BioC 2.12: CHECK report for rnaSeqMap on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rnaSeqMap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rnaSeqMap' version '2.14.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'rnaSeqMap' can be installed ... [33s/34s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
qq_derivative_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F):
  partial argument match of 'plot' to 'plot.it'
qq_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F): partial
  argument match of 'plot' to 'plot.it'
bam2sig: no visible global function definition for 'dbGetQuery'
* 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 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 examples ... [17s/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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck/00check.log'
for details.

* installing *source* package 'rnaSeqMap' ...
** libs
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  -c Rinit.c -o Rinit.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  -c gcoverage.c -o gcoverage.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  -c ghistogram.c -o ghistogram.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  -c regionmining.c -o regionmining.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  -c splicingind.c -o splicingind.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rnaSeqMap)

name	user	system	elapsed
NDplots	0.170	0.020	0.253
RleList2matrix	0.020	0.002	0.023
addBamData	0.014	0.001	0.017
addDataToReadset	0.192	0.002	0.224
addExperimentsToReadset	0.007	0.002	0.014
averageND	0.012	0.002	0.016
bam2sig	0.018	0.001	0.021
buildDESeq	0.008	0.004	0.012
buildDGEList	0.007	0.003	0.012
findRegionsAsIR	0.012	0.002	0.014
findRegionsAsND	0.012	0.002	0.016
gRanges2CamelMeasures	0.007	0.001	0.008
geneInChromosome	0.007	0.002	0.010
generators	0.013	0.003	0.017
getBamData	0.012	0.003	0.016
getCoverageFromRS	0.007	0.002	0.012
getFCFromND	0.008	0.003	0.010
getSIFromND	0.014	0.002	0.019
getSumsExp	0.012	0.002	0.014
measures	0.007	0.002	0.010
normalizations	0.008	0.003	0.011
normalizeBySum	0.008	0.002	0.010
parseGff3	0.012	0.002	0.013
plotGeneCoverage	0.013	0.003	0.020
readsInRange	0.007	0.001	0.009
regionBasedCoverage	0.013	0.002	0.016
regionCoverage	0.013	0.002	0.016
rs.list	0.134	0.012	0.148
setSpecies	0.007	0.002	0.009
spaceInChromosome	0.015	0.002	0.017

BioC 2.12: CHECK report for rnaSeqMap on petty

Summary

Command output