pRoloc 1.6.2
Laurent Gatto
| 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/pRoloc | | Last Changed Rev: 100962 / Revision: 102249 | | Last Changed Date: 2015-03-21 00:48:21 -0700 (Sat, 21 Mar 2015) |
| 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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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.6.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/pRoloc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pRoloc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRoloc’ version ‘1.6.2’
* 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 ‘pRoloc’ can be installed ... [37s/40s] 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 ‘synapter’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’
‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.isbig: no visible global function definition for ‘fData’
addLegend: no visible global function definition for ‘fData’
addLegend: no visible global function definition for ‘fData<-’
addLegend: no visible global function definition for ‘fvarLabels’
addLegend_v1: no visible global function definition for ‘fvarLabels’
addLegend_v1: no visible global function definition for ‘fData’
addMarkers: no visible global function definition for ‘fvarLabels’
addMarkers: no visible global function definition for ‘featureNames’
addMarkers: no visible global function definition for ‘fData’
addMarkers: no visible global function definition for ‘fData<-’
anyUnknown: no visible global function definition for ‘fData’
diffscores: no visible global function definition for ‘fvarLabels’
diffscores: no visible global function definition for ‘fData’
difftorand: no visible global function definition for ‘fvarLabels’
difftorand: no visible global function definition for ‘fData’
getMarkers: no visible global function definition for ‘fData’
getMarkers: no visible global function definition for ‘featureNames’
getPredictions: no visible global function definition for ‘fData’
highlightOnPlot: no visible global function definition for
‘featureNames’
knnClassification: no visible global function definition for ‘fData’
knnClassification: no visible global function definition for ‘knnI’
knnClassification: no visible global function definition for ‘fData<-’
knnClassification: no visible global function definition for
‘predictions’
knnClassification: no visible global function definition for
‘predScores’
ksvmClassification: no visible global function definition for ‘fData’
ksvmClassification: no visible binding for global variable ‘ksvmI’
ksvmClassification: no visible global function definition for ‘fData<-’
ksvmClassification: no visible global function definition for
‘predictions’
ksvmClassification: no visible global function definition for
‘predScores’
lopims: no visible global function definition for ‘fvarLabels’
lopims1: no visible global function definition for ‘estimateMasterFdr’
lopims1: no visible global function definition for ‘makeMaster’
lopims1: no visible global function definition for ‘bestComb’
lopims2 : <anonymous>: no visible global function definition for
‘synergise’
lopims3 : <anonymous>: no visible global function definition for
‘sampleNames<-’
lopims4: no visible global function definition for ‘exprs’
lopims4: no visible global function definition for ‘fData’
lopims4: no visible global function definition for ‘exprs<-’
lopims4: no visible global function definition for ‘sampleNames<-’
lopims4: no visible global function definition for ‘sampleNames’
makeNaData: no visible global function definition for ‘featureNames’
makeNaData: no visible global function definition for ‘fData’
makeNaData: no visible global function definition for ‘fData<-’
makeNaData: no visible global function definition for ‘exprs’
makeNaData: no visible global function definition for ‘exprs<-’
makeNaData2: no visible global function definition for ‘featureNames’
makeNaData2: no visible global function definition for ‘fData’
makeNaData2: no visible global function definition for ‘fData<-’
makeNaData2: no visible global function definition for ‘exprs’
makeNaData2: no visible global function definition for ‘exprs<-’
markerMSnSet: no visible global function definition for ‘fData’
markerMSnSet: no visible global function definition for ‘fData<-’
minClassScore: no visible global function definition for ‘fData’
minClassScore: no visible global function definition for ‘fData<-’
minMarkers: no visible global function definition for ‘fData’
minMarkers: no visible global function definition for ‘fData<-’
nbClassification: no visible global function definition for ‘fData’
nbClassification: no visible binding for global variable ‘naiveBayesI’
nbClassification: no visible global function definition for ‘fData<-’
nbClassification: no visible global function definition for
‘predictions’
nbClassification: no visible global function definition for
‘predScores’
nndist_msnset: no visible global function definition for ‘exprs’
nndist_msnset: no visible global function definition for ‘fData<-’
nndist_msnset: no visible global function definition for ‘fData’
nnetClassification: no visible global function definition for ‘fData’
nnetClassification: no visible binding for global variable ‘nnetI’
nnetClassification: no visible global function definition for ‘fData<-’
nnetClassification: no visible global function definition for
‘predictions’
nnetClassification: no visible global function definition for
‘predScores’
perTurboClassification: no visible global function definition for
‘fData’
perTurboClassification: no visible global function definition for
‘fData<-’
phenoDisco: no visible global function definition for ‘fvarLabels’
phenoDisco: no visible global function definition for ‘exprs’
phenoDisco: no visible global function definition for ‘fData’
phenoDisco: no visible global function definition for ‘fData<-’
phenoDisco: no visible global function definition for ‘featureNames’
phenoDisco : <anonymous>: no visible global function definition for
‘exprs’
plot2D: no visible global function definition for ‘fvarLabels’
plot2D: no visible global function definition for ‘exprs’
plot2D: no visible global function definition for ‘fData’
plot2D: no visible global function definition for ‘fData<-’
plot2D_v1: no visible global function definition for ‘fvarLabels’
plot2D_v1: no visible global function definition for ‘exprs’
plot2D_v1: no visible global function definition for ‘fData’
plotDist: no visible global function definition for ‘exprs’
plotDist: no visible global function definition for ‘pData’
plsdaClassification: no visible global function definition for ‘fData’
plsdaClassification: no visible binding for global variable ‘plsdaI’
plsdaClassification: no visible global function definition for
‘fData<-’
plsdaClassification: no visible global function definition for
‘predictions’
plsdaClassification: no visible global function definition for
‘predScores’
rfClassification: no visible global function definition for ‘fData’
rfClassification: no visible binding for global variable
‘randomForestI’
rfClassification: no visible global function definition for ‘fData<-’
rfClassification: no visible global function definition for
‘predictions’
rfClassification: no visible global function definition for
‘predScores’
sampleMSnSet: no visible global function definition for ‘sampleNames’
sampleMSnSet: no visible global function definition for ‘exprs’
sampleMSnSet: no visible global function definition for ‘fData’
subsetAsDataFrame: no visible global function definition for
‘sampleNames’
subsetAsDataFrame: no visible global function definition for ‘exprs’
subsetAsDataFrame: no visible global function definition for ‘fData’
svmClassification: no visible global function definition for ‘fData’
svmClassification: no visible binding for global variable ‘svmI’
svmClassification: no visible global function definition for ‘fData<-’
svmClassification: no visible global function definition for
‘predictions’
svmClassification: no visible global function definition for
‘predScores’
testMSnSet: no visible global function definition for ‘fData’
testMSnSet: no visible global function definition for ‘fData<-’
testMarkers: no visible global function definition for ‘fData’
tracking: no visible global function definition for ‘fData’
tracking: no visible global function definition for ‘exprs’
tracking : <anonymous>: no visible global function definition for
‘fData’
unknownMSnSet: no visible global function definition for ‘fData’
unknownMSnSet: no visible global function definition for ‘fData<-’
updateobject: no visible global function definition for ‘fData’
updateobject : <anonymous> : <anonymous>: no visible global function
definition for ‘featureNames’
updateobject: no visible global function definition for ‘fData<-’
viction: no visible global function definition for ‘fvarLabels’
viction: no visible global function definition for ‘fData’
whichNA: no visible global function definition for ‘exprs’
MLearn,formula-MSnSet-clusteringSchema-missing: no visible global
function definition for ‘exprs’
kmeansClustering,MSnSet-missing: no visible global function definition
for ‘exprs’
kmeansClustering,MSnSet-missing: no visible global function definition
for ‘fData’
kmeansClustering,MSnSet-missing: no visible global function definition
for ‘fData<-’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/89s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
perTurboClassification 21.753 0.012 22.355
rfClassification 8.684 0.032 10.902
nnetClassification 7.793 0.000 7.847
svmClassification 7.353 0.000 7.380
ksvmClassification 5.504 0.008 5.556
nbClassification 4.996 0.016 5.029
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘testthat.R’ [258s/265s]
[259s/265s] 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
‘/home/biocbuild/bbs-3.0-bioc/meat/pRoloc.Rcheck/00check.log’
for details.
* installing *source* package ‘pRoloc’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c pRoloc.cpp -o pRoloc.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o pRoloc.so pRoloc.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pRoloc)