BioC 3.4: CHECK report for pRoloc on morelia

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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_1.14.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/pRoloc.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.6’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
* 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’
  ‘caret:::predict.plsda’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘checkSortedFeatureNames’ ‘opt’
* 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 20.653  0.041  20.708
SpatProtVis-class       8.124  0.171   8.306
svmClassification       7.595  0.035   7.635
rfClassification        7.087  0.191   7.365
nnetClassification      6.852  0.019   6.926
ClustDist-class         5.890  0.219  13.241
ksvmClassification      5.115  0.080   5.202
clustDist               4.872  0.174  12.950
addGoAnnotations        4.628  0.179  13.237
ClustDistList-class     4.402  0.146  11.559
AnnotationParams-class  0.688  0.026   7.531
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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-3.4-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.688	0.026	7.531
ClustDist-class	5.890	0.219	13.241
ClustDistList-class	4.402	0.146	11.559
GenRegRes-class	0.003	0.000	0.004
QSep-class	1.195	0.047	1.245
SpatProtVis-class	8.124	0.171	8.306
addGoAnnotations	4.628	0.179	13.237
addMarkers	0.145	0.014	0.160
checkFeatureNamesOverlap	0.531	0.023	0.657
checkFvarOverlap	0.033	0.008	0.042
chi2-methods	0.007	0.001	0.007
classWeights	0.155	0.027	0.183
clustDist	4.872	0.174	12.950
empPvalues	0.537	0.017	0.557
exprsToRatios-methods	0.238	0.006	0.245
fDataToUnknown	0.053	0.005	0.058
filterBinMSnSet	0.300	0.009	0.309
filterZeroCols	0.158	0.019	0.176
getGOFromFeatures	0.058	0.010	0.521
getMarkerClasses	0.042	0.006	0.049
getMarkers	0.046	0.007	0.054
getPredictions	0.427	0.022	0.450
getStockcol	0.083	0.009	0.092
goIdToTerm	3.320	0.133	3.456
highlightOnPlot	0.355	0.041	0.435
knnClassification	1.962	0.011	2.017
knntlClassification	0.001	0.000	0.001
ksvmClassification	5.115	0.080	5.202
makeGoSet	1.080	0.017	1.859
markerMSnSet	0.358	0.007	0.364
markers	0.052	0.006	0.058
minMarkers	0.045	0.005	0.051
move2Ds	2.095	0.049	2.211
mrkHClust	0.333	0.007	0.341
nbClassification	4.215	0.030	4.314
nndist-methods	0.167	0.006	0.174
nnetClassification	6.852	0.019	6.926
orgQuants	0.296	0.009	0.305
pRolocmarkers	0.008	0.001	0.010
perTurboClassification	20.653	0.041	20.708
phenoDisco	0.000	0.000	0.001
plot2D	2.486	0.099	2.591
plot2Ds	0.444	0.036	0.482
plotDist	0.192	0.007	0.199
plsdaClassification	0.001	0.000	0.001
rfClassification	7.087	0.191	7.365
sampleMSnSet	0.076	0.003	0.080
showGOEvidenceCodes	0	0	0
svmClassification	7.595	0.035	7.635
testMSnSet	0.565	0.006	0.571
testMarkers	0.038	0.004	0.042
thetas	0.008	0.002	0.011
zerosInBinMSnSet	2.934	0.107	3.064

BioC 3.4: CHECK report for pRoloc on morelia

Summary

Command output