Package: Starr

Version: 1.15.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Starr_1.15.2.tar.gz

StartedAt: 2013-03-25 04:53:30 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:00:24 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 414.6 seconds

RetCode: 0

Status:  OK

CheckDir: Starr.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Starr.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.15.2’
* 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 ... [35s/36s] 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [96s/97s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 28.786  0.148  29.355
plot.gcBias  22.594  0.004  22.752
plot.ma       8.340  0.104   8.475
plot.boxes    4.960  0.040   5.015
* 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

* 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  -Wall -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  -Wall -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  -Wall -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  -Wall -c sort_by_genomic.c -o sort_by_genomic.o
gcc -std=gnu99 -shared -L/usr/local/lib -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 /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	0.012	0.015
cmarrt.ma	0.516	0.004	0.555
cmarrt.peak	0.016	0.000	0.015
correlationPlot	0.044	0.000	0.046
densityscatter	4.460	0.076	4.542
filterGenes	0.000	0.000	0.004
getMeans	0.012	0.000	0.014
getProfiles	0.008	0.000	0.008
getRatio	0.008	0.000	0.007
kde2dplot	0.848	0.004	0.852
makeSplines	0.012	0.000	0.013
normalize.Probes	0.008	0.000	0.006
plot.Density	0.484	0.004	0.489
plot.boxes	4.960	0.040	5.015
plot.cmarrt	0.016	0.000	0.015
plot.gcBias	22.594	0.004	22.752
plot.image	0.036	0.004	0.040
plot.ma	8.340	0.104	8.475
plot.posBias	28.786	0.148	29.355
plot.ratioScatter	2.976	0.048	3.077
plot.scatter	2.788	0.020	2.808
plotProfiles	0.360	0.008	0.368
profileplot	0.640	0.008	0.651
read.gffAnno	0.020	0.000	0.022
readCelFile	0.016	0.000	0.017
remap	0.016	0.000	0.016