Lei Huang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GeneAnswers |
| Branch: RELEASE_3_12 |
| Last Commit: a310951 |
| Last Changed Date: 2020-10-27 10:36:41 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:35:03 -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: /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_2.32.0.tar.gz |
| StartedAt: 2021-05-06 01:59:23 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:11:17 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 714.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeneAnswers.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_2.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneAnswers.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.32.0’
* 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 ‘/Users/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 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
geneAnswersReadable 66.639 1.596 68.334
GeneAnswers-class 38.643 1.873 40.742
geneAnswersConcepts 38.962 1.061 40.072
geneAnswersConceptRelation 38.512 0.769 39.338
geneAnswersChartPlots 37.999 0.784 38.843
GeneAnswers-package 36.634 1.050 37.738
geneAnswersConceptNet 35.890 0.698 36.643
geneAnswersHomoMapping 34.616 0.946 35.597
buildNet 34.496 0.934 35.491
geneAnswersBuilder 34.528 0.858 35.448
getConnectedGraph 34.897 0.465 35.422
getMultiLayerGraphIDs 34.566 0.609 35.230
geneAnswersHeatmap 34.151 0.653 34.840
geneAnswersSort 33.767 0.695 34.506
getGOList 18.466 1.043 20.232
* 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
‘/Users/biocbuild/bbs-3.12-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/4.0/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 | 0.433 | 0.014 | 0.448 | |
| DOLite | 0.036 | 0.003 | 0.038 | |
| DOLiteTerm | 0.003 | 0.003 | 0.007 | |
| DmIALite | 0.073 | 0.004 | 0.078 | |
| GeneAnswers-class | 38.643 | 1.873 | 40.742 | |
| GeneAnswers-package | 36.634 | 1.050 | 37.738 | |
| HsIALite | 0.227 | 0.007 | 0.234 | |
| MmIALite | 0.012 | 0.006 | 0.018 | |
| RnIALite | 0.007 | 0.006 | 0.013 | |
| buildNet | 34.496 | 0.934 | 35.491 | |
| caBIO.PATHGenes | 0 | 0 | 0 | |
| caBIO2entrez | 0.001 | 0.000 | 0.000 | |
| categoryNet | 0.000 | 0.000 | 0.001 | |
| chartPlots | 0.059 | 0.029 | 0.117 | |
| drawTable | 0.829 | 0.053 | 0.883 | |
| entrez2caBIO | 0.000 | 0.001 | 0.000 | |
| geneAnnotationHeatmap | 0.002 | 0.000 | 0.003 | |
| geneAnswersBuilder | 34.528 | 0.858 | 35.448 | |
| geneAnswersChartPlots | 37.999 | 0.784 | 38.843 | |
| geneAnswersConceptNet | 35.890 | 0.698 | 36.643 | |
| geneAnswersConceptRelation | 38.512 | 0.769 | 39.338 | |
| geneAnswersConcepts | 38.962 | 1.061 | 40.072 | |
| geneAnswersHeatmap | 34.151 | 0.653 | 34.840 | |
| geneAnswersHomoMapping | 34.616 | 0.946 | 35.597 | |
| geneAnswersReadable | 66.639 | 1.596 | 68.334 | |
| geneAnswersSort | 33.767 | 0.695 | 34.506 | |
| geneConceptNet | 0 | 0 | 0 | |
| getCategoryList | 0.411 | 0.035 | 0.448 | |
| getCategoryTerms | 0.042 | 0.002 | 0.046 | |
| getConceptTable | 0.699 | 0.046 | 0.748 | |
| getConnectedGraph | 34.897 | 0.465 | 35.422 | |
| getDOLiteTerms | 0.006 | 0.003 | 0.011 | |
| getGOList | 18.466 | 1.043 | 20.232 | |
| getHomoGeneIDs | 0.163 | 0.005 | 0.167 | |
| getListGIF | 0.000 | 0.000 | 0.001 | |
| getMultiLayerGraphIDs | 34.566 | 0.609 | 35.230 | |
| getNextGOIDs | 0.073 | 0.001 | 0.075 | |
| getPATHList | 0.030 | 0.001 | 0.030 | |
| getPATHTerms | 0.016 | 0.001 | 0.017 | |
| getREACTOMEPATHList | 0.000 | 0.001 | 0.000 | |
| getREACTOMEPATHTerms | 0.001 | 0.000 | 0.001 | |
| getSingleLayerGraphIDs | 0.002 | 0.001 | 0.003 | |
| getSymbols | 0.019 | 0.001 | 0.020 | |
| getTotalGeneNumber | 0.245 | 0.002 | 0.248 | |
| getcaBIOPATHList | 0 | 0 | 0 | |
| getcaBIOPATHTerms | 0 | 0 | 0 | |
| groupReport | 0.570 | 0.042 | 0.615 | |
| humanExpr | 0.004 | 0.003 | 0.007 | |
| humanGeneInput | 0.003 | 0.002 | 0.005 | |
| mouseExpr | 0.004 | 0.003 | 0.006 | |
| mouseGeneInput | 0.003 | 0.002 | 0.004 | |
| sampleGroupsData | 0.082 | 0.069 | 0.151 | |
| searchEntrez | 0 | 0 | 0 | |
| topCategory | 0.000 | 0.000 | 0.001 | |
| topCategoryGenes | 0.000 | 0.000 | 0.001 | |
| topDOLITE | 0.000 | 0.001 | 0.000 | |
| topDOLITEGenes | 0 | 0 | 0 | |
| topGO | 0 | 0 | 0 | |
| topGOGenes | 0.001 | 0.000 | 0.000 | |
| topPATH | 0 | 0 | 0 | |
| topPATHGenes | 0 | 0 | 0 | |
| topREACTOME.PATH | 0.000 | 0.000 | 0.001 | |
| topREACTOME.PATHGenes | 0.000 | 0.001 | 0.000 | |
| topcaBIO.PATH | 0 | 0 | 0 | |