BioC 2.11: CHECK report for Starr on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Starr.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Starr/DESCRIPTION' ... OK
* this is package 'Starr' version '1.14.1'
* 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 whether package 'Starr' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.11-bioc/meat/Starr.Rcheck/Starr/libs/i386/Starr.so':
  Found '_exit', possibly from 'exit' (C)
    Object: 'ahocorasick.o'
  Found '_printf', possibly from 'printf' (C)
    Object: 'ahocorasick.o'
  Found '_puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'ahocorasick.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 20.976  0.441  21.906
plot.gcBias  15.976  0.121  16.331
plot.ma       6.368  0.512   7.401
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/Starr.Rcheck/00check.log'
for details.

* installing *source* package 'Starr' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c ahocorasick.c -o ahocorasick.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c collect.c -o collect.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c rm_small_peak.c -o rm_small_peak.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c sort_by_genomic.c -o sort_by_genomic.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/Starr.Rcheck/Starr/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Starr.Rnw' 
** testing if installed package can be loaded

* DONE (Starr)

name	user	system	elapsed
bpmapToProbeAnno	0	0	0
cmarrt.ma	0	0	0
cmarrt.peak	0.000	0.000	0.001
correlationPlot	0.033	0.002	0.036
densityscatter	3.154	0.160	3.372
filterGenes	0	0	0
getMeans	0.000	0.000	0.001
getProfiles	0.000	0.001	0.000
getRatio	0	0	0
kde2dplot	0.488	0.077	0.571
makeSplines	0	0	0
normalize.Probes	0	0	0
plot.Density	0.987	0.163	1.171
plot.boxes	3.559	0.345	3.964
plot.cmarrt	0.000	0.000	0.001
plot.gcBias	15.976	0.121	16.331
plot.image	0	0	0
plot.ma	6.368	0.512	7.401
plot.posBias	20.976	0.441	21.906
plot.ratioScatter	1.700	0.184	2.018
plot.scatter	1.811	0.173	2.010
plotProfiles	0.357	0.031	0.397
profileplot	0.798	0.026	0.828
read.gffAnno	0.000	0.000	0.001
readCelFile	0	0	0
remap	0	0	0

Summary

Command output