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BioC 2.12: CHECK report for Starr on george2

This page was generated on 2013-10-09 09:37:35 -0700 (Wed, 09 Oct 2013).

Package 625/671HostnameOS / ArchBUILDCHECKBUILD BIN
Starr 1.16.0
Benedikt Zacher
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Starr
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Starr
Version: 1.16.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Starr_1.16.0.tar.gz
StartedAt: 2013-10-09 05:11:22 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:18:35 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 433.6 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 3.0.1 (2013-05-16)
* 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 ‘1.16.0’
* 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 ... [36s/38s] 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 ... [101s/105s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plot.posBias   27.458  0.180  28.032
plot.gcBias    23.422  0.052  24.834
plot.ma         8.264  0.156   8.644
densityscatter  6.144  0.112   6.770
plot.boxes      4.944  0.044   5.531
* 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
** testing if installed package can be loaded
* DONE (Starr)

Starr.Rcheck/Starr-Ex.timings:

nameusersystemelapsed
bpmapToProbeAnno0.6930.0000.772
cmarrt.ma0.0120.0040.018
cmarrt.peak0.020.000.02
correlationPlot0.0680.0000.100
densityscatter6.1440.1126.770
filterGenes0.0040.0000.006
getMeans0.0160.0000.018
getProfiles0.0120.0000.012
getRatio0.0160.0000.016
kde2dplot0.3360.0200.365
makeSplines0.0080.0000.011
normalize.Probes0.0120.0000.012
plot.Density0.5000.0160.518
plot.boxes4.9440.0445.531
plot.cmarrt0.0080.0000.010
plot.gcBias23.422 0.05224.834
plot.image0.0360.0040.040
plot.ma8.2640.1568.644
plot.posBias27.458 0.18028.032
plot.ratioScatter3.6560.0563.794
plot.scatter2.8690.0083.017
plotProfiles0.3280.0160.377
profileplot0.6160.0120.650
read.gffAnno0.0080.0000.007
readCelFile0.0080.0000.008
remap0.0120.0000.020