BioC 3.2: CHECK report for pRoloc on zin1

Package: pRoloc

Version: 1.10.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.10.3.tar.gz

StartedAt: 2016-04-23 04:02:06 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:08:40 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 394.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pRoloc.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.10.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/pRoloc.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.10.3’
* 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 ... [28s/28s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘pRoloc’
  Warning: replacing previous import ‘ggplot2::alpha’ by ‘kernlab::alpha’ when loading ‘pRoloc’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/pRoloc.Rcheck/00install.out’ for details.
* 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 ... [77s/111s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 15.968  0.012  16.004
SpatProtVis-class       9.953  0.171  10.181
rfClassification        7.141  0.020   7.156
nnetClassification      7.102  0.012   7.109
svmClassification       5.637  0.000   5.633
AnnotationParams-class  0.247  0.005  32.529
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [65s/63s]
 [66s/63s] 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c pRoloc.cpp -o pRoloc.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o pRoloc.so pRoloc.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘pRoloc’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘kernlab::alpha’ when loading ‘pRoloc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘pRoloc’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘kernlab::alpha’ when loading ‘pRoloc’
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.247	0.005	32.529
GenRegRes-class	0.003	0.000	0.003
SpatProtVis-class	9.953	0.171	10.181
addMarkers	0.103	0.000	0.106
checkFeatureNamesOverlap	0.417	0.008	0.430
checkFvarOverlap	0.035	0.000	0.035
chi2-methods	0.009	0.000	0.008
empPvalues	0.161	0.000	0.161
exprsToRatios-methods	0.201	0.000	0.201
filterBinMSnSet	0.288	0.000	0.288
filterZeroCols	0.131	0.008	0.139
getGOFromFeatures	0.054	0.000	0.880
getMarkerClasses	0.038	0.000	0.039
getMarkers	0.039	0.004	0.043
getPredictions	0.249	0.008	0.257
getStockcol	0.062	0.000	0.063
goIdToTerm	2.475	0.012	2.486
highlightOnPlot	0.116	0.000	0.115
knnClassification	1.044	0.004	1.048
knntlClassification	0	0	0
ksvmClassification	4.597	0.040	4.634
makeGoSet	0.345	0.004	0.983
makeNaData	1.129	0.004	1.133
markerMSnSet	0.305	0.000	0.304
markers	0.05	0.00	0.05
minClassScore	0.058	0.000	0.058
minMarkers	0.048	0.000	0.047
move2Ds	1.790	0.008	1.797
nbClassification	3.306	0.004	3.308
nndist-methods	0.213	0.008	0.221
nnetClassification	7.102	0.012	7.109
pRolocmarkers	0.01	0.00	0.01
perTurboClassification	15.968	0.012	16.004
phenoDisco	0.001	0.000	0.001
plot2D	2.583	0.028	2.609
plot2Ds	0.438	0.012	0.449
plotDist	0.107	0.000	0.108
plsdaClassification	0.001	0.000	0.000
rfClassification	7.141	0.020	7.156
sampleMSnSet	0.108	0.000	0.108
showGOEvidenceCodes	0.002	0.000	0.002
svmClassification	5.637	0.000	5.633
testMSnSet	0.478	0.000	0.478
testMarkers	0.042	0.000	0.042
thetas	0.014	0.000	0.014