BioC 3.2: CHECK report for pRoloc on linux1.bioconductor.org

Package: pRoloc

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.10.0.tar.gz

StartedAt: 2015-10-27 06:52:46 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:59:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 379.5 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

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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_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.10.0’
* 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 ... [29s/29s] 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 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 ... [82s/84s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 15.941  0.020  15.981
SpatProtVis-class       8.966  0.072   9.039
nnetClassification      7.354  0.004   7.362
rfClassification        6.303  0.004   6.313
svmClassification       6.115  0.016   6.135
ksvmClassification      5.055  0.000   5.066
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [66s/61s]
 [67s/61s] 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-3.2-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
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
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	0.267	0.008	0.641
GenRegRes-class	0.003	0.000	0.003
SpatProtVis-class	8.966	0.072	9.039
addMarkers	0.091	0.000	0.091
checkFeatureNamesOverlap	0.735	0.016	0.752
checkFvarOverlap	0.037	0.008	0.046
chi2-methods	0.010	0.000	0.011
empPvalues	0.197	0.000	0.197
exprsToRatios-methods	0.290	0.000	0.289
filterBinMSnSet	0.352	0.004	0.357
filterZeroCols	0.156	0.000	0.156
getGOFromFeatures	0.069	0.000	0.950
getMarkerClasses	0.050	0.004	0.053
getMarkers	0.056	0.000	0.056
getPredictions	0.342	0.000	0.342
getStockcol	0.085	0.000	0.085
goIdToTerm	3.143	0.031	3.175
highlightOnPlot	0.111	0.007	0.120
knnClassification	1.146	0.016	1.168
knntlClassification	0.000	0.000	0.001
ksvmClassification	5.055	0.000	5.066
makeGoSet	0.310	0.004	1.590
makeNaData	1.005	0.000	1.006
markerMSnSet	0.437	0.000	0.438
markers	0.075	0.000	0.075
minClassScore	0.079	0.000	0.079
minMarkers	0.065	0.004	0.068
move2Ds	2.534	0.008	2.542
nbClassification	4.806	0.004	4.810
nndist-methods	0.183	0.000	0.183
nnetClassification	7.354	0.004	7.362
pRolocmarkers	0.015	0.000	0.016
perTurboClassification	15.941	0.020	15.981
phenoDisco	0.000	0.000	0.001
plot2D	2.272	0.020	2.295
plot2Ds	0.374	0.012	0.387
plotDist	0.103	0.000	0.103
plsdaClassification	0	0	0
rfClassification	6.303	0.004	6.313
sampleMSnSet	0.076	0.004	0.079
showGOEvidenceCodes	0.001	0.000	0.001
svmClassification	6.115	0.016	6.135
testMSnSet	0.372	0.000	0.373
testMarkers	0.032	0.000	0.032
thetas	0.012	0.000	0.012