BioC 3.3: CHECK report for pRoloc on morelia

Package: pRoloc

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.11.0.tar.gz

StartedAt: 2015-10-22 09:47:46 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 09:53:34 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 347.9 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

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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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.11.0’
* 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 ... [27s/28s] 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 ... [73s/80s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 14.775  0.056  14.842
SpatProtVis-class       8.409  0.153   8.586
nnetClassification      6.810  0.035   6.860
rfClassification        5.744  0.194   5.938
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [60s/52s]
 [60s/52s] 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-3.3-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

* installing *source* package ‘pRoloc’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pRoloc.cpp -o pRoloc.o
clang++ -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 -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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.231	0.010	3.291
GenRegRes-class	0.004	0.000	0.004
SpatProtVis-class	8.409	0.153	8.586
addMarkers	0.095	0.004	0.100
checkFeatureNamesOverlap	0.699	0.017	0.733
checkFvarOverlap	0.027	0.002	0.029
chi2-methods	0.006	0.000	0.006
empPvalues	0.125	0.000	0.126
exprsToRatios-methods	0.175	0.017	0.192
filterBinMSnSet	0.315	0.001	0.316
filterZeroCols	0.111	0.007	0.118
getGOFromFeatures	0.058	0.004	1.615
getMarkerClasses	0.031	0.002	0.032
getMarkers	0.032	0.002	0.034
getPredictions	0.251	0.007	0.258
getStockcol	0.079	0.006	0.085
goIdToTerm	2.358	0.139	2.498
highlightOnPlot	0.123	0.012	0.137
knnClassification	1.205	0.011	1.218
knntlClassification	0	0	0
ksvmClassification	4.837	0.104	4.946
makeGoSet	0.423	0.010	2.313
makeNaData	1.523	0.010	1.534
markerMSnSet	0.324	0.007	0.332
markers	0.043	0.005	0.048
minClassScore	0.048	0.005	0.054
minMarkers	0.042	0.005	0.047
move2Ds	1.508	0.040	1.578
nbClassification	4.072	0.020	4.096
nndist-methods	0.243	0.012	0.279
nnetClassification	6.810	0.035	6.860
pRolocmarkers	0.014	0.002	0.015
perTurboClassification	14.775	0.056	14.842
phenoDisco	0	0	0
plot2D	1.738	0.076	1.819
plot2Ds	0.351	0.049	0.403
plotDist	0.106	0.012	0.119
plsdaClassification	0	0	0
rfClassification	5.744	0.194	5.938
sampleMSnSet	0.074	0.007	0.081
showGOEvidenceCodes	0.000	0.000	0.001
svmClassification	4.962	0.033	4.999
testMSnSet	0.513	0.008	0.522
testMarkers	0.027	0.007	0.034
thetas	0.006	0.002	0.008