BioC 3.2: CHECK report for pRoloc on perceval

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/pRoloc.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.10.0’
* 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 ... [36s/36s] 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
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
Found the following possibly unsafe calls:
File ‘pRoloc/R/annotation.R’:
  unlockBinding("params", .pRolocEnv)
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'pRoloc2'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [104s/110s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 21.888  0.041  21.932
SpatProtVis-class      12.152  0.240  12.414
nnetClassification      9.483  0.019   9.504
rfClassification        9.204  0.285   9.490
svmClassification       7.130  0.056   7.188
ksvmClassification      5.554  0.055   5.610
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [113s/85s]
 [113s/85s] 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
  ‘/Users/biocbuild/bbs-3.2-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/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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-3.2-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.286	0.016	2.337
GenRegRes-class	0.004	0.000	0.004
SpatProtVis-class	12.152	0.240	12.414
addMarkers	0.173	0.010	0.183
checkFeatureNamesOverlap	0.589	0.046	0.650
checkFvarOverlap	0.077	0.007	0.083
chi2-methods	0.011	0.001	0.012
empPvalues	0.225	0.001	0.227
exprsToRatios-methods	0.304	0.011	0.315
filterBinMSnSet	0.353	0.001	0.355
filterZeroCols	0.193	0.009	0.202
getGOFromFeatures	0.100	0.009	1.824
getMarkerClasses	0.082	0.007	0.089
getMarkers	0.079	0.005	0.085
getPredictions	0.346	0.007	0.354
getStockcol	0.115	0.011	0.127
goIdToTerm	3.714	0.219	3.933
highlightOnPlot	0.169	0.013	0.185
knnClassification	1.393	0.019	1.413
knntlClassification	0	0	0
ksvmClassification	5.554	0.055	5.610
makeGoSet	0.445	0.009	2.373
makeNaData	1.628	0.008	1.636
markerMSnSet	0.443	0.006	0.448
markers	0.088	0.005	0.093
minClassScore	0.108	0.006	0.114
minMarkers	0.087	0.006	0.093
move2Ds	2.354	0.056	2.447
nbClassification	4.693	0.012	4.708
nndist-methods	0.290	0.014	0.304
nnetClassification	9.483	0.019	9.504
pRolocmarkers	0.012	0.001	0.013
perTurboClassification	21.888	0.041	21.932
phenoDisco	0.001	0.000	0.001
plot2D	3.250	0.087	3.340
plot2Ds	0.595	0.044	0.643
plotDist	0.185	0.010	0.196
plsdaClassification	0.001	0.001	0.001
rfClassification	9.204	0.285	9.490
sampleMSnSet	0.152	0.006	0.158
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	7.130	0.056	7.188
testMSnSet	0.632	0.005	0.637
testMarkers	0.069	0.003	0.072
thetas	0.015	0.004	0.018

BioC 3.2: CHECK report for pRoloc on perceval

Summary

Command output