BioC 3.1: CHECK report for ArrayExpress on moscato2
This page was generated on 2015-10-09 09:28:23 -0700 (Fri, 09 Oct 2015).
ArrayExpress 1.28.1 Ugis Sarkans
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ArrayExpress | Last Changed Rev: 102784 / Revision: 109384 | Last Changed Date: 2015-04-20 03:20:19 -0700 (Mon, 20 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: ArrayExpress
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Version: 1.28.1
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Command: rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.28.1.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.28.1.tar.gz
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StartedAt: 2015-10-08 23:22:41 -0700 (Thu, 08 Oct 2015)
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EndedAt: 2015-10-08 23:26:33 -0700 (Thu, 08 Oct 2015)
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EllapsedTime: 231.9 seconds
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RetCode: 0
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Status: OK
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CheckDir: ArrayExpress.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.28.1.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.28.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.28.1'
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' ... [87s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 12.59 0.87 57.63
queryAE 3.25 0.53 5.80
getAE 3.30 0.25 21.98
** running examples for arch 'x64' ... [91s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 14.96 0.85 60.37
queryAE 3.91 0.44 6.55
getAE 3.01 0.27 21.69
* 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: 3 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.
ArrayExpress.Rcheck/00install.out:
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_1.28.1.zip
* DONE (ArrayExpress)
ArrayExpress.Rcheck/examples_i386/ArrayExpress-Ex.timings:
name | user | system | elapsed
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ArrayExpress | 12.59 | 0.87 | 57.63 |
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ae2bioc | 0 | 0 | 0 |
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getAE | 3.30 | 0.25 | 21.98 |
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procset | 0 | 0 | 0 |
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queryAE | 3.25 | 0.53 | 5.80 |
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ArrayExpress.Rcheck/examples_x64/ArrayExpress-Ex.timings:
name | user | system | elapsed
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ArrayExpress | 14.96 | 0.85 | 60.37 |
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ae2bioc | 0 | 0 | 0 |
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getAE | 3.01 | 0.27 | 21.69 |
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procset | 0 | 0 | 0 |
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queryAE | 3.91 | 0.44 | 6.55 |
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