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Package 613/658HostnameOS / ArchBUILDCHECKBUILD BIN
Starr 1.15.2
Benedikt Zacher
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Starr
Last Changed Rev: 73963 / Revision: 74774
Last Changed Date: 2013-03-06 01:59:25 -0800 (Wed, 06 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

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

Command output

* 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

Starr.Rcheck/00install.out:

* 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)

Starr.Rcheck/Starr-Ex.timings:

nameusersystemelapsed
bpmapToProbeAnno0.0040.0120.015
cmarrt.ma0.5160.0040.555
cmarrt.peak0.0160.0000.015
correlationPlot0.0440.0000.046
densityscatter4.4600.0764.542
filterGenes0.0000.0000.004
getMeans0.0120.0000.014
getProfiles0.0080.0000.008
getRatio0.0080.0000.007
kde2dplot0.8480.0040.852
makeSplines0.0120.0000.013
normalize.Probes0.0080.0000.006
plot.Density0.4840.0040.489
plot.boxes4.9600.0405.015
plot.cmarrt0.0160.0000.015
plot.gcBias22.594 0.00422.752
plot.image0.0360.0040.040
plot.ma8.3400.1048.475
plot.posBias28.786 0.14829.355
plot.ratioScatter2.9760.0483.077
plot.scatter2.7880.0202.808
plotProfiles0.3600.0080.368
profileplot0.6400.0080.651
read.gffAnno0.0200.0000.022
readCelFile0.0160.0000.017
remap0.0160.0000.016