BioC 3.1: CHECK report for pRoloc on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.8.0’
* 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 ... [46s/46s] 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 ... [119s/126s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 28.771  0.061  28.852
rfClassification       12.309  0.345  12.671
nnetClassification     12.074  0.034  12.121
svmClassification       9.802  0.040   9.848
ksvmClassification      7.411  0.061   7.589
nbClassification        6.833  0.032   6.907
plot2D                  5.251  0.110   5.446
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [107s/82s]
 [107s/83s] 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
  ‘/Users/biocbuild/bbs-3.1-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/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/Library/Frameworks/R.framework/Resources/lib -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-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	0.982	0.025	3.011
GenRegRes-class	0.006	0.001	0.006
addMarkers	0.399	0.019	0.421
checkFeatureNamesOverlap	1.864	0.038	1.949
checkFvarOverlap	0.115	0.011	0.127
chi2-methods	0.013	0.001	0.013
empPvalues	0.305	0.009	0.313
exprsToRatios-methods	0.381	0.053	0.434
filterBinMSnSet	0.443	0.001	0.445
filterZeroCols	0.301	0.019	0.322
getGOFromFeatures	0.140	0.013	1.984
getMarkerClasses	0.105	0.010	0.114
getMarkers	0.098	0.008	0.106
getPredictions	1.099	0.020	1.121
getStockcol	0.149	0.013	0.163
highlightOnPlot	0.245	0.015	0.274
knnClassification	2.081	0.030	2.140
knntlClassification	0.002	0.001	0.003
ksvmClassification	7.411	0.061	7.589
makeGoSet	0.385	0.016	2.457
makeNaData	2.205	0.016	2.305
markerMSnSet	0.229	0.010	0.239
minClassScore	0.150	0.010	0.161
minMarkers	0.137	0.010	0.147
nbClassification	6.833	0.032	6.907
nndist-methods	0.413	0.026	0.491
nnetClassification	12.074	0.034	12.121
pRolocmarkers	0.019	0.002	0.021
perTurboClassification	28.771	0.061	28.852
phenoDisco	0.001	0.000	0.001
plot2D	5.251	0.110	5.446
plot2D_v1	4.217	0.072	4.295
plotDist	0.227	0.006	0.233
plsdaClassification	0.000	0.001	0.001
rfClassification	12.309	0.345	12.671
sampleMSnSet	0.172	0.006	0.178
showGOEvidenceCodes	0.002	0.000	0.002
svmClassification	9.802	0.040	9.848
testMSnSet	1.003	0.008	1.013
testMarkers	0.109	0.008	0.117
thetas	0.024	0.003	0.027

BioC 3.1: CHECK report for pRoloc on petty

Summary

Command output