GeneAnswers 2.4.0
Gang Feng , Pan Du and Tian Xia
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GeneAnswers | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '2.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* checking installed package size ... NOTE
installed size is 35.3Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.0Mb
doc 1.4Mb
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'Biobase' 'Heatplus' 'MASS' 'RColorBrewer' 'XML' 'annotate' 'igraph'
Please remove these calls from your code.
Packages in Depends field not imported from:
'Biobase' 'Heatplus' 'MASS' 'RColorBrewer' 'RCurl' 'RSQLite' 'XML'
'igraph'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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'.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'geneAnswers.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [515s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 53.64 0.95 54.91
GeneAnswers-class 33.93 1.22 35.17
geneAnswersSort 28.10 0.94 29.03
getMultiLayerGraphIDs 27.44 1.16 28.60
getConnectedGraph 24.73 0.78 25.51
geneAnswersConcepts 24.63 0.83 25.48
geneAnswersHeatmap 24.66 0.65 25.32
geneAnswersConceptRelation 24.36 0.84 25.21
geneAnswersConceptNet 24.16 0.80 24.96
GeneAnswers-package 23.65 0.81 24.46
geneAnswersChartPlots 23.61 0.64 24.26
buildNet 22.95 0.58 23.52
geneAnswersBuilder 22.50 0.76 23.26
geneAnswersHomoMapping 22.01 0.89 23.26
getGOList 13.81 0.98 108.77
** running examples for arch 'x64' ... [520s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 82.72 2.08 84.78
GeneAnswers-class 34.67 1.51 36.21
getConnectedGraph 32.74 1.57 34.32
getMultiLayerGraphIDs 32.06 1.25 33.30
geneAnswersHomoMapping 31.75 1.48 33.23
geneAnswersConcepts 31.65 0.96 32.63
geneAnswersConceptRelation 31.10 1.07 32.18
geneAnswersBuilder 29.59 1.06 30.67
geneAnswersSort 29.06 1.45 31.34
geneAnswersConceptNet 28.99 1.06 30.05
geneAnswersHeatmap 27.99 0.83 28.82
buildNet 27.72 0.91 28.65
GeneAnswers-package 25.71 0.81 26.52
geneAnswersChartPlots 25.38 0.84 26.22
getGOList 17.06 0.97 18.08
* 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
NOTE: There were 5 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.4.0.zip
* DONE (GeneAnswers)