BioC 2.12: CHECK report for rnaSeqMap on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* 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 '2.13.1'
* 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 ... 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 ... [29s/30s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [16s/16s] 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 -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
   'rnaSeqMap.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (rnaSeqMap)

name	user	system	elapsed
NDplots	0.140	0.019	0.160
RleList2matrix	0.013	0.002	0.015
addBamData	0.386	0.003	0.390
addDataToReadset	0.149	0.005	0.155
addExperimentsToReadset	0.012	0.004	0.017
averageND	0.012	0.004	0.017
bam2sig	0.012	0.002	0.014
buildDESeq	0.011	0.001	0.012
buildDGEList	0.014	0.002	0.015
findRegionsAsIR	0.009	0.003	0.011
findRegionsAsND	0.008	0.002	0.011
gRanges2CamelMeasures	0.007	0.001	0.009
geneInChromosome	0.011	0.002	0.015
generators	0.020	0.003	0.022
getBamData	0.009	0.003	0.012
getCoverageFromRS	0.009	0.003	0.011
getFCFromND	0.008	0.003	0.011
getSIFromND	0.007	0.003	0.010
getSumsExp	0.011	0.003	0.014
measures	0.012	0.002	0.013
normalizations	0.389	0.005	0.398
normalizeBySum	0.011	0.004	0.015
parseGff3	0.011	0.003	0.014
plotGeneCoverage	0.010	0.003	0.014
readsInRange	0.011	0.004	0.015
regionBasedCoverage	0.013	0.003	0.016
regionCoverage	0.011	0.002	0.013
rs.list	0.114	0.013	0.127
setSpecies	0.014	0.001	0.014
spaceInChromosome	0.013	0.003	0.015

Summary

Command output