BioC 2.13: CHECK report for pRoloc on perceval

Package: pRoloc

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pRoloc_1.2.1.tar.gz

StartedAt: 2014-04-05 03:31:20 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:42:37 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 676.8 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/pRoloc.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.1’
* 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 ... [49s/53s] 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:
  ‘e1071:::predict.naiveBayes’ ‘e1071:::predict.svm’
  ‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’
  ‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’ ‘nnet:::predict.nnet’
  ‘randomForest:::predict.randomForest’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... 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’ ... OK
* checking examples ... [75s/76s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 15.928  0.109  16.246
svmClassification       6.419  0.103   6.663
nnetClassification      6.058  0.043   6.203
rfClassification        5.703  0.284   6.103
ksvmClassification      5.163  0.086   5.290
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [183s/188s]
 [184s/188s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pRoloc.cpp -o pRoloc.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
Warning: replacing previous import by ‘MLInterfaces::plot’ when loading ‘pRoloc’
Warning: replacing previous import by ‘scales::alpha’ when loading ‘pRoloc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
Warning: replacing previous import by ‘MLInterfaces::plot’ when loading ‘pRoloc’
Warning: replacing previous import by ‘scales::alpha’ when loading ‘pRoloc’
* DONE (pRoloc)

name	user	system	elapsed
GenRegRes-class	0.033	0.004	0.038
chi2-methods	0.022	0.007	0.030
empPvalues	0.274	0.027	0.305
exprsToRatios-methods	0.514	0.024	0.565
getMarkers	0.107	0.012	0.120
getStockcol	0.137	0.018	0.158
knnClassification	1.613	0.028	1.656
ksvmClassification	5.163	0.086	5.290
makeNaData	2.117	0.027	2.168
markerSet	0.162	0.012	0.175
minClassScore	0.130	0.012	0.142
minMarkers	0.110	0.008	0.118
nbClassification	4.816	0.050	4.968
nnetClassification	6.058	0.043	6.203
perTurboClassification	15.928	0.109	16.246
phenoDisco	0.009	0.003	0.013
plot2D	3.465	0.053	3.557
plotDist	0.187	0.020	0.209
plsdaClassification	0.008	0.008	0.017
rfClassification	5.703	0.284	6.103
svmClassification	6.419	0.103	6.663
testMarkers	0.084	0.013	0.098