Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:41 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the GeneAnswers package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 682/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneAnswers 2.32.0 (landing page) Lei Huang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: GeneAnswers |
Version: 2.32.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneAnswers_2.32.0.tar.gz |
StartedAt: 2021-05-06 01:47:20 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:59:43 -0400 (Thu, 06 May 2021) |
EllapsedTime: 743.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GeneAnswers.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneAnswers_2.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GeneAnswers.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (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 ‘2.32.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'igraph', '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 ... OK * 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 ‘/home/biocbuild/bbs-3.12-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’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘GO.db’ ‘KEGG.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'. .catsCluster: no visible global function definition for ‘par’ .defaultHeatmapColors: no visible global function definition for ‘rgb’ .drawHTMLtable: no visible global function definition for ‘colorRampPalette’ .drawTable: no visible global function definition for ‘par’ .drawTable: no visible global function definition for ‘image’ .drawTable: no visible global function definition for ‘abline’ .drawTable: no visible global function definition for ‘axis’ .drawTable: no visible global function definition for ‘points’ .heatmap.mds: no visible global function definition for ‘colorRampPalette’ .heatmap.mds: no visible global function definition for ‘layout’ .heatmap.mds: no visible global function definition for ‘par’ .heatmap.mds: no visible global function definition for ‘image’ .heatmap.mds: no visible global function definition for ‘axis’ .heatmap.mds: no visible global function definition for ‘box’ buildNet: no visible global function definition for ‘colorRampPalette’ chartPlots: no visible global function definition for ‘x11’ chartPlots: no visible global function definition for ‘pie’ chartPlots: no visible global function definition for ‘rainbow’ chartPlots: no visible global function definition for ‘barplot’ drawTable: no visible global function definition for ‘colorRampPalette’ drawTable: no visible global function definition for ‘x11’ drawTable: no visible global function definition for ‘par’ drawTable: no visible global function definition for ‘image’ drawTable: no visible global function definition for ‘abline’ drawTable: no visible global function definition for ‘axis’ drawTable: no visible global function definition for ‘text’ drawTable: no visible global function definition for ‘box’ drawTable: no visible global function definition for ‘dev.set’ drawTable: no visible global function definition for ‘dev.prev’ geneAnnotationHeatmap: no visible global function definition for ‘colorRampPalette’ geneAnnotationHeatmap: no visible global function definition for ‘layout’ geneConceptNet: no visible global function definition for ‘colorRampPalette’ 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’ groupReport: no visible global function definition for ‘png’ groupReport: no visible global function definition for ‘dev.off’ groupReport: no visible global function definition for ‘rgb’ groupReport: no visible global function definition for ‘col2rgb’ Undefined global functions or variables: abline axis barplot box col2rgb colorRampPalette count.mappedkeys dev.off dev.prev dev.set getLDS image layout par pie png points rainbow reactomePATHNAME2ID rgb text toTable useMart x11 Consider adding importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off", "dev.prev", "dev.set", "png", "rainbow", "rgb", "x11") importFrom("graphics", "abline", "axis", "barplot", "box", "image", "layout", "par", "pie", "points", "text") to your NAMESPACE file. * 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 geneAnswersReadable 67.736 0.096 67.918 GeneAnswers-class 41.564 0.892 42.658 geneAnswersHeatmap 41.964 0.024 42.085 geneAnswersChartPlots 40.176 0.004 40.282 buildNet 40.060 0.032 40.219 GeneAnswers-package 39.920 0.080 40.102 getMultiLayerGraphIDs 39.712 0.060 39.820 geneAnswersBuilder 39.052 0.040 39.209 geneAnswersHomoMapping 38.924 0.048 39.054 geneAnswersConceptRelation 38.640 0.008 38.711 getConnectedGraph 38.184 0.044 38.300 geneAnswersSort 37.456 0.116 37.648 geneAnswersConceptNet 37.088 0.032 37.166 geneAnswersConcepts 36.852 0.016 36.930 getGOList 20.584 0.220 22.822 * 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 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.12-bioc/meat/GeneAnswers.Rcheck/00check.log’ for details.
GeneAnswers.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GeneAnswers ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 | 0.436 | 0.004 | 0.444 | |
DOLite | 0.024 | 0.000 | 0.024 | |
DOLiteTerm | 0.004 | 0.000 | 0.002 | |
DmIALite | 0.052 | 0.004 | 0.058 | |
GeneAnswers-class | 41.564 | 0.892 | 42.658 | |
GeneAnswers-package | 39.920 | 0.080 | 40.102 | |
HsIALite | 0.2 | 0.0 | 0.2 | |
MmIALite | 0.012 | 0.000 | 0.011 | |
RnIALite | 0.004 | 0.000 | 0.005 | |
buildNet | 40.060 | 0.032 | 40.219 | |
caBIO.PATHGenes | 0 | 0 | 0 | |
caBIO2entrez | 0 | 0 | 0 | |
categoryNet | 0 | 0 | 0 | |
chartPlots | 0.072 | 0.016 | 0.221 | |
drawTable | 0.924 | 0.004 | 0.930 | |
entrez2caBIO | 0 | 0 | 0 | |
geneAnnotationHeatmap | 0.000 | 0.000 | 0.002 | |
geneAnswersBuilder | 39.052 | 0.040 | 39.209 | |
geneAnswersChartPlots | 40.176 | 0.004 | 40.282 | |
geneAnswersConceptNet | 37.088 | 0.032 | 37.166 | |
geneAnswersConceptRelation | 38.640 | 0.008 | 38.711 | |
geneAnswersConcepts | 36.852 | 0.016 | 36.930 | |
geneAnswersHeatmap | 41.964 | 0.024 | 42.085 | |
geneAnswersHomoMapping | 38.924 | 0.048 | 39.054 | |
geneAnswersReadable | 67.736 | 0.096 | 67.918 | |
geneAnswersSort | 37.456 | 0.116 | 37.648 | |
geneConceptNet | 0 | 0 | 0 | |
getCategoryList | 0.420 | 0.008 | 0.453 | |
getCategoryTerms | 0.052 | 0.000 | 0.060 | |
getConceptTable | 0.936 | 0.008 | 0.946 | |
getConnectedGraph | 38.184 | 0.044 | 38.300 | |
getDOLiteTerms | 0.004 | 0.000 | 0.004 | |
getGOList | 20.584 | 0.220 | 22.822 | |
getHomoGeneIDs | 0.120 | 0.012 | 0.133 | |
getListGIF | 0 | 0 | 0 | |
getMultiLayerGraphIDs | 39.712 | 0.060 | 39.820 | |
getNextGOIDs | 0.092 | 0.000 | 0.093 | |
getPATHList | 0.052 | 0.000 | 0.050 | |
getPATHTerms | 0.028 | 0.000 | 0.026 | |
getREACTOMEPATHList | 0 | 0 | 0 | |
getREACTOMEPATHTerms | 0.000 | 0.000 | 0.001 | |
getSingleLayerGraphIDs | 0.000 | 0.000 | 0.002 | |
getSymbols | 0.020 | 0.000 | 0.021 | |
getTotalGeneNumber | 0.412 | 0.000 | 0.430 | |
getcaBIOPATHList | 0.000 | 0.000 | 0.001 | |
getcaBIOPATHTerms | 0.000 | 0.000 | 0.001 | |
groupReport | 0.640 | 0.008 | 0.651 | |
humanExpr | 0.004 | 0.000 | 0.005 | |
humanGeneInput | 0.004 | 0.000 | 0.002 | |
mouseExpr | 0.000 | 0.000 | 0.003 | |
mouseGeneInput | 0.000 | 0.000 | 0.003 | |
sampleGroupsData | 0.048 | 0.016 | 0.062 | |
searchEntrez | 0 | 0 | 0 | |
topCategory | 0 | 0 | 0 | |
topCategoryGenes | 0 | 0 | 0 | |
topDOLITE | 0.004 | 0.000 | 0.000 | |
topDOLITEGenes | 0 | 0 | 0 | |
topGO | 0 | 0 | 0 | |
topGOGenes | 0 | 0 | 0 | |
topPATH | 0 | 0 | 0 | |
topPATHGenes | 0 | 0 | 0 | |
topREACTOME.PATH | 0 | 0 | 0 | |
topREACTOME.PATHGenes | 0 | 0 | 0 | |
topcaBIO.PATH | 0.000 | 0.000 | 0.001 | |