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 3.4.2 (2017-09-28)
* 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 13.232  0.103  13.600
SpatProtVis-class       6.323  0.171   6.586
rfClassification        5.668  0.204   5.969
ClustDist-class         5.507  0.201  13.851
svmClassification       5.439  0.067   5.606
nnetClassification      5.333  0.032   5.504
ksvmClassification      4.884  0.048   5.026
addGoAnnotations        3.455  0.148   8.820
ClustDistList-class     3.405  0.143   8.187
clustDist               3.329  0.139   8.099
AnnotationParams-class  0.541  0.022  56.707
* 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	0.541	0.022	56.707
ClustDist-class	5.507	0.201	13.851
ClustDistList-class	3.405	0.143	8.187
GenRegRes-class	0.002	0.000	0.002
QSep-class	0.750	0.049	0.818
SpatProtVis-class	6.323	0.171	6.586
addGoAnnotations	3.455	0.148	8.820
addMarkers	0.115	0.004	0.122
checkFeatureNamesOverlap	0.401	0.018	0.433
checkFvarOverlap	0.036	0.004	0.041
chi2-methods	0.005	0.001	0.006
classWeights	0.117	0.012	0.134
clustDist	3.329	0.139	8.099
empPvalues	0.085	0.002	0.089
exprsToRatios-methods	0.169	0.007	0.180
fDataToUnknown	0.042	0.005	0.048
filterBinMSnSet	0.164	0.002	0.169
filterZeroCols	0.115	0.012	0.132
getGOFromFeatures	0.044	0.009	0.446
getMarkerClasses	0.028	0.004	0.031
getMarkers	0.043	0.005	0.048
getPredictions	0.411	0.006	0.419
getStockcol	0.043	0.006	0.050
goIdToTerm	2.436	0.094	2.605
highlightOnPlot	0.578	0.026	0.637
knnClassification	1.754	0.016	1.811
knntlClassification	0.001	0.000	0.001
ksvmClassification	4.884	0.048	5.026
makeGoSet	0.746	0.011	1.136
markerMSnSet	0.244	0.005	0.255
markers	0.044	0.004	0.049
minMarkers	0.042	0.004	0.045
move2Ds	2.064	0.043	2.163
mrkConsProfiles	0.162	0.006	0.173
mrkHClust	0.184	0.004	0.195
nbClassification	2.958	0.020	3.057
nndist-methods	0.177	0.007	0.188
nnetClassification	5.333	0.032	5.504
orgQuants	0.518	0.006	0.539
pRolocmarkers	0.039	0.001	0.043
perTurboClassification	13.232	0.103	13.600
phenoDisco	0.001	0.000	0.001
plot2D	1.809	0.062	1.911
plot2Ds	0.363	0.028	0.400
plotDist	0.130	0.004	0.140
plsdaClassification	0.000	0.001	0.000
rfClassification	5.668	0.204	5.969
sampleMSnSet	0.066	0.003	0.070
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	5.439	0.067	5.606
testMSnSet	0.356	0.007	0.369
testMarkers	0.026	0.005	0.033
thetas	0.057	0.004	0.062
zerosInBinMSnSet	1.975	0.101	2.122

BioC 3.5: CHECK report for pRoloc on veracruz2

Summary

Command output