PREDA 1.16.0
Francesco Ferrari
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/PREDA | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PREDA_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/PREDA.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PREDA/DESCRIPTION’ ... OK
* this is package ‘PREDA’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rsprng’
* 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 ‘PREDA’ can be installed ... [10s/10s] 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' calls to packages already attached by Depends:
‘annotate’ ‘lokern’ ‘multtest’ ‘stats’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Rmpi’ ‘affy’ ‘caTools’ ‘limma’ ‘quantsmooth’ ‘qvalue’ ‘rsprng’
‘samr’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘Biobase’ ‘annotate’ ‘lokern’ ‘methods’ ‘multtest’
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 ... NOTE
Foreign function call to a different package:
.Call("mpi_finalize", ..., PACKAGE = "Rmpi")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
genomePlot_improved: warning in axis(1, seq(from = 0, to = max(len), by
= (10 * scale.positions)), label = as.integer(((seq(from = 0, to =
max(len), by = (10 * scale.positions))/scale.positions)))): partial
argument match of 'label' to 'labels'
genomePlot,GenomicAnnotationsForPREDA : .local: warning in axis(1,
seq(from = 0, to = max(len), by = (10 * scale.positions)), label =
as.integer(((seq(from = 0, to = max(len), by = (10 *
scale.positions))/scale.positions)))): partial argument match of
'label' to 'labels'
GE_computeStatistic_onMatrix: no visible global function definition for
‘lmFit’
GE_computeStatistic_onMatrix: no visible global function definition for
‘makeContrasts’
GE_computeStatistic_onMatrix: no visible global function definition for
‘contrasts.fit’
GE_computeStatistic_onMatrix: no visible global function definition for
‘eBayes’
GE_computeStatistic_onMatrix: no visible global function definition for
‘topTable’
GE_computeStatistic_onMatrix: no visible global function definition for
‘samr’
GE_computeStatistic_onMatrix: no visible global function definition for
‘samr.compute.delta.table’
GE_computeStatistic_onMatrix: no visible global function definition for
‘samr.compute.siggenes.table’
GenomicAnnotationsFromLibrary: no visible global function definition
for ‘annPkgName’
GenomicAnnotationsFromLibrary: no visible global function definition
for ‘keys’
GenomicAnnotationsFromLibrary: no visible global function definition
for ‘lookUp’
PREDA_main : .Last: no visible global function definition for
‘mpi.comm.size’
PREDA_main : .Last: no visible global function definition for
‘mpi.close.Rslaves’
PREDA_main: no visible global function definition for
‘mpi.spawn.Rslaves’
PREDA_main: no visible global function definition for
‘mpi.bcast.Robj2slave’
PREDA_main: no visible global function definition for ‘mpi.remote.exec’
PREDA_main: no visible global function definition for ‘init.sprng’
PREDA_main: no visible global function definition for ‘mpi.comm.size’
PREDA_main: no visible global function definition for ‘mpi.comm.rank’
PREDA_main : Listen_on_slaves: no visible global function definition
for ‘mpi.recv.Robj’
PREDA_main : Listen_on_slaves: no visible global function definition
for ‘mpi.any.tag’
PREDA_main : Listen_on_slaves: no visible global function definition
for ‘mpi.get.sourcetag’
PREDA_main : Listen_on_slaves: no visible global function definition
for ‘mpi.send.Robj’
PREDA_main: no visible global function definition for ‘mpi.isend.Robj’
PREDA_main: no visible global function definition for ‘mpi.bcast.cmd’
PREDA_main: no visible global function definition for ‘mpi.recv.Robj’
PREDA_main: no visible global function definition for ‘mpi.any.source’
PREDA_main: no visible global function definition for ‘mpi.any.tag’
PREDA_main: no visible global function definition for
‘mpi.get.sourcetag’
PREDA_main: no visible global function definition for ‘free.sprng’
PREDA_main: no visible global function definition for
‘mpi.close.Rslaves’
PREDA_main_permRows: no visible global function definition for
‘mpi.spawn.Rslaves’
PREDA_main_permRows: no visible global function definition for
‘mpi.bcast.Robj2slave’
PREDA_main_permRows: no visible global function definition for
‘mpi.remote.exec’
PREDA_main_permRows: no visible global function definition for
‘init.sprng’
PREDA_main_permRows: no visible global function definition for
‘mpi.comm.size’
PREDA_main_permRows: no visible global function definition for
‘mpi.comm.rank’
PREDA_main_permRows : Listen_on_slaves: no visible global function
definition for ‘mpi.recv.Robj’
PREDA_main_permRows : Listen_on_slaves: no visible global function
definition for ‘mpi.any.tag’
PREDA_main_permRows : Listen_on_slaves: no visible global function
definition for ‘mpi.get.sourcetag’
PREDA_main_permRows : Listen_on_slaves: no visible global function
definition for ‘mpi.send.Robj’
PREDA_main_permRows: no visible global function definition for
‘mpi.isend.Robj’
PREDA_main_permRows: no visible global function definition for
‘mpi.bcast.cmd’
PREDA_main_permRows: no visible global function definition for
‘mpi.recv.Robj’
PREDA_main_permRows: no visible global function definition for
‘mpi.any.source’
PREDA_main_permRows: no visible global function definition for
‘mpi.any.tag’
PREDA_main_permRows: no visible global function definition for
‘mpi.get.sourcetag’
PREDA_main_permRows: no visible global function definition for
‘free.sprng’
PREDA_main_permRows: no visible global function definition for
‘mpi.close.Rslaves’
PREDA_main_permSamples: no visible global function definition for
‘mpi.spawn.Rslaves’
PREDA_main_permSamples: no visible global function definition for
‘mpi.bcast.Robj2slave’
PREDA_main_permSamples: no visible global function definition for
‘mpi.remote.exec’
PREDA_main_permSamples: no visible global function definition for
‘init.sprng’
PREDA_main_permSamples: no visible global function definition for
‘mpi.comm.size’
PREDA_main_permSamples: no visible global function definition for
‘mpi.comm.rank’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
definition for ‘mpi.recv.Robj’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
definition for ‘mpi.any.tag’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
definition for ‘mpi.get.sourcetag’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
definition for ‘mpi.send.Robj’
PREDA_main_permSamples: no visible global function definition for
‘mpi.isend.Robj’
PREDA_main_permSamples: no visible global function definition for
‘mpi.bcast.cmd’
PREDA_main_permSamples: no visible global function definition for
‘mpi.recv.Robj’
PREDA_main_permSamples: no visible global function definition for
‘mpi.any.source’
PREDA_main_permSamples: no visible global function definition for
‘mpi.any.tag’
PREDA_main_permSamples: no visible global function definition for
‘mpi.get.sourcetag’
PREDA_main_permSamples: no visible global function definition for
‘free.sprng’
PREDA_main_permSamples: no visible global function definition for
‘mpi.close.Rslaves’
PREDA_multTestCorrection: no visible global function definition for
‘qvalue’
PREDA_multTestCorrection: no visible global function definition for
‘mt.rawp2adjp’
PREDA_quantsmoothStat: no visible global function definition for
‘quantsmooth’
PREDA_quantsmoothStatPerm: no visible global function definition for
‘quantsmooth’
PREDA_smoothStat: no visible global function definition for ‘lokerns’
PREDA_smoothStatPerm: no visible global function definition for
‘lokerns’
RMAwithCDFfilter: no visible global function definition for
‘cleancdfname’
RMAwithCDFfilter: no visible global function definition for
‘multiassign’
RMAwithCDFfilter: no visible global function definition for
‘annotation<-’
RMAwithCDFfilter: no visible global function definition for ‘pData’
RMAwithCDFfilter: no visible global function definition for
‘sampleNames’
RMAwithCDFfilter: no visible global function definition for
‘phenoData<-’
RMAwithCDFfilter: no visible global function definition for ‘rma’
RMAwithCDFfilter: no visible global function definition for ‘justRMA’
getExpectedSmoothFunction_runmean : PREDA_runmeanStatPerm_fun: no
visible global function definition for ‘runmean’
getObservedSmoothFunction_runmean : PREDA_runmeanStat_fun: no visible
global function definition for ‘runmean’
GE_computeStatistic,ExpressionSet : .local: no visible global function
definition for ‘pData’
GE_computeStatistic,ExpressionSet : .local: no visible global function
definition for ‘sampleNames’
GE_computeStatistic,ExpressionSet : .local: no visible global function
definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet : .local: no visible
global function definition for ‘pData’
GE_simulations_samplingColumns,ExpressionSet : .local: no visible
global function definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet : .local: no visible
global function definition for ‘exprs<-’
GE_standardize,ExpressionSet : .local: no visible global function
definition for ‘exprs’
GE_standardize,ExpressionSet : .local: no visible global function
definition for ‘exprs<-’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
definition for ‘pData’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
definition for ‘exprs’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
definition for ‘samr’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
definition for ‘sampleNames’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
definition for ‘featureNames’
eset2GenomicAnnotations,ExpressionSet : .local: no visible global
function definition for ‘featureNames’
eset2GenomicAnnotations,ExpressionSet : .local: no visible global
function definition for ‘annotation’
statisticsForPREDAfromEset,ExpressionSet : .local: no visible global
function definition for ‘pData’
statisticsForPREDAfromEset,ExpressionSet : .local: no visible global
function definition for ‘sampleNames’
statisticsForPREDAfromEset,ExpressionSet : .local: 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/PREDA.Rcheck/00check.log’
for details.