BioC 3.3: CHECK report for pRoloc on zin2

Package: pRoloc

Version: 1.12.4

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.12.4.tar.gz

StartedAt: 2016-10-13 05:24:14 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:32:16 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 481.9 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.12.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.4’
* 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 ... OK
* 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’
  See the note in ?`:::` about the use of this operator.
* 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 17.603  0.004  17.617
SpatProtVis-class       8.489  0.033   8.524
nnetClassification      8.314  0.000   8.345
svmClassification       7.311  0.000   7.320
rfClassification        7.306  0.004   7.305
ClustDist-class         4.455  0.032  11.105
addGoAnnotations        3.105  0.012   8.912
clustDist               3.069  0.032   9.205
ClustDistList-class     2.976  0.043   8.999
AnnotationParams-class  0.216  0.008   6.180
* 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c pRoloc.cpp -o pRoloc.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o pRoloc.so pRoloc.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.216	0.008	6.180
ClustDist-class	4.455	0.032	11.105
ClustDistList-class	2.976	0.043	8.999
GenRegRes-class	0.002	0.000	0.002
SpatProtVis-class	8.489	0.033	8.524
addGoAnnotations	3.105	0.012	8.912
addMarkers	0.119	0.000	0.121
checkFeatureNamesOverlap	0.398	0.020	0.434
checkFvarOverlap	0.034	0.000	0.034
chi2-methods	0.006	0.000	0.006
classWeights	0.118	0.000	0.118
clustDist	3.069	0.032	9.205
empPvalues	0.094	0.000	0.094
exprsToRatios-methods	0.168	0.000	0.168
fDataToUnknown	0.039	0.000	0.039
filterBinMSnSet	0.222	0.000	0.222
filterZeroCols	0.117	0.000	0.117
getGOFromFeatures	0.040	0.004	0.527
getMarkerClasses	0.034	0.000	0.037
getMarkers	0.038	0.004	0.041
getPredictions	0.318	0.000	0.318
getStockcol	0.063	0.004	0.067
goIdToTerm	2.316	0.004	2.333
highlightOnPlot	0.145	0.000	0.144
knnClassification	1.586	0.003	1.624
knntlClassification	0.000	0.000	0.001
ksvmClassification	4.586	0.004	4.595
makeGoSet	0.327	0.008	0.965
markerMSnSet	0.304	0.000	0.305
markers	0.049	0.000	0.050
minMarkers	0.039	0.000	0.039
move2Ds	1.747	0.012	1.759
nbClassification	3.929	0.004	3.933
nndist-methods	0.216	0.000	0.216
nnetClassification	8.314	0.000	8.345
orgQuants	0.254	0.004	0.257
pRolocmarkers	0.011	0.000	0.012
perTurboClassification	17.603	0.004	17.617
phenoDisco	0.001	0.000	0.000
plot2D	2.232	0.020	2.278
plot2Ds	0.423	0.016	0.438
plotDist	0.111	0.000	0.110
plsdaClassification	0.001	0.000	0.000
rfClassification	7.306	0.004	7.305
sampleMSnSet	0.079	0.004	0.084
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	7.311	0.000	7.320
testMSnSet	0.479	0.000	0.479
testMarkers	0.030	0.000	0.031
thetas	0.005	0.000	0.006