Francesco Ferrari
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/PREDA |
| git_branch: RELEASE_3_14 |
| git_last_commit: 65d1da0 |
| git_last_commit_date: 2021-10-26 11:59:54 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:33 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the PREDA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PREDA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1452/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PREDA 1.40.0 (landing page) Francesco Ferrari
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: PREDA |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PREDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PREDA_1.40.0.tar.gz |
| StartedAt: 2022-04-12 16:56:08 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:59:22 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 193.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PREDA.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PREDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PREDA_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PREDA.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PREDA/DESCRIPTION’ ... OK
* this is package ‘PREDA’ version ‘1.40.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PREDA’ can be installed ... 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’
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
GE_computeStatistic_onMatrix : <anonymous>: no visible global function
definition for ‘t.test’
GE_computeStatistic_onMatrix : <anonymous>: no visible global function
definition for ‘median’
GE_computeStatistic_onMatrix: no visible global function definition for
‘model.matrix’
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’
GenomicAnnotationsForPREDAFromfile: no visible global function
definition for ‘read.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’
GenomicAnnotationsFromLibrary: no visible global function definition
for ‘slot’
GenomicAnnotationsFromdataframe: no visible global function definition
for ‘new’
GenomicAnnotationsFromfile: no visible global function definition for
‘read.table’
GenomicRegions2dataframe: no visible global function definition for
‘slot’
GenomicRegionsFromdataframe: no visible global function definition for
‘new’
GenomicRegionsFromfile: no visible global function definition for
‘read.table’
MergeStatisticAnnotations2DataForPREDA: no visible global function
definition for ‘slot’
MergeStatisticAnnotations2DataForPREDA: no visible global function
definition for ‘new’
PREDA_main: no visible global function definition for ‘slot’
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 ‘txtProgressBar’
PREDA_main: no visible global function definition for
‘setTxtProgressBar’
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 ‘slot’
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
‘txtProgressBar’
PREDA_main_permRows: no visible global function definition for
‘setTxtProgressBar’
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
‘slot’
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
‘txtProgressBar’
PREDA_main_permSamples: no visible global function definition for
‘setTxtProgressBar’
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’
PREDA_splineStat: no visible global function definition for
‘smooth.spline’
PREDA_splineStat: no visible global function definition for ‘predict’
PREDA_splineStatPerm: no visible global function definition for
‘smooth.spline’
PREDA_splineStatPerm: no visible global function definition for
‘predict’
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 ‘new’
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
‘read.table’
RMAwithCDFfilter: no visible global function definition for ‘justRMA’
StatisticsForPREDAFromdataframe: no visible global function definition
for ‘new’
StatisticsForPREDAFromfile: no visible global function definition for
‘read.table’
datasetSignatureFromFlags : <anonymous>: no visible global function
definition for ‘dbinom’
genomePlot_improved: no visible global function definition for
‘rainbow’
genomePlot_improved: no visible global function definition for ‘slot’
genomePlot_improved: no visible global function definition for ‘par’
genomePlot_improved : <anonymous>: no visible global function
definition for ‘lines’
genomePlot_improved : <anonymous>: no visible global function
definition for ‘slot’
genomePlot_improved: no visible global function definition for ‘lines’
genomePlot_improved: no visible global function definition for ‘axis’
genomePlot_improved: no visible global function definition for
‘polygon’
getExpectedSmoothFunction: no visible global function definition for
‘existsFunction’
getExpectedSmoothFunction_runmean : PREDA_runmeanStatPerm_fun: no
visible global function definition for ‘runmean’
getObservedSmoothFunction: no visible global function definition for
‘existsFunction’
getObservedSmoothFunction_runmean : PREDA_runmeanStat_fun: no visible
global function definition for ‘runmean’
getPermutationMatrix: no visible global function definition for ‘combn’
getStardadizeFunction : my_standardize: no visible global function
definition for ‘sd’
getStardadizeFunction : my_standardize: no visible global function
definition for ‘median’
DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA: no visible global
function definition for ‘new’
DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA: no visible global
function definition for ‘slot’
DataForPREDA2StatisticsForPREDA,DataForPREDA: no visible global
function definition for ‘new’
DataForPREDA2StatisticsForPREDA,DataForPREDA: no visible global
function definition for ‘slot’
DataForPREDAAddEffect_single,DataForPREDA: no visible global function
definition for ‘slot’
DataForPREDAAddEffect_single,DataForPREDA: no visible global function
definition for ‘runif’
DataForPREDAAddEffect_single,DataForPREDA: no visible global function
definition for ‘slot<-’
DataForPREDAAddEffects,DataForPREDA-GenomicRegions: no visible global
function definition for ‘slot’
DataForPREDAMedianCenter,DataForPREDA: no visible global function
definition for ‘slot’
DataForPREDAMedianCenter,DataForPREDA: no visible binding for global
variable ‘median’
DataForPREDAMedianCenter,DataForPREDA: no visible global function
definition for ‘slot<-’
DataForPREDARandomShuffle,DataForPREDA: no visible global function
definition for ‘slot’
DataForPREDARandomShuffle,DataForPREDA: no visible global function
definition for ‘slot<-’
DataForPREDASimulationGetExpectedFlags,DataForPREDA-GenomicRegions: no
visible global function definition for ‘slot’
GE_computeStatistic,ExpressionSet: no visible global function
definition for ‘pData’
GE_computeStatistic,ExpressionSet: no visible global function
definition for ‘sampleNames’
GE_computeStatistic,ExpressionSet: no visible global function
definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet: no visible global
function definition for ‘pData’
GE_simulations_samplingColumns,ExpressionSet: no visible global
function definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet: no visible global
function definition for ‘exprs<-’
GE_standardize,ExpressionSet: no visible global function definition for
‘exprs’
GE_standardize,ExpressionSet: no visible global function definition for
‘exprs<-’
GE_standardize,StatisticsForPREDA: no visible global function
definition for ‘slot’
GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations: no
visible global function definition for ‘new’
GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations: no
visible global function definition for ‘slot’
GenomicAnnotations2dataframe,GenomicAnnotations: no visible global
function definition for ‘slot’
GenomicAnnotations2dataframe,GenomicAnnotationsForPREDA: no visible
global function definition for ‘slot’
GenomicAnnotations2reference_positions,GenomicAnnotations: no visible
global function definition for ‘slot’
GenomicAnnotationsExtract,GenomicAnnotations: no visible global
function definition for ‘slot’
GenomicAnnotationsFilter_neg,GenomicAnnotations: no visible global
function definition for ‘slot’
GenomicAnnotationsFilter_neg,GenomicAnnotationsForPREDA: no visible
global function definition for ‘slot’
GenomicAnnotationsFilter_pos,DataForPREDA: no visible global function
definition for ‘slot’
GenomicAnnotationsFilter_pos,GenomicAnnotations: no visible global
function definition for ‘slot’
GenomicAnnotationsFilter_pos,GenomicAnnotationsForPREDA: no visible
global function definition for ‘slot’
GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotationsForPREDA:
no visible global function definition for ‘new’
GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotationsForPREDA:
no visible global function definition for ‘slot’
GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA: no
visible global function definition for ‘new’
GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA: no
visible global function definition for ‘slot’
GenomicAnnotationsForPREDAGetExpectedFlags,GenomicAnnotationsForPREDA:
no visible global function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,GenomicAnnotations: no visible global
function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,GenomicAnnotationsForPREDA: no visible
global function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults: no visible global
function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults: no visible global
function definition for ‘new’
GenomicAnnotationsSortAndCleanNA,PREDAResults: no visible global
function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,PREDAResults: no visible global
function definition for ‘new’
GenomicRegionsAnnotate,GenomicRegions-GenomicAnnotations: no visible
global function definition for ‘slot’
GenomicRegionsAnnotate,GenomicRegions-GenomicAnnotations: no visible
global function definition for ‘new’
GenomicRegionsChrNumber,GenomicRegions: no visible global function
definition for ‘slot’
GenomicRegionsCreateRegionsIds,GenomicRegions: no visible global
function definition for ‘slot’
GenomicRegionsFilter_neg,GenomicRegions: no visible global function
definition for ‘slot’
GenomicRegionsFilter_pos,GenomicRegions: no visible global function
definition for ‘slot’
GenomicRegionsNumber,GenomicRegions: no visible global function
definition for ‘slot’
GenomicRegionsSpan,GenomicRegions: no visible global function
definition for ‘slot’
PREDADataAndResults2dataframe,PREDADataAndResults: no visible global
function definition for ‘slot’
PREDAResults2GenomicRegions,PREDAResults: no visible global function
definition for ‘slot’
PREDAResults2GenomicRegionsSingle,PREDAResults: no visible global
function definition for ‘slot’
PREDAResults2PREDADataAndResults,PREDAResults: no visible global
function definition for ‘slot’
PREDAResults2PREDADataAndResults,PREDAResults: no visible global
function definition for ‘new’
PREDAResults2dataframe,PREDAResults: no visible global function
definition for ‘slot’
PREDAResultsGetObservedFlags,PREDAResults: no visible global function
definition for ‘slot’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
definition for ‘pData’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
definition for ‘sampleNames’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
definition for ‘featureNames’
StatisticsForPREDA2dataframe,StatisticsForPREDA: no visible global
function definition for ‘slot’
StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA: no visible
global function definition for ‘slot’
StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA: no visible
global function definition for ‘new’
StatisticsForPREDAFilterColumns_pos,DataForPREDA: no visible global
function definition for ‘slot’
StatisticsForPREDAFilterColumns_pos,StatisticsForPREDA: no visible
global function definition for ‘slot’
analysesNames,PREDAResults: no visible global function definition for
‘slot’
analysesNames,StatisticsForPREDA: no visible global function definition
for ‘slot’
compareFunctionFromStatisticsForPREDA,StatisticsForPREDA: no visible
global function definition for ‘slot’
computeDatasetSignature,GenomicAnnotationsForPREDA: no visible global
function definition for ‘slot’
computeDatasetSignature,GenomicAnnotationsForPREDA: no visible global
function definition for ‘new’
eset2GenomicAnnotations,ExpressionSet: no visible global function
definition for ‘featureNames’
eset2GenomicAnnotations,ExpressionSet: no visible global function
definition for ‘annotation’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
definition for ‘slot’
genomePlot,GenomicAnnotationsForPREDA : <anonymous>: no visible global
function definition for ‘slot’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
definition for ‘rainbow’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
definition for ‘par’
genomePlot,GenomicAnnotationsForPREDA : <anonymous>: no visible global
function definition for ‘lines’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
definition for ‘lines’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
definition for ‘axis’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
definition for ‘polygon’
getStatisticByName,StatisticsForPREDA: no visible global function
definition for ‘slot’
initialize,DataForPREDA: no visible global function definition for
‘new’
initialize,DataForPREDA: no visible global function definition for
‘slot’
initialize,GenomicAnnotationsForPREDA: no visible global function
definition for ‘new’
initialize,GenomicAnnotationsForPREDA: no visible global function
definition for ‘slot’
initialize,PREDADataAndResults: no visible global function definition
for ‘new’
initialize,PREDADataAndResults: no visible global function definition
for ‘slot’
initialize,PREDAResults: no visible global function definition for
‘new’
initialize,PREDAResults: no visible global function definition for
‘slot’
statisticsForPREDAfromEset,ExpressionSet: no visible global function
definition for ‘pData’
statisticsForPREDAfromEset,ExpressionSet: no visible global function
definition for ‘sampleNames’
statisticsForPREDAfromEset,ExpressionSet: no visible global function
definition for ‘featureNames’
Undefined global functions or variables:
annPkgName annotation annotation<- axis cleancdfname combn
contrasts.fit dbinom eBayes existsFunction exprs exprs<- featureNames
free.sprng init.sprng justRMA keys lines lmFit lokerns lookUp
makeContrasts median model.matrix mpi.any.source mpi.any.tag
mpi.bcast.Robj2slave mpi.bcast.cmd mpi.close.Rslaves mpi.comm.rank
mpi.comm.size mpi.get.sourcetag mpi.isend.Robj mpi.recv.Robj
mpi.remote.exec mpi.send.Robj mpi.spawn.Rslaves mt.rawp2adjp
multiassign new pData par phenoData<- polygon predict quantsmooth
qvalue rainbow read.table rma runif runmean sampleNames sd
setTxtProgressBar slot slot<- smooth.spline t.test topTable
txtProgressBar
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "axis", "lines", "par", "polygon")
importFrom("methods", "existsFunction", "new", "slot", "slot<-")
importFrom("stats", "dbinom", "median", "model.matrix", "predict",
"runif", "sd", "smooth.spline", "t.test")
importFrom("utils", "combn", "read.table", "setTxtProgressBar",
"txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'StatisticsForPREDAFromdataframe':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.14-bioc/meat/PREDA.Rcheck/00check.log’
for details.
PREDA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PREDA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘PREDA’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘PREDAclasses.Rnw’ using ‘latin1’ ‘PREDAtutorial.Rnw’ using ‘latin1’ ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PREDA)
PREDA.Rcheck/PREDA-Ex.timings
| name | user | system | elapsed | |
| DataForPREDA-class | 0.003 | 0.001 | 0.004 | |
| GenomicAnnotations-class | 0.001 | 0.001 | 0.002 | |
| GenomicAnnotations2GenomicAnnotationsForPREDA | 0.000 | 0.001 | 0.000 | |
| GenomicAnnotationsForPREDA-class | 0.001 | 0.001 | 0.002 | |
| GenomicAnnotationsForPREDAFromfile | 0.000 | 0.001 | 0.000 | |
| GenomicAnnotationsFromLibrary | 0.000 | 0.000 | 0.001 | |
| GenomicAnnotationsFromfile | 0.000 | 0.001 | 0.001 | |
| GenomicRegions-class | 0.000 | 0.000 | 0.001 | |
| GenomicRegions2dataframe | 0.000 | 0.001 | 0.000 | |
| GenomicRegionsFindOverlap | 0.001 | 0.000 | 0.001 | |
| PREDADataAndResults-class | 0.001 | 0.001 | 0.003 | |
| PREDAResults-class | 0.001 | 0.001 | 0.002 | |
| PREDAResults2GenomicRegions | 0.001 | 0.000 | 0.000 | |
| PREDA_main | 0 | 0 | 0 | |
| SODEGIRpreprocessingGE | 0.000 | 0.001 | 0.001 | |
| StatisticsForPREDA-class | 0.001 | 0.000 | 0.002 | |
| StatisticsForPREDAFromdataframe | 0.001 | 0.000 | 0.001 | |
| StatisticsForPREDAFromfile | 0 | 0 | 0 | |
| analysesNames | 0.865 | 0.036 | 0.904 | |
| computeDatasetSignature | 0.000 | 0.001 | 0.001 | |
| eset2GenomicAnnotations | 0 | 0 | 0 | |
| genomePlot | 0 | 0 | 0 | |
| preprocessingGE | 0.001 | 0.001 | 0.001 | |
| statisticsForPREDAfromEset | 0 | 0 | 0 | |