Francesco Ferrari
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/PREDA |
| git_branch: devel |
| git_last_commit: 431f3f6 |
| git_last_commit_date: 2024-10-29 09:37:56 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 | ||||
| Package 1576/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PREDA 1.53.0 (landing page) Francesco Ferrari
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the PREDA package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: PREDA |
| Version: 1.53.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PREDA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PREDA_1.53.0.tar.gz |
| StartedAt: 2024-11-28 03:36:28 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 03:38:36 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 128.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PREDA.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PREDA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PREDA_1.53.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/PREDA.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PREDA/DESCRIPTION' ... OK
* this is package 'PREDA' version '1.53.0'
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 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 code 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
SODEGIR_GEstatistics.Rd: ExpressionSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'StatisticsForPREDAFromdataframe.Rd':
'...'
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 ... NOTE
Argument items with no description in Rd file 'DataForPREDAMedianCenter.Rd':
'\dots'
Argument items with no description in Rd file 'GenomicRegionsCreateRegionsIds.Rd':
'\dots'
Argument items with no description in Rd file 'GenomicRegionsSpan.Rd':
'\dots'
Argument items with no description in Rd file 'GenomicRegionsTotalSpan.Rd':
'\dots'
* 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 ... 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
'E:/biocbuild/bbs-3.21-bioc/meat/PREDA.Rcheck/00check.log'
for details.
PREDA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL PREDA ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 ** 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 | 0 | 0 | |
| GenomicAnnotations-class | 0 | 0 | 0 | |
| GenomicAnnotations2GenomicAnnotationsForPREDA | 0 | 0 | 0 | |
| GenomicAnnotationsForPREDA-class | 0 | 0 | 0 | |
| GenomicAnnotationsForPREDAFromfile | 0 | 0 | 0 | |
| GenomicAnnotationsFromLibrary | 0 | 0 | 0 | |
| GenomicAnnotationsFromfile | 0 | 0 | 0 | |
| GenomicRegions-class | 0 | 0 | 0 | |
| GenomicRegions2dataframe | 0 | 0 | 0 | |
| GenomicRegionsFindOverlap | 0 | 0 | 0 | |
| PREDADataAndResults-class | 0 | 0 | 0 | |
| PREDAResults-class | 0 | 0 | 0 | |
| PREDAResults2GenomicRegions | 0 | 0 | 0 | |
| PREDA_main | 0 | 0 | 0 | |
| SODEGIRpreprocessingGE | 0 | 0 | 0 | |
| StatisticsForPREDA-class | 0 | 0 | 0 | |
| StatisticsForPREDAFromdataframe | 0 | 0 | 0 | |
| StatisticsForPREDAFromfile | 0 | 0 | 0 | |
| analysesNames | 0.61 | 0.03 | 0.68 | |
| computeDatasetSignature | 0 | 0 | 0 | |
| eset2GenomicAnnotations | 0 | 0 | 0 | |
| genomePlot | 0 | 0 | 0 | |
| preprocessingGE | 0 | 0 | 0 | |
| statisticsForPREDAfromEset | 0 | 0 | 0 | |