BioC 3.5: CHECK report for pRoloc on veracruz2

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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_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pRoloc.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.1’
* 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  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
* 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 17.218  0.043  17.664
rfClassification        7.874  0.225   8.283
svmClassification       7.636  0.042   7.914
SpatProtVis-class       6.653  0.136   6.984
ClustDist-class         6.321  0.225  11.332
nnetClassification      6.236  0.021   6.398
ksvmClassification      5.915  0.032   6.103
ClustDistList-class     4.149  0.164   9.102
clustDist               4.009  0.158   8.887
addGoAnnotations        3.936  0.152  10.489
AnnotationParams-class  0.611  0.022   9.236
* 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-3.5-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.611	0.022	9.236
ClustDist-class	6.321	0.225	11.332
ClustDistList-class	4.149	0.164	9.102
GenRegRes-class	0.002	0.001	0.003
QSep-class	0.802	0.040	0.872
SpatProtVis-class	6.653	0.136	6.984
addGoAnnotations	3.936	0.152	10.489
addMarkers	0.115	0.004	0.123
checkFeatureNamesOverlap	0.481	0.020	0.514
checkFvarOverlap	0.036	0.004	0.042
chi2-methods	0.007	0.000	0.008
classWeights	0.135	0.014	0.150
clustDist	4.009	0.158	8.887
empPvalues	0.121	0.000	0.123
exprsToRatios-methods	0.233	0.015	0.249
fDataToUnknown	0.052	0.008	0.060
filterBinMSnSet	0.203	0.001	0.207
filterZeroCols	0.126	0.013	0.140
getGOFromFeatures	0.057	0.015	0.377
getMarkerClasses	0.033	0.005	0.039
getMarkers	0.058	0.007	0.065
getPredictions	0.496	0.007	0.513
getStockcol	0.050	0.007	0.057
goIdToTerm	2.778	0.121	2.974
highlightOnPlot	0.620	0.024	0.667
knnClassification	2.00	0.02	2.08
knntlClassification	0.001	0.000	0.001
ksvmClassification	5.915	0.032	6.103
makeGoSet	1.041	0.017	1.940
markerMSnSet	0.282	0.006	0.291
markers	0.044	0.006	0.050
minMarkers	0.050	0.007	0.057
move2Ds	2.481	0.048	2.591
mrkConsProfiles	0.217	0.009	0.233
mrkHClust	0.228	0.008	0.239
nbClassification	3.450	0.021	3.576
nndist-methods	0.191	0.009	0.201
nnetClassification	6.236	0.021	6.398
orgQuants	0.561	0.009	0.596
pRolocmarkers	0.029	0.001	0.030
perTurboClassification	17.218	0.043	17.664
phenoDisco	0.001	0.000	0.001
plot2D	2.394	0.057	2.547
plot2Ds	0.553	0.036	0.603
plotDist	0.200	0.006	0.213
plsdaClassification	0	0	0
rfClassification	7.874	0.225	8.283
sampleMSnSet	0.087	0.005	0.093
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	7.636	0.042	7.914
testMSnSet	0.495	0.005	0.506
testMarkers	0.036	0.006	0.042
thetas	0.046	0.002	0.048
zerosInBinMSnSet	2.635	0.116	2.819

BioC 3.5: CHECK report for pRoloc on veracruz2

Summary

Command output