Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:47 -0500 (Fri, 08 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
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 5/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
annotate 1.80.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
To the developers/maintainers of the annotate package: - 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: 1.80.0 |
Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings annotate_1.80.0.tar.gz |
StartedAt: 2024-03-08 16:01:13 -0500 (Fri, 08 Mar 2024) |
EndedAt: 2024-03-08 16:14:17 -0500 (Fri, 08 Mar 2024) |
EllapsedTime: 783.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings annotate_1.80.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/annotate.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘annotate/DESCRIPTION’ ... OK * this is package ‘annotate’ version ‘1.80.0’ * 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 loading without being on the library search path ... 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed blastSequences 168.655 1.405 443.754 chrCats 8.764 0.024 8.789 * 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 ... NOTE Error(s) in re-building vignettes: --- re-building ‘GOusage.Rnw’ using Sweave Loading required package: BiocGenerics 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")'. Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML Attaching package: ‘graph’ The following object is masked from ‘package:XML’: addNode Attaching package: ‘Rgraphviz’ The following object is masked from ‘package:annotate’: toFile The following objects are masked from ‘package:IRanges’: from, to The following objects are masked from ‘package:S4Vectors’: from, to Loading required package: org.Hs.eg.db --- finished re-building ‘GOusage.Rnw’ --- re-building ‘annotate.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML Loading required package: org.Hs.eg.db --- finished re-building ‘annotate.Rnw’ --- re-building ‘chromLoc.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML --- finished re-building ‘chromLoc.Rnw’ --- re-building ‘prettyOutput.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML --- finished re-building ‘prettyOutput.Rnw’ --- re-building ‘query.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML Loading required package: org.Hs.eg.db Read 4 items Warning in file(file, "r") : cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062': HTTP status was '400 Bad Request' Error: processing vignette 'query.Rnw' failed with diagnostics: chunk 6 Error in file(file, "r") : cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062' --- failed re-building ‘query.Rnw’ --- re-building ‘useDataPkgs.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML Loading required package: org.Hs.eg.db --- finished re-building ‘useDataPkgs.Rnw’ --- re-building ‘useProbeInfo.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML Loading required package: org.Rn.eg.db Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit --- finished re-building ‘useProbeInfo.Rnw’ SUMMARY: processing the following file failed: ‘query.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/hpages/bbs-3.18-bioc-R41/meat/annotate.Rcheck/00check.log’ for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-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 -- Fri Mar 8 16:11:57 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 8.230 0.389 8.608
annotate.Rcheck/annotate-Ex.timings
name | user | system | elapsed | |
ACCNUMStats | 1.25 | 0.06 | 1.31 | |
GO2heatmap | 0.255 | 0.012 | 0.267 | |
GOmnplot | 0.046 | 0.004 | 0.050 | |
HTMLPage-class | 0 | 0 | 0 | |
LL2homology | 0 | 0 | 0 | |
PMIDAmat | 0.094 | 0.007 | 0.103 | |
PWAmat | 2.354 | 0.110 | 2.465 | |
UniGeneQuery | 0.001 | 0.000 | 0.001 | |
accessionToUID | 0.505 | 0.011 | 2.699 | |
annPkgName | 0.001 | 0.000 | 0.000 | |
aqListGOIDs | 0.181 | 0.020 | 0.201 | |
blastSequences | 168.655 | 1.405 | 443.754 | |
buildChromLocation | 0.762 | 0.067 | 0.829 | |
buildPubMedAbst | 0.087 | 0.004 | 0.498 | |
chrCats | 8.764 | 0.024 | 8.789 | |
chromLocation-class | 0.810 | 0.004 | 0.814 | |
compatibleVersions | 0.033 | 0.004 | 0.037 | |
dropECode | 0.041 | 0.004 | 0.045 | |
entrezGeneByID | 0.000 | 0.000 | 0.001 | |
entrezGeneQuery | 0 | 0 | 0 | |
filterGOByOntology | 0.052 | 0.000 | 0.052 | |
findNeighbors | 0.052 | 0.000 | 0.055 | |
genbank | 0.361 | 0.000 | 1.044 | |
getAnnMap | 0.041 | 0.000 | 0.041 | |
getEvidence | 0.081 | 0.000 | 0.080 | |
getGOTerm | 0.621 | 0.012 | 0.633 | |
getOntology | 0.043 | 0.000 | 0.043 | |
getPMInfo | 0.359 | 0.000 | 0.773 | |
getSYMBOL | 0.100 | 0.004 | 0.105 | |
getSeq4Acc | 0.087 | 0.000 | 0.557 | |
hasGOannote | 0.021 | 0.000 | 0.022 | |
hgByChroms | 0.011 | 0.004 | 0.014 | |
hgCLengths | 0.001 | 0.000 | 0.001 | |
hgu95Achroloc | 0.056 | 0.004 | 0.060 | |
hgu95Achrom | 0.049 | 0.000 | 0.050 | |
hgu95All | 0.054 | 0.008 | 0.065 | |
hgu95Asym | 0.050 | 0.012 | 0.062 | |
homoData-class | 0.002 | 0.000 | 0.003 | |
htmlpage | 0.013 | 0.004 | 0.017 | |
isValidkey | 0.001 | 0.000 | 0.000 | |
makeAnchor | 0.001 | 0.000 | 0.001 | |
organism | 0.616 | 0.024 | 0.640 | |
p2LL | 0.000 | 0.000 | 0.001 | |
pm.abstGrep | 0.949 | 0.056 | 1.849 | |
pm.getabst | 1.038 | 0.040 | 1.863 | |
pm.titles | 1.024 | 0.074 | 1.817 | |
pmAbst2HTML | 0.128 | 0.000 | 0.502 | |
pmid2MIAME | 0 | 0 | 0 | |
pmidQuery | 0.001 | 0.000 | 0.001 | |
pubMedAbst-class | 0.119 | 0.016 | 0.491 | |
pubmed | 0.066 | 0.004 | 0.466 | |
readGEOAnn | 0 | 0 | 0 | |
serializeEnv | 0.002 | 0.000 | 0.002 | |
setRepository | 0.001 | 0.000 | 0.001 | |
updateSymbolsToValidKeys | 0 | 0 | 0 | |
usedChromGenes | 0.071 | 0.012 | 0.083 | |