BioC 3.3: CHECK report for pRoloc on morelia

Package: pRoloc

Version: 1.11.22

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.11.22.tar.gz

StartedAt: 2016-04-21 06:14:24 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:27:18 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 774.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pRoloc.Rcheck

Warnings: 1

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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_1.11.22.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.11.22’
* 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 ... [31s/32s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/pRoloc.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 ... [70s/413s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 13.731  0.068  13.829
SpatProtVis-class       7.590  0.154   7.750
rfClassification        5.873  0.171   6.046
svmClassification       5.154  0.036   5.195
AnnotationParams-class  0.399  0.032 341.553
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [114s/101s]
 [114s/101s] 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: 1 WARNING, 3 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
** 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (pRoloc)

name	user	system	elapsed
AnnotationParams-class	0.399	0.032	341.553
GenRegRes-class	0.002	0.001	0.002
SpatProtVis-class	7.590	0.154	7.750
addMarkers	0.097	0.006	0.103
checkFeatureNamesOverlap	0.376	0.013	0.404
checkFvarOverlap	0.031	0.004	0.035
chi2-methods	0.007	0.001	0.008
classWeights	0.094	0.008	0.102
empPvalues	0.343	0.006	0.349
exprsToRatios-methods	0.169	0.005	0.174
fDataToUnknown	0.039	0.005	0.044
filterBinMSnSet	0.226	0.013	0.240
filterZeroCols	0.092	0.004	0.096
getGOFromFeatures	0.192	0.009	0.703
getMarkerClasses	0.031	0.004	0.035
getMarkers	0.031	0.004	0.035
getPredictions	0.241	0.007	0.248
getStockcol	0.059	0.010	0.069
goIdToTerm	2.336	0.144	2.481
highlightOnPlot	0.143	0.009	0.153
knnClassification	0.963	0.012	0.978
knntlClassification	0.000	0.000	0.001
ksvmClassification	4.079	0.104	4.183
makeGoSet	0.324	0.014	0.994
makeNaData	1.036	0.005	1.041
markerMSnSet	0.260	0.004	0.263
markers	0.057	0.006	0.064
minMarkers	0.040	0.004	0.044
move2Ds	1.798	0.039	1.861
nbClassification	3.127	0.033	3.163
nndist-methods	0.175	0.005	0.186
nnetClassification	4.792	0.012	4.806
orgQuants	0.199	0.004	0.203
pRolocmarkers	0.011	0.002	0.012
perTurboClassification	13.731	0.068	13.829
phenoDisco	0	0	0
plot2D	2.506	0.070	2.607
plot2Ds	0.363	0.028	0.394
plotDist	0.100	0.004	0.105
plsdaClassification	0	0	0
rfClassification	5.873	0.171	6.046
sampleMSnSet	0.077	0.003	0.081
showGOEvidenceCodes	0.000	0.000	0.001
svmClassification	5.154	0.036	5.195
testMSnSet	0.365	0.009	0.374
testMarkers	0.032	0.012	0.044
thetas	0.006	0.002	0.008