affyPara 1.30.0
Markus Schmidberger
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/affyPara | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 affyPara_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/affyPara.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.30.0’
* 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 ‘affyPara’ can be installed ... [5s/68s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘affy’
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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘affy’ ‘aplpack’ ‘snow’ ‘vsn’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘affyio’ ‘aplpack’ ‘methods’ ‘snow’ ‘vsn’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘vsn:::isSmall’ ‘vsn:::optimparNames’ ‘vsn:::pstartHeuristic’
‘vsn:::vsnLTS’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.doSummarizationPara: no visible global function definition for
‘clusterCall’
.doSummarizationPara: no visible global function definition for
‘phenoData’
.doSummarizationPara: no visible global function definition for
‘experimentData’
.doSummarizationPara: no visible global function definition for
‘annotation’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.permArrays: no visible global function definition for ‘clusterCall’
.permMatrix: no visible global function definition for ‘clusterCall’
.resetABSF: no visible global function definition for ‘exprs<-’
.resetABSF: no visible global function definition for ‘sampleNames<-’
.rowMeansPara: no visible global function definition for ‘clusterCall’
.rowVPara: no visible global function definition for ‘clusterCall’
bgCorrectPara: no visible global function definition for ‘checkCluster’
bgCorrectPara: no visible global function definition for ‘clusterApply’
bgCorrectPara: no visible global function definition for ‘clusterCall’
bgCorrectPara: no visible global function definition for ‘pData’
boxplotPara: no visible global function definition for ‘checkCluster’
boxplotPara: no visible global function definition for ‘clusterApply’
boxplotPara: no visible global function definition for ‘clusterCall’
boxplotParagMedIQR: no visible global function definition for ‘bagplot’
computeExprSetPara: no visible global function definition for
‘checkCluster’
computeExprSetPara: no visible global function definition for
‘clusterApply’
distributeFiles: no visible global function definition for
‘checkCluster’
distributeFiles: no visible global function definition for
‘clusterEvalQ’
distributeFiles: no visible global function definition for
‘clusterCall’
distributeFiles: no visible global function definition for
‘clusterSplit’
grad_loglikPara: no visible global function definition for
‘clusterCall’
justvsnPara: no visible global function definition for ‘clusterCall’
logikPara: no visible global function definition for ‘clusterCall’
MAplotPara: no visible global function definition for ‘checkCluster’
MAplotPara: no visible global function definition for ‘clusterApply’
MAplotPara: no visible global function definition for ‘clusterCall’
mergeAffyBatches: no visible global function definition for ‘phenoData’
mergeAffyBatches: no visible global function definition for ‘notes<-’
mergeAffyBatches: no visible global function definition for ‘pData<-’
mergeAffyBatches: no visible global function definition for ‘pData’
mergeAffyBatches: no visible global function definition for ‘exprs<-’
mergeAffyBatches: no visible global function definition for
‘phenoData<-’
mergeAffyBatches: no visible global function definition for
‘experimentData<-’
normalizeAffyBatchConstantPara: no visible global function definition
for ‘checkCluster’
normalizeAffyBatchConstantPara: no visible global function definition
for ‘clusterApply’
normalizeAffyBatchConstantPara: no visible global function definition
for ‘clusterCall’
normalizeAffyBatchInvariantsetPara: no visible global function
definition for ‘checkCluster’
normalizeAffyBatchInvariantsetPara: no visible global function
definition for ‘clusterApply’
normalizeAffyBatchInvariantsetPara: no visible global function
definition for ‘clusterCall’
normalizeAffyBatchLoessIterPara: no visible global function definition
for ‘checkCluster’
normalizeAffyBatchLoessIterPara: no visible global function definition
for ‘clusterApply’
normalizeAffyBatchLoessIterPara: no visible global function definition
for ‘clusterCall’
normalizeAffyBatchLoessPara: no visible global function definition for
‘checkCluster’
normalizeAffyBatchLoessPara: no visible global function definition for
‘clusterApply’
normalizeAffyBatchLoessPara: no visible global function definition for
‘clusterCall’
normalizeAffyBatchQuantilesPara: no visible global function definition
for ‘checkCluster’
normalizeAffyBatchQuantilesPara: no visible global function definition
for ‘clusterApply’
normalizeAffyBatchQuantilesPara: no visible global function definition
for ‘clusterCall’
normalizeConstantPara: no visible global function definition for
‘clusterCall’
normalizeInvariantsetPara: no visible global function definition for
‘clusterCall’
normalizeInvariantsetPara: no visible global function definition for
‘rowMedians’
normalizeLoessIterPara: no visible global function definition for
‘clusterCall’
normalizeLoessPara: no visible global function definition for
‘clusterCall’
normalizeQuantilesPara: no visible global function definition for
‘clusterCall’
preproPara: no visible global function definition for ‘checkCluster’
preproPara: no visible global function definition for ‘clusterApply’
preproPara: no visible global function definition for ‘clusterCall’
read.affybatchPara: no visible global function definition for
‘checkCluster’
read.affybatchPara: no visible global function definition for
‘clusterApply’
read.affybatchPara: no visible global function definition for
‘clusterCall’
read.affybatchPara: no visible global function definition for
‘phenoData<-’
read.affybatchPara: no visible global function definition for ‘notes<-’
removeDistributedFiles: no visible global function definition for
‘checkCluster’
removeDistributedFiles: no visible global function definition for
‘clusterEvalQ’
removeDistributedFiles: no visible global function definition for
‘clusterCall’
setupPara: no visible global function definition for ‘clusterCall’
splitAffyBatch: no visible global function definition for
‘splitIndices’
splitFileVector: no visible global function definition for
‘splitIndices’
splitMatrix: no visible global function definition for ‘splitCols’
stopCluster: no visible global function definition for ‘checkCluster’
vsn2Para: no visible global function definition for ‘checkCluster’
vsn2Para: no visible global function definition for ‘clusterApply’
vsn2Para: no visible global function definition for ‘clusterCall’
vsn2trsfPara: no visible global function definition for ‘clusterCall’
vsnColumnByColumnPara: no visible global function definition for
‘clusterCall’
vsnLTSPara: no visible global function definition for ‘clusterCall’
vsnMatrixPara: no visible global function definition for
‘scalingFactorTransformation’
vsnrmaPara: no visible global function definition for ‘checkCluster’
vsnrmaPara: no visible global function definition for ‘clusterApply’
vsnrmaPara: no visible global function definition for ‘clusterCall’
vsnSamplePara: no visible global function definition for ‘clusterCall’
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘vsnStudy.pdf’ from 2095Kb to 318Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/11s] 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
Status: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/affyPara.Rcheck/00check.log’
for details.