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This page was generated on 2021-10-15 15:06:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GeneAnswers package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneAnswers.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 708/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneAnswers 2.34.0 (landing page) Lei Huang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: GeneAnswers |
Version: 2.34.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAnswers_2.34.0.tar.gz |
StartedAt: 2021-10-14 19:18:06 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:45:44 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 1658.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GeneAnswers.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAnswers_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.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 ‘GeneAnswers/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneAnswers’ version ‘2.34.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'igraph', 'KEGGREST', 'RCurl', 'annotate', 'Biobase', 'XML', 'RSQLite', 'MASS', 'Heatplus', 'RColorBrewer' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GeneAnswers’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ See ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 34.2Mb sub-directories of 1Mb or more: External 32.4Mb data 1.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘annotate’ A package should be listed in only one of these fields. * 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 'library' or 'require' calls to packages already attached by Depends: ‘Biobase’ ‘Heatplus’ ‘KEGGREST’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘GO.db’ ‘biomaRt’ ‘reactome.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘GeneAnswers/R/zzz.R’: .onLoad calls: require(Biobase) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. getHomoGeneIDs: no visible global function definition for ‘useMart’ getHomoGeneIDs: no visible global function definition for ‘getLDS’ getTotalGeneNumber: no visible global function definition for ‘count.mappedkeys’ getTotalGeneNumber: no visible global function definition for ‘toTable’ getTotalGeneNumber: no visible binding for global variable ‘reactomePATHNAME2ID’ Undefined global functions or variables: count.mappedkeys getLDS reactomePATHNAME2ID toTable useMart * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘queryKegg’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... ERROR Running examples in ‘GeneAnswers-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getPATHTerms > ### Title: Get Pathway names of given KEGG IDs > ### Aliases: getPATHTerms > ### Keywords: methods > > ### ** Examples > > getPATHTerms(c('04916', '05221')) Error in names(temp) <- sapply(temp, function(x) return(x$ENTRY)) : attempt to set an attribute on NULL Calls: getPATHTerms -> lapply -> queryKegg Execution halted * 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 ERROR, 2 WARNINGs, 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck/00check.log’ for details.
GeneAnswers.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneAnswers ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘GeneAnswers’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ ** testing if installed package keeps a record of temporary installation path * DONE (GeneAnswers)
GeneAnswers.Rcheck/GeneAnswers-Ex.timings
name | user | system | elapsed | |
DO | 0.398 | 0.012 | 0.410 | |
DOLite | 0.036 | 0.003 | 0.039 | |
DOLiteTerm | 0.003 | 0.002 | 0.005 | |
DmIALite | 0.075 | 0.003 | 0.078 | |
GeneAnswers-class | 38.953 | 1.368 | 40.431 | |
GeneAnswers-package | 38.268 | 1.113 | 39.441 | |
HsIALite | 0.226 | 0.009 | 0.235 | |
MmIALite | 0.017 | 0.021 | 0.071 | |
RnIALite | 0.007 | 0.007 | 0.014 | |
buildNet | 36.442 | 0.869 | 37.368 | |
caBIO.PATHGenes | 0.001 | 0.000 | 0.000 | |
caBIO2entrez | 0.000 | 0.001 | 0.000 | |
categoryNet | 0.000 | 0.000 | 0.001 | |
chartPlots | 0.067 | 0.028 | 0.123 | |
drawTable | 307.789 | 1.087 | 442.151 | |
entrez2caBIO | 0 | 0 | 0 | |
geneAnnotationHeatmap | 0.002 | 0.001 | 0.003 | |
geneAnswersBuilder | 36.968 | 0.899 | 37.902 | |
geneAnswersChartPlots | 35.273 | 0.533 | 35.867 | |
geneAnswersConceptNet | 34.677 | 0.848 | 35.630 | |
geneAnswersConceptRelation | 34.329 | 0.613 | 34.999 | |
geneAnswersConcepts | 35.848 | 0.784 | 36.770 | |
geneAnswersHeatmap | 36.782 | 0.857 | 37.835 | |
geneAnswersHomoMapping | 34.458 | 0.845 | 35.462 | |
geneAnswersReadable | 65.867 | 1.744 | 67.874 | |
geneAnswersSort | 33.841 | 0.704 | 34.611 | |
geneConceptNet | 0.000 | 0.000 | 0.001 | |
getCategoryList | 0.147 | 0.019 | 0.169 | |
getCategoryTerms | 0 | 0 | 0 | |
getConceptTable | 315.152 | 1.262 | 456.615 | |
getConnectedGraph | 34.894 | 0.397 | 35.315 | |
getDOLiteTerms | 0.005 | 0.004 | 0.009 | |
getGOList | 19.853 | 0.706 | 20.678 | |
getHomoGeneIDs | 0.234 | 0.007 | 0.241 | |
getListGIF | 0.000 | 0.000 | 0.001 | |
getMultiLayerGraphIDs | 36.688 | 0.606 | 37.320 | |
getNextGOIDs | 0.212 | 0.018 | 0.231 | |
getPATHList | 5.848 | 0.019 | 9.216 | |