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Package 293/389HostnameOS / ArchBUILDCHECKBUILD BIN
puma 2.0.0
Richard Pearson , Li Zhang
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/puma
Last Changed Rev: 46467 / Revision: 49923
Last Changed Date: 2010-04-23 09:18:01 -0700 (Fri, 23 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: puma
Version: 2.0.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings puma_2.0.0.tar.gz
StartedAt: 2010-10-04 19:17:56 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 19:23:25 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 329.4 seconds
RetCode: 0
Status:  OK 
CheckDir: puma.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/puma.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'puma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'puma' version '2.0.0'
* 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 ... NOTE
just.mgmos: possible error in gsub("^/?([^/]*/)*", "",
  unlist(filenames), extended = TRUE): unused argument(s) (extended =
  TRUE)
just.mmgmos: possible error in gsub("^/?([^/]*/)*", "",
  unlist(filenames), extended = TRUE): unused argument(s) (extended =
  TRUE)
* 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 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

puma.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'puma' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-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-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c multimgmos.c -o multimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-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-2.6-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-2.6-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-2.6-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-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-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)

puma.Rcheck/puma-Ex.timings:

nameusersystemelapsed
DEResult-class18.461 0.03218.526
bcomb0.0880.0640.154
calcAUC0.5600.0400.595
calculateFC6.3120.1126.503
calculateLimma5.1160.0645.191
calculateTtest0.2760.0000.278
clusterNormE0.0680.0000.070
clusterNormVar0.0930.0000.092
createContrastMatrix2.6360.0162.770
createDesignMatrix2.2320.0442.378
erfc000
exprReslt-class0.6520.0160.688
hcomb23.321 0.02823.372
legend20.0040.0000.005
license.puma0.0000.0040.003
matrixDistance0.0000.0000.002
mgmos000
mmgmos0.0000.0000.001
normalisation.gs0.0160.0040.022
numFP0.0040.0040.005
numOfFactorsToUse0.1320.0000.132
numTP0.0120.0000.011
orig_pplr0.1440.0000.142
plot-methods18.870 0.01218.919
plotErrorBars0.5000.0040.578
plotHistTwoClasses0.0120.0000.014
plotROC0.4880.0760.565
pplr0.1360.0040.138
puma-package64.872 0.04864.972
pumaClustii32.234 0.00432.253
pumaComb19.673 0.02420.027
pumaCombImproved16.097 0.01216.145
pumaDE36.054 0.02836.218
pumaFull000
pumaNormalize0.5840.0000.582
pumaPCA17.805 0.00417.954
pumaclust3.1520.0003.156
removeUninformativeFactors0.0880.0000.087