Package: puma

Version: 2.2.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings puma_2.2.0.tar.gz

StartedAt: 2011-02-24 22:01:11 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:06:57 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 345.4 seconds

RetCode: 0

Status:  OK

CheckDir: puma.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/puma.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘2.2.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘puma’ can be installed ... 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

* installing *source* package ‘puma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ipplr_c.c -o ipplr_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c multimgmos.c -o multimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c pplr_c.c -o pplr_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c pumaclustii_c.c -o pumaclustii_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c user_eval.c -o user_eval.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o puma.so cregistration.o donlp2.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/puma.Rcheck/puma/libs
** R
** data
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (puma)

name	user	system	elapsed
DEResult-class	18.649	0.056	18.846
bcomb	0.100	0.000	0.102
calcAUC	0.448	0.052	0.493
calculateFC	5.360	0.100	5.569
calculateLimma	4.364	0.080	4.480
calculateTtest	0.204	0.004	0.208
clusterNormE	0.240	0.004	0.242
clusterNormVar	0.068	0.000	0.069
createContrastMatrix	2.001	0.028	2.048
createDesignMatrix	1.552	0.024	1.578
erfc	0	0	0
exprReslt-class	0.648	0.020	0.687
hcomb	31.118	0.020	31.229
legend2	0.004	0.000	0.006
license.puma	0.004	0.000	0.004
matrixDistance	0.000	0.000	0.001
mgmos	0	0	0
mmgmos	0	0	0
normalisation.gs	0.024	0.000	0.023
numFP	0.004	0.000	0.005
numOfFactorsToUse	0.132	0.004	0.133
numTP	0.008	0.000	0.009
orig_pplr	0.188	0.004	0.191
plot-methods	17.273	0.020	17.311
plotErrorBars	0.392	0.000	0.393
plotHistTwoClasses	0.012	0.000	0.011
plotROC	0.416	0.076	0.504
pplr	0.236	0.000	0.236
puma-package	75.028	0.052	75.241
pumaClustii	30.458	0.076	30.788
pumaComb	20.254	0.052	20.408
pumaCombImproved	14.405	0.056	14.506
pumaDE	36.002	0.088	36.618
pumaFull	0	0	0
pumaNormalize	0.944	0.000	0.960
pumaPCA	17.041	0.052	17.300
pumaclust	3.048	0.004	3.056
removeUninformativeFactors	0.072	0.000	0.071