ArrayExpress 1.26.0
Ibrahim Emam
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ArrayExpress | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.26.0.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.26.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.26.0'
* 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 'ArrayExpress' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Package in Depends field not imported from: 'Biobase'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ae2bioc: no visible global function definition for 'varLabels'
ae2bioc: no visible global function definition for 'pData'
ae2bioc: no visible global function definition for 'sampleNames'
ae2bioc: no visible global function definition for 'phenoData<-'
ae2bioc: no visible global function definition for 'protocolData'
ae2bioc: no visible global function definition for 'sampleNames<-'
ae2bioc: no visible global function definition for 'protocolData<-'
ae2bioc: no visible global function definition for 'experimentData<-'
ae2bioc: no visible global function definition for 'featureData<-'
ae2bioc: no visible global function definition for 'featureNames'
ae2bioc: no visible global function definition for 'featureData'
getAE: no visible global function definition for
'read.AnnotatedDataFrame'
getAE: no visible global function definition for 'pData'
getAE: no visible global function definition for 'varLabels'
getPhenoDataPerAD: no visible global function definition for 'pData'
getPhenoDataPerAD: no visible global function definition for
'varLabels'
getcolproc: no visible global function definition for
'read.AnnotatedDataFrame'
getcolproc: no visible global function definition for 'varLabels'
isOneChannel: no visible global function definition for
'read.AnnotatedDataFrame'
isOneChannel: no visible global function definition for 'varLabels'
preparePhenoDataFor2channel: no visible global function definition for
'pData'
preparePhenoDataFor2channel: no visible global function definition for
'varLabels'
preparePhenoDataFor2channel: no visible global function definition for
'pData<-'
readPhenoData: no visible global function definition for
'read.AnnotatedDataFrame'
readPhenoData: no visible global function definition for 'pData'
readPhenoData : <anonymous>: no visible global function definition for
'pData'
readPhenoData: no visible global function definition for 'pData<-'
readPhenoData: no visible global function definition for 'varLabels'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [118s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 14.52 1.01 75.59
getAE 4.57 0.19 33.07
queryAE 3.50 0.01 7.24
** running examples for arch 'x64' ... [107s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 17.02 0.78 71.68
queryAE 4.88 0.05 8.14
getAE 4.15 0.25 24.37
* 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ArrayExpress' ...
** R
** 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 'ArrayExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.26.0.zip
* DONE (ArrayExpress)