BioC 3.2: CHECK report for pRoloc on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.9.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/pRoloc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.9.6’
* 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/37s] 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 ... [91s/96s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 22.903  0.079  23.108
rfClassification        8.046  0.213   8.268
nnetClassification      7.121  0.018   7.176
svmClassification       6.582  0.040   6.666
ksvmClassification      6.022  0.094   6.131
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [64s/56s]
 [64s/57s] 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
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/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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-3.2-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	1.359	0.013	3.379
GenRegRes-class	0.004	0.000	0.004
addMarkers	0.306	0.006	0.312
checkFeatureNamesOverlap	1.279	0.014	1.319
checkFvarOverlap	0.051	0.004	0.059
chi2-methods	0.010	0.001	0.011
empPvalues	0.186	0.010	0.197
exprsToRatios-methods	0.270	0.023	0.294
filterBinMSnSet	0.350	0.001	0.351
filterZeroCols	0.156	0.006	0.162
getGOFromFeatures	0.065	0.005	1.277
getMarkerClasses	0.049	0.004	0.053
getMarkers	0.055	0.005	0.059
getPredictions	0.693	0.011	0.714
getStockcol	0.090	0.007	0.097
goIdToTerm	3.584	0.184	3.801
highlightOnPlot	0.168	0.010	0.180
knnClassification	1.452	0.013	1.470
knntlClassification	0.000	0.000	0.001
ksvmClassification	6.022	0.094	6.131
makeGoSet	0.554	0.007	2.212
makeNaData	1.593	0.005	1.599
markerMSnSet	0.502	0.004	0.507
markers	0.073	0.004	0.078
minClassScore	0.088	0.005	0.093
minMarkers	0.079	0.005	0.083
move2Ds	2.518	0.049	2.594
nbClassification	4.776	0.015	4.806
nndist-methods	0.301	0.005	0.317
nnetClassification	7.121	0.018	7.176
pRolocmarkers	0.014	0.001	0.016
perTurboClassification	22.903	0.079	23.108
phenoDisco	0.001	0.000	0.001
plot2D	3.016	0.081	3.101
plot2Ds	0.557	0.047	0.607
plotDist	0.151	0.011	0.163
plsdaClassification	0.001	0.000	0.001
rfClassification	8.046	0.213	8.268
sampleMSnSet	0.115	0.005	0.120
showGOEvidenceCodes	0.001	0.001	0.002
svmClassification	6.582	0.040	6.666
testMSnSet	0.565	0.007	0.572
testMarkers	0.045	0.008	0.053
thetas	0.016	0.003	0.019

BioC 3.2: CHECK report for pRoloc on oaxaca

Summary

Command output