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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pRoloc_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/pRoloc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [56s/59s] 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’
testMarkers: no visible global function definition for ‘fData’
testMSnSet: no visible global function definition for ‘fData’
testMSnSet: 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’
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<-’
MLearn,formula-MSnSet-clusteringSchema-missing: no visible global
function definition for ‘exprs’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [116s/117s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
perTurboClassification 29.036 0.091 29.179
rfClassification 10.295 0.384 10.699
nnetClassification 9.606 0.025 9.664
plot2D 9.187 0.117 9.432
svmClassification 8.802 0.048 8.913
ksvmClassification 8.207 0.082 8.315
nbClassification 5.429 0.029 5.480
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘testthat.R’ [326s/324s]
[326s/325s] 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
‘/Users/biocbuild/bbs-3.0-bioc/meat/pRoloc.Rcheck/00check.log’
for details.
* installing *source* package ‘pRoloc’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -mtune=core2 -g -O2 -Wall -c pRoloc.cpp -o pRoloc.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o pRoloc.so pRoloc.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)