu95Achroloc | 0.099 | 0.008 | 0.107 | |
hgu95Achrom | 0.088 | 0.008 | 0.095 | |
hgu95All | 0.089 | 0.008 | 0.097 | |
hgu95Asym | 0.095 | 0.008 | 0.103 | |
homoData-class | 0.005 | 0.001 | 0.006 | |
htmlpage | 0.035 | 0.004 | 0.039 | |
isValidkey | 0.000 | 0.000 | 0.001 | |
makeAnchor | 0.001 | 0.000 | 0.002 | |
organism | 1.519 | 0.059 | 1.592 | |
p2LL | 0 | 0 | 0 | |
pm.abstGrep | 2.059 | 0.039 | 2.932 | |
pm.getabst | 2.114 | 0.045 | 2.949 | |
pm.titles | 2.059 | 0.038 | 2.909 | |
pmAbst2HTML | 0.128 | 0.007 | 0.749 | |
pmid2MIAME | 0.000 | 0.001 | 0.000 | |
pmidQuery | 0.002 | 0.001 | 0.002 | |
pubMedAbst-class | 0.065 | 0.004 | 0.514 | |
pubmed | 0.038 | 0.004 | 0.637 | |
readGEOAnn | 0.000 | 0.001 | 0.001 | |
serializeEnv | 0.002 | 0.001 | 0.003 | |
setRepository | 0.001 | 0.001 | 0.003 | |
updateSymbolsToValidKeys | 0.001 | 0.000 | 0.001 | |
usedChromGenes | 0.125 | 0.010 | 0.134 | |