BioC 3.0: CHECK report for ArrayExpress on zin1
This page was generated on 2015-04-10 09:38:17 -0700 (Fri, 10 Apr 2015).
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 |
Summary
Package: ArrayExpress |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpress_1.26.0.tar.gz |
StartedAt: 2015-04-09 21:36:23 -0700 (Thu, 09 Apr 2015) |
EndedAt: 2015-04-09 21:38:21 -0700 (Thu, 09 Apr 2015) |
EllapsedTime: 118.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ArrayExpress.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpress_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ArrayExpress’ can be installed ... [4s/4s] 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
* 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 ... [16s/78s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 8.212 0.644 50.681
queryAE 2.988 0.008 6.836
getAE 2.300 0.156 18.682
* 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
‘/home/biocbuild/bbs-3.0-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.
ArrayExpress.Rcheck/00install.out:
* 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
* DONE (ArrayExpress)
ArrayExpress.Rcheck/ArrayExpress-Ex.timings:
name | user | system | elapsed
|
ArrayExpress | 8.212 | 0.644 | 50.681 |
|
ae2bioc | 0.000 | 0.000 | 0.001 |
|
getAE | 2.300 | 0.156 | 18.682 |
|
procset | 0 | 0 | 0 |
|
queryAE | 2.988 | 0.008 | 6.836 |
|