BioC 2.14: CHECK report for Ringo on petty

Package: Ringo

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.28.0.tar.gz

StartedAt: 2014-10-07 23:50:22 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:56:49 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 386.9 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.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 --no-multiarch Ringo_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Ringo.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘RColorBrewer’ ‘limma’ ‘Matrix’ ‘grid’ ‘lattice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [35s/36s] 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/26s] 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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-2.14-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	0.563	0.009	0.571
asExprSet	0.428	0.015	0.447
autocorr	0.178	0.003	0.185
cherByThreshold	0.010	0.001	0.014
cherClass	0.740	0.005	0.749
chipAlongChrom	0.297	0.014	0.311
chipAlongChromOld	0.081	0.005	0.088
computeRunningMedians	0.980	0.014	1.036
compute_gc	0.003	0.000	0.004
compute_sliding_t	0.142	0.002	0.147
corrPlot	0.068	0.010	0.079
exportCherList	0.001	0.000	0.001
features2Probes	1.579	0.071	1.660
findChersOnSmoothed	0.195	0.003	0.206
ftr2xys	0.001	0.000	0.002
newCER	0.004	0.000	0.005
nonzero	0.025	0.002	0.027
plotAutocorr	0.001	0.000	0.001
plotBM	0.024	0.003	0.031
posToProbeAnnoEnvironment	0.113	0.004	0.117
preprocess	0.972	0.026	1.002
probeAnnoClass	0.060	0.002	0.063
qopS4	0.001	0.000	0.002
quantilesOverPositions	1.357	0.006	1.368
readNimblegen	0.542	0.026	0.571
regionoverlap	0.015	0.001	0.015
relateCERs	0.000	0.000	0.001
sigGOTable	0.002	0.000	0.002
sliding_meansd	0.005	0.000	0.005
sliding_quantile	0.020	0.001	0.023
twoGaussiansNull	0.327	0.011	0.338
upperBoundNull	0.144	0.013	0.157
validProbeAnno	0.039	0.003	0.042