GeneAnswers 2.12.0
Lei Huang and Gang Feng
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GeneAnswers | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.12.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.12.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '2.12.0'
* 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 by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import by 'igraph::decompose' when loading 'GeneAnswers'
See 'C:/biocbld/bbs-3.2-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'.
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'
* 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' ... [387s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 44.58 1.00 45.58
GeneAnswers-class 25.81 1.33 27.28
GeneAnswers-package 23.19 1.08 24.27
getConnectedGraph 23.36 0.75 24.12
geneAnswersConceptNet 23.08 0.87 23.95
buildNet 22.92 0.83 23.75
geneAnswersHeatmap 22.61 0.89 23.50
getMultiLayerGraphIDs 22.32 0.85 23.24
geneAnswersConceptRelation 22.14 0.82 22.95
geneAnswersBuilder 22.34 0.45 22.80
geneAnswersConcepts 21.39 0.89 22.30
geneAnswersSort 21.50 0.70 22.20
geneAnswersChartPlots 21.19 0.61 21.80
geneAnswersHomoMapping 20.97 0.75 21.72
getGOList 11.44 1.17 27.95
** running examples for arch 'x64' ... [419s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 53.37 1.38 54.80
getConnectedGraph 28.57 1.33 29.90
geneAnswersConcepts 27.43 1.47 28.89
GeneAnswers-class 27.74 1.14 28.87
geneAnswersHeatmap 26.64 1.08 27.72
geneAnswersHomoMapping 26.81 0.81 27.62
geneAnswersConceptRelation 26.03 1.31 27.34
getMultiLayerGraphIDs 25.36 1.25 26.61
geneAnswersSort 24.71 1.11 25.84
geneAnswersConceptNet 23.13 0.98 24.11
geneAnswersBuilder 23.23 0.86 24.10
GeneAnswers-package 22.69 1.23 23.92
geneAnswersChartPlots 22.03 0.83 22.86
buildNet 21.62 0.96 22.59
getGOList 13.67 0.90 14.59
* 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:/biocbld/bbs-3.2-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 by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 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 by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import by 'igraph::decompose' when loading 'GeneAnswers'
install for x64
* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'igraph::decompose' when loading 'GeneAnswers'
Warning: replacing previous import by 'igraph::spectrum' when loading 'GeneAnswers'
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.12.0.zip
* DONE (GeneAnswers)