BioC 3.6: CHECK report for pRoloc on veracruz1

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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_1.17.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.17.3’
* 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 13.8Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 17.626  0.034  18.237
SpatProtVis-class       7.192  0.108   7.499
svmClassification       6.628  0.033   6.864
rfClassification        6.391  0.184   6.742
ClustDist-class         6.147  0.201  11.305
nnetClassification      6.151  0.017   6.338
ksvmClassification      5.995  0.042   6.210
ClustDistList-class     4.305  0.179   9.280
addGoAnnotations        4.301  0.149   9.715
clustDist               3.963  0.140   8.762
AnnotationParams-class  0.596  0.021   7.449
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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-3.6-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	0.596	0.021	7.449
ClustDist-class	6.147	0.201	11.305
ClustDistList-class	4.305	0.179	9.280
GenRegRes-class	0.003	0.000	0.003
QSep-class	0.771	0.038	0.818
SpatProtVis-class	7.192	0.108	7.499
addGoAnnotations	4.301	0.149	9.715
addMarkers	0.139	0.004	0.146
checkFeatureNamesOverlap	0.419	0.021	0.453
checkFvarOverlap	0.039	0.004	0.044
chi2-methods	0.007	0.001	0.007
classWeights	0.109	0.008	0.120
clustDist	3.963	0.140	8.762
empPvalues	0.110	0.000	0.115
exprsToRatios-methods	0.201	0.006	0.209
fDataToUnknown	0.047	0.003	0.051
filterBinMSnSet	0.226	0.001	0.239
filterZeroCols	0.134	0.014	0.149
getGOFromFeatures	0.059	0.010	0.371
getMarkerClasses	0.037	0.003	0.041
getMarkers	0.070	0.005	0.076
getPredictions	0.581	0.008	0.610
getStockcol	0.054	0.006	0.062
goIdToTerm	2.736	0.106	2.928
highlightOnPlot	0.765	0.028	0.840
knnClassification	2.118	0.008	2.183
knntlClassification	0.000	0.001	0.000
ksvmClassification	5.995	0.042	6.210
makeGoSet	1.016	0.012	1.902
markerMSnSet	0.256	0.005	0.262
markers	0.046	0.005	0.055
minMarkers	0.037	0.003	0.040
move2Ds	2.007	0.039	2.104
mrkConsProfiles	0.207	0.005	0.217
mrkHClust	0.259	0.003	0.272
nbClassification	3.828	0.014	3.945
nndist-methods	0.223	0.008	0.236
nnetClassification	6.151	0.017	6.338
orgQuants	0.529	0.005	0.545
pRolocmarkers	0.027	0.001	0.029
perTurboClassification	17.626	0.034	18.237
phenoDisco	0.001	0.000	0.001
plot2D	3.298	0.063	3.482
plot2Ds	0.504	0.039	0.558
plotDist	0.136	0.007	0.147
plsdaClassification	0.001	0.000	0.001
rfClassification	6.391	0.184	6.742
sampleMSnSet	0.088	0.004	0.094
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	6.628	0.033	6.864
testMSnSet	0.509	0.004	0.529
testMarkers	0.035	0.005	0.039
thetas	0.062	0.002	0.064
zerosInBinMSnSet	2.215	0.094	2.356

BioC 3.6: CHECK report for pRoloc on veracruz1

Summary

Command output