Package: Starr

Version: 1.15.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Starr_1.15.0.tar.gz

StartedAt: 2013-01-16 06:37:36 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:42:24 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 288.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Starr.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Starr.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Starr/DESCRIPTION’ ... OK
* this is package ‘Starr’ version ‘1.15.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Starr’ can be installed ... 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 ... 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 ... WARNING
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Starr.Rcheck/Starr/libs/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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 21.966  0.072  22.043
plot.gcBias  17.329  0.032  17.392
plot.ma       6.744  0.052   6.849
* 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

WARNING: There was 1 warning.
See
  ‘/loc/home/biocbuild/bbs-2.12-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c ahocorasick.c -o ahocorasick.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c collect.c -o collect.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c rm_small_peak.c -o rm_small_peak.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c sort_by_genomic.c -o sort_by_genomic.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/Starr.Rcheck/Starr/libs
** 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	0.004	0.004	0.007
cmarrt.ma	0.416	0.004	0.420
cmarrt.peak	0.016	0.000	0.013
correlationPlot	0.044	0.000	0.047
densityscatter	3.900	0.044	3.940
filterGenes	0.004	0.000	0.005
getMeans	0.012	0.000	0.012
getProfiles	0.008	0.000	0.008
getRatio	0.005	0.000	0.006
kde2dplot	0.712	0.008	0.721
makeSplines	0.012	0.000	0.011
normalize.Probes	0.008	0.000	0.009
plot.Density	0.884	0.004	0.889
plot.boxes	2.712	0.008	2.720
plot.cmarrt	0.008	0.000	0.011
plot.gcBias	17.329	0.032	17.392
plot.image	0.024	0.000	0.022
plot.ma	6.744	0.052	6.849
plot.posBias	21.966	0.072	22.043
plot.ratioScatter	2.508	0.036	2.542
plot.scatter	1.872	0.012	1.888
plotProfiles	0.248	0.008	0.258
profileplot	0.484	0.000	0.482
read.gffAnno	0.004	0.000	0.004
readCelFile	0.004	0.000	0.004
remap	0.004	0.000	0.003