Lei Huang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneAnswers |
| Branch: RELEASE_3_8 |
| Last Commit: 95cfd23 |
| Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:55:07 -0400 (Tue, 16 Apr 2019).
| Package 590/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneAnswers 2.24.0 Lei Huang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GeneAnswers |
| Version: 2.24.0 |
| 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_2.24.0.tar.gz |
| StartedAt: 2019-04-16 00:06:44 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:20:26 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 821.2 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_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.24.0’
* 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-3.8-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 81.655 4.279 87.411
geneAnswersHomoMapping 42.572 1.551 45.108
geneAnswersHeatmap 41.449 1.959 44.197
geneAnswersConcepts 41.513 1.538 43.670
geneAnswersConceptRelation 40.739 1.715 42.891
getConnectedGraph 39.937 1.348 42.023
getMultiLayerGraphIDs 39.471 1.344 41.624
GeneAnswers-class 37.925 2.340 40.461
geneAnswersChartPlots 38.235 1.666 40.299
geneAnswersConceptNet 38.049 1.532 39.948
GeneAnswers-package 37.401 1.962 39.579
geneAnswersSort 37.483 1.627 39.532
geneAnswersBuilder 36.057 1.623 37.922
buildNet 35.617 1.612 37.403
getGOList 20.066 1.727 23.925
* 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-3.8-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/3.5/Resources/library’ * installing *source* package ‘GeneAnswers’ ... ** 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 Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ * DONE (GeneAnswers)
GeneAnswers.Rcheck/GeneAnswers-Ex.timings
| name | user | system | elapsed | |
| DO | 0.322 | 0.022 | 0.345 | |
| DOLite | 0.027 | 0.006 | 0.034 | |
| DOLiteTerm | 0.003 | 0.003 | 0.006 | |
| DmIALite | 0.063 | 0.005 | 0.068 | |
| GeneAnswers-class | 37.925 | 2.340 | 40.461 | |
| GeneAnswers-package | 37.401 | 1.962 | 39.579 | |
| HsIALite | 0.217 | 0.010 | 0.230 | |
| MmIALite | 0.011 | 0.007 | 0.017 | |
| RnIALite | 0.006 | 0.007 | 0.013 | |
| buildNet | 35.617 | 1.612 | 37.403 | |
| caBIO.PATHGenes | 0.001 | 0.000 | 0.001 | |
| caBIO2entrez | 0.001 | 0.000 | 0.001 | |
| categoryNet | 0.001 | 0.000 | 0.002 | |
| chartPlots | 0.049 | 0.026 | 0.099 | |
| drawTable | 0.707 | 0.032 | 0.741 | |
| entrez2caBIO | 0.000 | 0.000 | 0.001 | |
| geneAnnotationHeatmap | 0.003 | 0.000 | 0.003 | |
| geneAnswersBuilder | 36.057 | 1.623 | 37.922 | |
| geneAnswersChartPlots | 38.235 | 1.666 | 40.299 | |
| geneAnswersConceptNet | 38.049 | 1.532 | 39.948 | |
| geneAnswersConceptRelation | 40.739 | 1.715 | 42.891 | |
| geneAnswersConcepts | 41.513 | 1.538 | 43.670 | |
| geneAnswersHeatmap | 41.449 | 1.959 | 44.197 | |
| geneAnswersHomoMapping | 42.572 | 1.551 | 45.108 | |
| geneAnswersReadable | 81.655 | 4.279 | 87.411 | |
| geneAnswersSort | 37.483 | 1.627 | 39.532 | |
| geneConceptNet | 0.001 | 0.000 | 0.001 | |
| getCategoryList | 0.212 | 0.009 | 0.227 | |
| getCategoryTerms | 0.037 | 0.001 | 0.039 | |
| getConceptTable | 0.993 | 0.035 | 1.040 | |
| getConnectedGraph | 39.937 | 1.348 | 42.023 | |
| getDOLiteTerms | 0.005 | 0.002 | 0.007 | |
| getGOList | 20.066 | 1.727 | 23.925 | |
| getHomoGeneIDs | 0.249 | 0.010 | 0.263 | |
| getListGIF | 0.002 | 0.000 | 0.002 | |
| getMultiLayerGraphIDs | 39.471 | 1.344 | 41.624 | |
| getNextGOIDs | 0.093 | 0.002 | 0.096 | |
| getPATHList | 0.034 | 0.001 | 0.035 | |
| getPATHTerms | 0.014 | 0.000 | 0.015 | |
| getREACTOMEPATHList | 0.001 | 0.000 | 0.001 | |
| getREACTOMEPATHTerms | 0.001 | 0.000 | 0.001 | |
| getSingleLayerGraphIDs | 0.004 | 0.000 | 0.005 | |
| getSymbols | 0.030 | 0.001 | 0.033 | |
| getTotalGeneNumber | 0.314 | 0.011 | 0.327 | |
| getcaBIOPATHList | 0.001 | 0.000 | 0.002 | |
| getcaBIOPATHTerms | 0.001 | 0.000 | 0.002 | |
| groupReport | 0.637 | 0.043 | 0.694 | |
| humanExpr | 0.006 | 0.002 | 0.008 | |
| humanGeneInput | 0.005 | 0.002 | 0.007 | |
| mouseExpr | 0.008 | 0.003 | 0.010 | |
| mouseGeneInput | 0.006 | 0.003 | 0.009 | |
| sampleGroupsData | 0.115 | 0.039 | 0.154 | |
| searchEntrez | 0.001 | 0.001 | 0.001 | |
| topCategory | 0.001 | 0.000 | 0.001 | |
| topCategoryGenes | 0.001 | 0.000 | 0.001 | |
| topDOLITE | 0.001 | 0.000 | 0.001 | |
| topDOLITEGenes | 0.000 | 0.001 | 0.001 | |
| topGO | 0.001 | 0.000 | 0.001 | |
| topGOGenes | 0.001 | 0.000 | 0.001 | |
| topPATH | 0.001 | 0.000 | 0.001 | |
| topPATHGenes | 0.000 | 0.001 | 0.001 | |
| topREACTOME.PATH | 0.001 | 0.000 | 0.001 | |
| topREACTOME.PATHGenes | 0.001 | 0.000 | 0.001 | |
| topcaBIO.PATH | 0.001 | 0.000 | 0.001 | |