codelink 1.34.0
Diego Diez
| 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/codelink | | 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch codelink_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/codelink.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘codelink/DESCRIPTION’ ... OK
* this is package ‘codelink’ version ‘1.34.0’
* 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 ‘codelink’ can be installed ... [20s/22s] 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
'library' or 'require' call to ‘genefilter’ in package code.
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
Codelink2CodelinkSet: no visible global function definition for
‘phenoData<-’
Codelink2CodelinkSet: no visible global function definition for
‘featureData<-’
Codelink2CodelinkSet: no visible global function definition for
‘experimentData’
Codelink2CodelinkSet: no visible global function definition for
‘experimentData<-’
Codelink2eSet: no visible global function definition for
‘featureNames<-’
Codelink2eSet: no visible global function definition for
‘sampleNames<-’
Codelink2eSet: no visible global function definition for
‘experimentData’
Codelink2eSet: no visible global function definition for
‘experimentData<-’
averageProbes,CodelinkSet: no visible global function definition for
‘sampleNames’
averageProbes,CodelinkSet: no visible global function definition for
‘pData’
averageProbes,CodelinkSet: no visible global function definition for
‘featureData’
averageProbes,CodelinkSet: no visible global function definition for
‘varMetadata’
averageProbes,CodelinkSet: no visible global function definition for
‘featureNames<-’
averageProbes,CodelinkSet: no visible global function definition for
‘phenoData’
codCorrect,CodelinkSet: no visible global function definition for
‘assayDataElement<-’
codCorrect,CodelinkSet: no visible global function definition for
‘experimentData’
codCorrect,CodelinkSet: no visible global function definition for
‘experimentData<-’
createFlagWeights,CodelinkSet: no visible global function definition
for ‘sampleNames’
createFlagWeights,CodelinkSet: no visible global function definition
for ‘featureNames’
createTypeWeights,CodelinkSet: no visible global function definition
for ‘sampleNames’
createTypeWeights,CodelinkSet: no visible global function definition
for ‘featureNames’
exprs,CodelinkSet: no visible global function definition for
‘assayDataElement’
filterSNR,matrix: no visible global function definition for
‘genefilter’
filterSNR,matrix: no visible global function definition for ‘filterfun’
getBkg,CodelinkSet: no visible global function definition for
‘assayDataElement’
getFlag,CodelinkSet: no visible global function definition for
‘assayDataElement’
getInfo,CodelinkSet: no visible global function definition for
‘experimentData’
getSNR,CodelinkSet: no visible global function definition for
‘assayDataElement’
getWeight,CodelinkSet: no visible global function definition for
‘assayDataElement’
logicalCol,CodelinkSet: no visible global function definition for
‘pData’
logicalCol,CodelinkSet: no visible global function definition for
‘featureData’
logicalRow,CodelinkSet: no visible global function definition for
‘pData’
logicalRow,CodelinkSet: no visible global function definition for
‘featureData’
meanSNR,CodelinkSet: no visible global function definition for ‘pData’
meanSNR,CodelinkSet: no visible global function definition for
‘featureData’
probeNames,CodelinkSet: no visible global function definition for
‘pData’
probeNames,CodelinkSet: no visible global function definition for
‘featureData’
probeNames,CodelinkSetUnique: no visible global function definition for
‘featureNames’
probeTypes,CodelinkSet: no visible global function definition for
‘pData’
probeTypes,CodelinkSet: no visible global function definition for
‘featureData’
writeCodelink,CodelinkSet: no visible global function definition for
‘sampleNames’
writeCodelink,CodelinkSet: no visible global function definition for
‘featureNames’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* 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
‘/Users/biocbuild/bbs-3.0-bioc/meat/codelink.Rcheck/00check.log’
for details.
* installing *source* package ‘codelink’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘createWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
in method for ‘createFlagWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
in method for ‘createTypeWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
Creating a generic function for ‘summary’ from package ‘base’ in package ‘codelink’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (codelink)