BioC 2.13: CHECK report for Ringo on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Ringo.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 ‘Ringo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ringo’ version ‘1.26.1’
* 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 ‘Ringo’ can be installed ... [27s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* 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
‘library’ or ‘require’ call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘limma’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘lattice’ ‘limma’ ‘Matrix’ ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘clusters’
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 ... NOTE
sigGOTable: no visible binding for global variable ‘p.value’
* 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 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’ ... NOTE
The following files should probably not be installed:
  ‘Makefile’, ‘Ringo.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Ringo.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [23s/23s] 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 were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/Ringo.Rcheck/00check.log’
for details.

* installing *source* package ‘Ringo’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mmeansd.cpp -o mmeansd.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mmedian.cpp -o mmedian.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c region_overlap.c -o region_overlap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ringo_init.c -o ringo_init.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 Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/Ringo.Rcheck/Ringo/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Ringo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.639	0.013	0.652
asExprSet	0.774	0.032	0.806
autocorr	0.138	0.009	0.152
cherByThreshold	0.026	0.007	0.034
cherClass	0.738	0.016	0.755
chipAlongChrom	0.208	0.005	0.213
chipAlongChromOld	0.073	0.007	0.081
computeRunningMedians	0.372	0.031	0.402
compute_gc	0.025	0.005	0.030
compute_sliding_t	0.127	0.010	0.137
corrPlot	0.054	0.019	0.144
exportCherList	0.010	0.002	0.013
features2Probes	2.491	0.089	2.604
findChersOnSmoothed	0.120	0.013	0.134
ftr2xys	0.010	0.008	0.018
newCER	0.004	0.005	0.009
nonzero	0.026	0.010	0.036
plotAutocorr	0.002	0.004	0.005
plotBM	0.031	0.013	0.044
posToProbeAnnoEnvironment	0.075	0.015	0.090
preprocess	0.339	0.025	0.365
probeAnnoClass	0.044	0.014	0.059
qopS4	0.002	0.004	0.005
quantilesOverPositions	1.999	0.094	2.103
readNimblegen	0.100	0.009	0.110
regionoverlap	0.013	0.008	0.021
relateCERs	0.002	0.003	0.005
sigGOTable	0.004	0.007	0.011
sliding_meansd	0.01	0.01	0.02
sliding_quantile	0.017	0.010	0.027
twoGaussiansNull	0.230	0.022	0.253
upperBoundNull	0.089	0.008	0.099
validProbeAnno	0.033	0.012	0.046

BioC 2.13: CHECK report for Ringo on perceval

Summary

Command output