BioC 3.3: CHECK report for pRoloc on oaxaca

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.4’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 18.228  0.049  18.359
SpatProtVis-class       9.166  0.185   9.364
rfClassification        7.666  0.209   7.881
svmClassification       7.348  0.038   7.389
ClustDist-class         6.541  0.203  29.952
nnetClassification      6.302  0.020   6.359
ClustDistList-class     4.466  0.140  10.755
clustDist               4.098  0.152  13.331
addGoAnnotations        4.086  0.150  10.298
makeGoSet               0.937  0.017  13.833
AnnotationParams-class  0.283  0.021   6.848
getGOFromFeatures       0.045  0.008   7.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pRoloc.cpp -o pRoloc.o
clang++ -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 -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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-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: 'rgl_init' failed, running with rgl.useNULL = TRUE
** 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.283	0.021	6.848
ClustDist-class	6.541	0.203	29.952
ClustDistList-class	4.466	0.140	10.755
GenRegRes-class	0.002	0.000	0.003
SpatProtVis-class	9.166	0.185	9.364
addGoAnnotations	4.086	0.150	10.298
addMarkers	0.100	0.005	0.104
checkFeatureNamesOverlap	0.526	0.018	0.559
checkFvarOverlap	0.037	0.004	0.041
chi2-methods	0.007	0.000	0.007
classWeights	0.148	0.013	0.162
clustDist	4.098	0.152	13.331
empPvalues	0.103	0.008	0.112
exprsToRatios-methods	0.197	0.014	0.212
fDataToUnknown	0.056	0.005	0.061
filterBinMSnSet	0.257	0.001	0.258
filterZeroCols	0.149	0.009	0.157
getGOFromFeatures	0.045	0.008	7.285
getMarkerClasses	0.034	0.004	0.039
getMarkers	0.043	0.006	0.048
getPredictions	0.362	0.007	0.370
getStockcol	0.074	0.006	0.080
goIdToTerm	2.708	0.117	2.827
highlightOnPlot	0.174	0.012	0.187
knnClassification	1.722	0.027	1.755
knntlClassification	0.000	0.000	0.001
ksvmClassification	4.413	0.085	4.594
makeGoSet	0.937	0.017	13.833
markerMSnSet	0.339	0.008	0.347
markers	0.041	0.005	0.045
minMarkers	0.039	0.004	0.043
move2Ds	1.826	0.040	1.922
nbClassification	3.546	0.018	3.610
nndist-methods	0.160	0.008	0.196
nnetClassification	6.302	0.020	6.359
orgQuants	0.221	0.005	0.226
pRolocmarkers	0.009	0.001	0.009
perTurboClassification	18.228	0.049	18.359
phenoDisco	0.000	0.000	0.001
plot2D	2.507	0.069	2.582
plot2Ds	0.451	0.034	0.511
plotDist	0.123	0.006	0.129
plsdaClassification	0.001	0.000	0.000
rfClassification	7.666	0.209	7.881
sampleMSnSet	0.107	0.006	0.112
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	7.348	0.038	7.389
testMSnSet	0.579	0.004	0.584
testMarkers	0.039	0.003	0.043
thetas	0.009	0.002	0.011

BioC 3.3: CHECK report for pRoloc on oaxaca

Summary

Command output