BioC 3.1: CHECK report for pRoloc on zin2

Package: pRoloc

Version: 1.8.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.8.0.tar.gz

StartedAt: 2015-10-09 04:26:09 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:31:28 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 319.0 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.8.0’
* 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 ... [26s/26s] 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 ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'pRoloc2'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* 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 ... [66s/71s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 15.553  0.009  15.554
rfClassification        7.492  0.004   7.515
nnetClassification      7.181  0.000   7.190
svmClassification       5.747  0.004   5.755
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [48s/46s]
 [49s/46s] 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c pRoloc.cpp -o pRoloc.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o pRoloc.so pRoloc.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.234	0.004	2.275
GenRegRes-class	0.003	0.000	0.003
addMarkers	0.190	0.004	0.199
checkFeatureNamesOverlap	1.083	0.004	1.106
checkFvarOverlap	0.031	0.004	0.037
chi2-methods	0.008	0.000	0.008
empPvalues	0.145	0.000	0.145
exprsToRatios-methods	0.189	0.040	0.229
filterBinMSnSet	0.288	0.000	0.289
filterZeroCols	0.125	0.004	0.130
getGOFromFeatures	0.045	0.012	1.149
getMarkerClasses	0.030	0.000	0.031
getMarkers	0.025	0.004	0.029
getPredictions	0.596	0.000	0.596
getStockcol	0.072	0.000	0.073
highlightOnPlot	0.111	0.000	0.111
knnClassification	1.126	0.008	1.140
knntlClassification	0.001	0.000	0.001
ksvmClassification	4.775	0.016	4.806
makeGoSet	0.166	0.004	1.656
makeNaData	1.164	0.000	1.163
markerMSnSet	0.099	0.004	0.103
minClassScore	0.051	0.000	0.053
minMarkers	0.042	0.004	0.046
nbClassification	3.312	0.008	3.324
nndist-methods	0.213	0.004	0.227
nnetClassification	7.181	0.000	7.190
pRolocmarkers	0.011	0.000	0.011
perTurboClassification	15.553	0.009	15.554
phenoDisco	0.001	0.000	0.000
plot2D	2.918	0.024	2.943
plot2D_v1	2.840	0.011	2.855
plotDist	0.088	0.004	0.093
plsdaClassification	0.001	0.000	0.001
rfClassification	7.492	0.004	7.515
sampleMSnSet	0.075	0.000	0.075
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	5.747	0.004	5.755
testMSnSet	0.484	0.000	0.485
testMarkers	0.028	0.008	0.034
thetas	0.012	0.000	0.013