puma 1.10.1
Richard Pearson
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/puma | | Last Changed Rev: 39953 / Revision: 42512 | | Last Changed Date: 2009-06-05 04:01:09 -0700 (Fri, 05 Jun 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/puma.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49419)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'puma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'puma' version '1.10.1'
* 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 name space can be loaded with stated dependencies ... 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c cregistration.c -o cregistration.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c donlp2.c -o donlp2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c multimgmos.c -o multimgmos.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c newx.c -o newx.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c pplr_c.c -o pplr_c.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c user_eval.c -o user_eval.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o puma.so cregistration.o donlp2.o multimgmos.o newx.o pplr_c.o pumaclust_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c cregistration.c -o cregistration.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c donlp2.c -o donlp2.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c multimgmos.c -o multimgmos.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c newx.c -o newx.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c pplr_c.c -o pplr_c.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c user_eval.c -o user_eval.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o puma.so cregistration.o donlp2.o multimgmos.o newx.o pplr_c.o pumaclust_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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)'.
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
Class "ExpressionSet" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported? Making a copy in package "puma"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
Class "eSet" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported? Making a copy in package "puma"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
Class "VersionedBiobase" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported? Making a copy in package "puma"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
Class "Versioned" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported? Making a copy in package "puma"
** help
*** installing help indices
>>> Building/Updating help pages for package 'puma'
Formats: text html latex example
Clust.exampleE text html latex
Clust.exampleStd text html latex
DEResult-class text html latex example
bcomb text html latex example
calcAUC text html latex example
calculateFC text html latex example
calculateLimma text html latex example
calculateTtest text html latex example
clusterApplyLBDots text html latex
clusterNormE text html latex example
clusterNormVar text html latex example
compareLimmapumaDE text html latex
createContrastMatrix text html latex example
createDesignMatrix text html latex example
create_eset_r text html latex
erfc text html latex example
eset_mmgmos text html latex
exampleE text html latex
exampleStd text html latex
exprReslt-class text html latex example
hgu95aphis text html latex
Note: removing empty section \examples in file 'justmgMOS.Rd'
justmgMOS text html latex
Note: removing empty section \examples in file 'justmmgMOS.Rd'
justmmgMOS text html latex
legend2 text html latex example
Note: removing empty section \details in file 'license.puma.Rd'
Note: removing empty section \arguments in file 'license.puma.Rd'
Note: removing empty section \seealso in file 'license.puma.Rd'
license.puma text html latex example
matrixDistance text html latex example
mgmos text html latex example
mmgmos text html latex example
normalisation.gs text html latex example
numFP text html latex example
numOfFactorsToUse text html latex example
numTP text html latex example
orig_pplr text html latex example
plot-methods text html latex example
plotErrorBars text html latex example
plotHistTwoClasses text html latex example
plotROC text html latex example
plotWhiskers text html latex
pplr text html latex example
pplrUnsorted text html latex
puma-package text html latex example
pumaComb text html latex example
pumaDE text html latex example
pumaDEUnsorted text html latex
pumaFull text html latex example
pumaNormalize text html latex example
pumaPCA text html latex example
pumaPCAExpectations-class text html latex
pumaPCAModel-class text html latex
pumaPCARes-class text html latex
pumaclust text html latex example
removeUninformativeFactors text html latex example
** building package indices ...
* DONE (puma)