BioC 3.5: CHECK report for pRoloc on oaxaca

Package: pRoloc

Version: 1.15.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.15.6.tar.gz

StartedAt: 2017-03-04 07:20:06 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:29:44 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 577.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pRoloc.Rcheck

Warnings: 2

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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_1.15.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pRoloc.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.15.6’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘pRoloc’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/pRoloc.Rcheck/00install.out’ for details.
* 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)

.plotQSep: no visible global function definition for ‘strwidth’
Undefined global functions or variables:
  strwidth
Consider adding
  importFrom("graphics", "strwidth")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotDist':
plotDist
  Code: function(object, markers, mcol = "steelblue", pcol =
                 getUnknowncol(), alpha = 0.3, type = "b", lty = 1,
                 fractions = sampleNames(object), ylab = "Intensity",
                 xlab = "Fractions", ylim, ...)
  Docs: function(object, markers, mcol = "steelblue", pcol =
                 getUnknowncol(), alpha = 0.3, type = "b", lty = 1,
                 fractions = sampleNames(object), ylim, ...)
  Argument names in code not in docs:
    ylab xlab
  Mismatches in argument names:
    Position: 9 Code: ylab Docs: ylim
    Position: 10 Code: xlab Docs: ...

* 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 18.069  0.047  18.123
rfClassification        8.042  0.227   8.273
svmClassification       8.190  0.029   8.223
SpatProtVis-class       7.869  0.182   8.114
ksvmClassification      7.433  0.084   7.608
nnetClassification      7.168  0.026   7.198
ClustDist-class         6.366  0.221  13.971
addGoAnnotations        5.547  0.176  13.004
ClustDistList-class     4.256  0.169  11.880
clustDist               4.021  0.152  11.323
AnnotationParams-class  0.867  0.024   6.826
* 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: 2 WARNINGs, 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 -I/usr/local/include/freetype2 -I/opt/X11/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-3.5-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’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘pRoloc’
** 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’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘pRoloc’
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.867	0.024	6.826
ClustDist-class	6.366	0.221	13.971
ClustDistList-class	4.256	0.169	11.880
GenRegRes-class	0.002	0.001	0.002
QSep-class	0.880	0.049	0.930
SpatProtVis-class	7.869	0.182	8.114
addGoAnnotations	5.547	0.176	13.004
addMarkers	0.152	0.004	0.156
checkFeatureNamesOverlap	0.560	0.028	0.610
checkFvarOverlap	0.046	0.005	0.051
chi2-methods	0.006	0.000	0.006
classWeights	0.132	0.010	0.142
clustDist	4.021	0.152	11.323
empPvalues	0.119	0.000	0.119
exprsToRatios-methods	0.235	0.008	0.242
fDataToUnknown	0.040	0.004	0.044
filterBinMSnSet	0.217	0.001	0.218
filterZeroCols	0.140	0.014	0.155
getGOFromFeatures	0.061	0.011	0.543
getMarkerClasses	0.028	0.003	0.032
getMarkers	0.047	0.003	0.051
getPredictions	0.620	0.011	0.631
getStockcol	0.061	0.007	0.109
goIdToTerm	3.212	0.117	3.330
highlightOnPlot	0.830	0.034	0.912
knnClassification	2.686	0.013	2.702
knntlClassification	0	0	0
ksvmClassification	7.433	0.084	7.608
makeGoSet	1.713	0.015	2.339
markerMSnSet	0.310	0.006	0.315
markers	0.048	0.005	0.053
minMarkers	0.050	0.005	0.055
move2Ds	2.260	0.048	2.334
mrkHClust	0.241	0.005	0.245
nbClassification	4.212	0.021	4.234
nndist-methods	0.302	0.014	0.317
nnetClassification	7.168	0.026	7.198
orgQuants	0.503	0.005	0.509
pRolocmarkers	0.041	0.001	0.043
perTurboClassification	18.069	0.047	18.123
phenoDisco	0	0	0
plot2D	3.107	0.091	3.227
plot2Ds	0.615	0.039	0.675
plotDist	0.205	0.006	0.212
plsdaClassification	0.000	0.000	0.001
rfClassification	8.042	0.227	8.273
sampleMSnSet	0.100	0.010	0.111
showGOEvidenceCodes	0.001	0.001	0.001
svmClassification	8.190	0.029	8.223
testMSnSet	0.632	0.004	0.635
testMarkers	0.028	0.002	0.031
thetas	0.044	0.003	0.047
zerosInBinMSnSet	2.357	0.105	2.485