Package: puma

Version: 2.2.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings puma_2.2.0.tar.gz

StartedAt: 2011-03-31 07:57:20 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 08:02:38 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 318.0 seconds

RetCode: 0

Status:  OK

CheckDir: puma.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/puma.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

* installing *source* package ‘puma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c multimgmos.c -o multimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-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-2.7-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-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-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
  'openVignette()'. 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	17.901	0.028	17.945
bcomb	0.100	0.000	0.099
calcAUC	0.460	0.028	0.488
calculateFC	5.228	0.116	5.361
calculateLimma	5.068	0.036	5.128
calculateTtest	0.196	0.000	0.194
clusterNormE	0.080	0.000	0.082
clusterNormVar	0.060	0.000	0.061
createContrastMatrix	2.101	0.012	2.114
createDesignMatrix	1.472	0.016	1.493
erfc	0	0	0
exprReslt-class	0.648	0.012	0.661
hcomb	22.657	0.012	22.669
legend2	0.004	0.000	0.005
license.puma	0.000	0.004	0.004
matrixDistance	0.004	0.000	0.001
mgmos	0	0	0
mmgmos	0	0	0
normalisation.gs	0.024	0.000	0.021
numFP	0.004	0.000	0.005
numOfFactorsToUse	0.132	0.000	0.133
numTP	0.008	0.000	0.009
orig_pplr	0.148	0.000	0.148
plot-methods	16.677	0.004	16.680
plotErrorBars	0.436	0.008	0.445
plotHistTwoClasses	0.012	0.000	0.011
plotROC	0.388	0.076	0.464
pplr	0.144	0.000	0.146
puma-package	62.836	0.100	62.947
pumaClustii	29.710	0.004	29.727
pumaComb	18.485	0.004	18.503
pumaCombImproved	15.733	0.012	15.745
pumaDE	34.314	0.016	34.388
pumaFull	0	0	0
pumaNormalize	0.876	0.004	0.883
pumaPCA	16.873	0.004	16.882
pumaclust	3.045	0.008	3.050
removeUninformativeFactors	0.064	0.000	0.065