Lei Huang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GeneAnswers |
| Branch: RELEASE_3_9 |
| Last Commit: 0ebcc3c |
| Last Changed Date: 2019-05-02 11:53:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:45 -0400 (Wed, 16 Oct 2019).
| Package 622/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneAnswers 2.26.0 Lei Huang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GeneAnswers |
| Version: 2.26.0 |
| 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_2.26.0.tar.gz |
| StartedAt: 2019-10-16 03:02:19 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:16:40 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 861.6 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_2.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.26.0’
* 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-3.9-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 34.1Mb
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’
.catsCluster: no visible global function definition for ‘plot’
.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’
buildNet: no visible global function definition for ‘plot’
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 plot 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", "plot", "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 or elapsed time > 5s
user system elapsed
geneAnswersReadable 85.987 7.358 94.262
GeneAnswers-class 41.613 4.338 45.983
geneAnswersHomoMapping 40.877 3.434 44.368
getMultiLayerGraphIDs 40.875 3.345 44.348
geneAnswersBuilder 40.119 3.466 43.590
getConnectedGraph 40.027 2.895 43.006
buildNet 39.860 2.726 42.591
geneAnswersConcepts 39.256 3.163 42.473
geneAnswersConceptNet 38.936 2.948 41.885
geneAnswersSort 38.952 2.844 41.872
geneAnswersChartPlots 39.003 2.619 41.626
geneAnswersHeatmap 38.023 2.853 40.875
GeneAnswers-package 37.406 3.265 40.690
geneAnswersConceptRelation 37.320 2.866 40.187
getGOList 23.866 2.527 28.452
* 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-3.9-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/3.6/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 | 0.411 | 0.040 | 0.451 | |
| DOLite | 0.039 | 0.010 | 0.048 | |
| DOLiteTerm | 0.005 | 0.006 | 0.011 | |
| DmIALite | 0.077 | 0.011 | 0.088 | |
| GeneAnswers-class | 41.613 | 4.338 | 45.983 | |
| GeneAnswers-package | 37.406 | 3.265 | 40.690 | |
| HsIALite | 0.283 | 0.017 | 0.300 | |
| MmIALite | 0.014 | 0.009 | 0.024 | |
| RnIALite | 0.008 | 0.007 | 0.016 | |
| buildNet | 39.860 | 2.726 | 42.591 | |
| caBIO.PATHGenes | 0.000 | 0.000 | 0.001 | |
| caBIO2entrez | 0.001 | 0.000 | 0.000 | |
| categoryNet | 0.001 | 0.000 | 0.001 | |
| chartPlots | 0.089 | 0.069 | 0.200 | |
| drawTable | 1.099 | 0.084 | 1.183 | |
| entrez2caBIO | 0.001 | 0.000 | 0.000 | |
| geneAnnotationHeatmap | 0.003 | 0.000 | 0.003 | |
| geneAnswersBuilder | 40.119 | 3.466 | 43.590 | |
| geneAnswersChartPlots | 39.003 | 2.619 | 41.626 | |
| geneAnswersConceptNet | 38.936 | 2.948 | 41.885 | |
| geneAnswersConceptRelation | 37.320 | 2.866 | 40.187 | |
| geneAnswersConcepts | 39.256 | 3.163 | 42.473 | |
| geneAnswersHeatmap | 38.023 | 2.853 | 40.875 | |
| geneAnswersHomoMapping | 40.877 | 3.434 | 44.368 | |
| geneAnswersReadable | 85.987 | 7.358 | 94.262 | |
| geneAnswersSort | 38.952 | 2.844 | 41.872 | |
| geneConceptNet | 0.001 | 0.000 | 0.001 | |
| getCategoryList | 0.490 | 0.131 | 0.624 | |
| getCategoryTerms | 0.058 | 0.003 | 0.060 | |
| getConceptTable | 0.875 | 0.040 | 0.916 | |
| getConnectedGraph | 40.027 | 2.895 | 43.006 | |
| getDOLiteTerms | 0.008 | 0.004 | 0.011 | |
| getGOList | 23.866 | 2.527 | 28.452 | |
| getHomoGeneIDs | 0.312 | 0.027 | 0.338 | |
| getListGIF | 0.001 | 0.000 | 0.001 | |
| getMultiLayerGraphIDs | 40.875 | 3.345 | 44.348 | |
| getNextGOIDs | 0.133 | 0.003 | 0.136 | |
| getPATHList | 0.058 | 0.003 | 0.061 | |
| getPATHTerms | 0.032 | 0.001 | 0.033 | |
| getREACTOMEPATHList | 0.000 | 0.000 | 0.001 | |
| getREACTOMEPATHTerms | 0 | 0 | 0 | |
| getSingleLayerGraphIDs | 0.003 | 0.001 | 0.004 | |
| getSymbols | 0.037 | 0.003 | 0.040 | |
| getTotalGeneNumber | 0.354 | 0.034 | 0.387 | |
| getcaBIOPATHList | 0 | 0 | 0 | |
| getcaBIOPATHTerms | 0 | 0 | 0 | |
| groupReport | 0.887 | 0.090 | 0.976 | |
| humanExpr | 0.010 | 0.005 | 0.015 | |
| humanGeneInput | 0.006 | 0.005 | 0.011 | |
| mouseExpr | 0.008 | 0.006 | 0.015 | |
| mouseGeneInput | 0.007 | 0.007 | 0.014 | |
| sampleGroupsData | 0.208 | 0.126 | 0.334 | |
| searchEntrez | 0.000 | 0.001 | 0.000 | |
| topCategory | 0.000 | 0.000 | 0.001 | |
| topCategoryGenes | 0 | 0 | 0 | |
| topDOLITE | 0.000 | 0.000 | 0.001 | |
| topDOLITEGenes | 0.000 | 0.001 | 0.001 | |
| topGO | 0 | 0 | 0 | |
| topGOGenes | 0 | 0 | 0 | |
| topPATH | 0 | 0 | 0 | |
| topPATHGenes | 0 | 0 | 0 | |
| topREACTOME.PATH | 0.000 | 0.000 | 0.001 | |
| topREACTOME.PATHGenes | 0.000 | 0.001 | 0.001 | |
| topcaBIO.PATH | 0 | 0 | 0 | |