GeneAnswers 2.18.0
Lei Huang and Gang Feng
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GeneAnswers | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && mkdir GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.18.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '2.18.0'
* 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 whether package 'GeneAnswers' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 35.5Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.0Mb
doc 1.6Mb
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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'.
.defaultHeatmapColors: no visible global function definition for 'rgb'
.drawHTMLtable: no visible global function definition for
'colorRampPalette'
.heatmap.mds: no visible global function definition for
'colorRampPalette'
buildNet: no visible global function definition for 'colorRampPalette'
chartPlots: no visible global function definition for 'x11'
chartPlots: no visible global function definition for 'rainbow'
drawTable: no visible global function definition for 'colorRampPalette'
drawTable: no visible global function definition for 'x11'
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'
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:
col2rgb colorRampPalette count.mappedkeys dev.off dev.prev dev.set
getLDS png rainbow reactomePATHNAME2ID rgb toTable useMart x11
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
"dev.prev", "dev.set", "png", "rainbow", "rgb", "x11")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 56.19 1.68 57.87
GeneAnswers-class 30.22 1.89 45.61
getMultiLayerGraphIDs 27.79 1.13 28.97
geneAnswersHeatmap 27.50 0.93 28.42
geneAnswersSort 27.30 0.94 28.24
geneAnswersConcepts 27.13 0.95 28.08
geneAnswersHomoMapping 26.95 1.00 27.95
geneAnswersChartPlots 26.94 0.89 27.83
geneAnswersConceptNet 25.55 1.00 26.61
geneAnswersConceptRelation 25.59 0.84 26.44
GeneAnswers-package 24.56 1.25 25.82
buildNet 24.16 0.92 25.08
geneAnswersBuilder 24.31 0.69 25.01
getConnectedGraph 23.88 0.90 24.81
getGOList 14.54 1.63 365.37
getCategoryList 0.36 0.00 9.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 67.51 1.74 69.26
geneAnswersChartPlots 30.23 1.50 31.73
getConnectedGraph 29.76 1.25 31.02
geneAnswersHomoMapping 29.65 1.20 30.85
geneAnswersConcepts 29.51 1.09 30.61
getMultiLayerGraphIDs 29.09 1.25 30.35
geneAnswersConceptRelation 29.06 1.18 30.23
geneAnswersSort 28.92 1.22 30.17
GeneAnswers-package 28.77 1.25 30.01
geneAnswersConceptNet 28.05 1.26 29.36
GeneAnswers-class 27.52 1.79 29.29
geneAnswersHeatmap 27.35 1.03 28.38
geneAnswersBuilder 26.03 1.28 27.31
buildNet 24.81 1.50 26.32
getGOList 14.66 0.70 15.35
* 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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
install for x64
* installing *source* package 'GeneAnswers' ...
** 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'
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.18.0.zip
* DONE (GeneAnswers)