pamr 1.36.0
Rob Tibshirani
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/pamr | | Last Changed Rev: 27709 / Revision: 30966 | | Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | [ OK ] | OK |
* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/pamr.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.36.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pamr' 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 ... NOTE
pamr.makeclasses: no visible global function definition for
'plot.hclust'
pamr.xl.derive.adjusted.prior: no visible binding for global variable
'pamr.xl.survival.setting'
pamr.xl.derive.adjusted.prior: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.get.class.labels: no visible binding for global variable
'pamr.xl.data'
pamr.xl.get.class.names: no visible binding for global variable
'pamr.xl.survival.setting'
pamr.xl.get.class.names: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.get.class.names: no visible binding for global variable
'pamr.xl.data'
pamr.xl.get.default.training.parameters: no visible binding for global
variable 'pamr.xl.survival.setting'
pamr.xl.get.default.training.parameters: no visible binding for global
variable 'pamr.xl.regression.setting'
pamr.xl.get.number.of.classes: no visible binding for global variable
'pamr.xl.survival.setting'
pamr.xl.get.number.of.classes: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.get.number.of.classes: no visible binding for global variable
'pamr.xl.data'
pamr.xl.get.offset: no visible binding for global variable 'x.train'
pamr.xl.get.offset: no visible binding for global variable
'pamr.xl.data'
pamr.xl.get.offset: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.is.a.subset: no visible binding for global variable
'pamr.xl.survival.setting'
pamr.xl.is.a.subset: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.plot.test.probs.compute: no visible binding for global variable
'pamr.xl.survival.setting'
pamr.xl.plot.test.probs.compute: no visible binding for global variable
'pamr.xl.test.survival.times'
pamr.xl.plot.test.probs.compute: no visible binding for global variable
'pamr.xl.test.censoring.status'
pamr.xl.plot.test.probs.compute: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.plot.training.error.compute: no visible binding for global
variable 'pamr.xl.survival.setting'
pamr.xl.plotcv.compute: no visible binding for global variable
'pamr.xl.survival.setting'
pamr.xl.plotcvprob.compute: no visible binding for global variable 'aa'
pamr.xl.predict.test.surv.class: no visible binding for global variable
'pamr.xl.training.parameters'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.class.labels'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.survival.times'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.raw.data'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.gene.names'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.gene.ids'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.sample.labels'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.batch.labels'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.censoring.status'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.data.has.missing.values'
pamr.xl.process.data: no visible binding for global variable
'pamr.xl.knn.neighbors'
pamr.xl.test.data.impute: no visible binding for global variable
'pamr.xl.knn.neighbors'
pamr.xl.test.errors.surv.compute: no visible binding for global
variable 'pamr.xl.training.parameters'
pamr.xl.transform.data: no visible binding for global variable
'pamr.xl.take.cube.root'
pamr.xl.transform.data: no visible binding for global variable
'pamr.xl.batch.labels.present'
pamr.xl.transform.data: no visible binding for global variable
'pamr.xl.center.columns'
pamr.xl.transform.data: no visible binding for global variable
'pamr.xl.scale.columns'
pamr.xl.transform.test.data: no visible binding for global variable
'pamr.xl.take.cube.root'
pamr.xl.transform.test.data: no visible binding for global variable
'pamr.xl.center.columns'
pamr.xl.transform.test.data: no visible binding for global variable
'pamr.xl.scale.columns'
* checking Rd files ... 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
* creating pamr-Ex.R ... OK
* checking examples ... OK
* creating pamr-manual.tex ... OK
* checking pamr-manual.tex ... OK
* Installing *source* package 'pamr' ...
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -march=nocona -c cox_func.c -o cox_func.o
gfortran -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fPIC -g -O2 -march=nocona -c knnimpute.f -o knnimpute.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.1 -lgfortran -lgcc_s.10.4 -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c cox_func.c -o cox_func.o
gfortran -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fPIC -g -O2 -c knnimpute.f -o knnimpute.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.1 -lgfortran -lgcc_s.10.4 -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R
** R
** data
** inst
** help
Note: unmatched right brace in 'pamr.confusion.survival' on or after line 24
Note: unmatched right brace in 'pamr.listgenes' on or after line 8
Note: unmatched right brace in 'pamr.plotcen' on or after line 7
Note: unmatched right brace in 'pamr.predict' on or after line 8
Note: unmatched right brace in 'pamr.predictmany' on or after line 8
>>> Building/Updating help pages for package 'pamr'
Formats: text html latex example
khan text html latex
pamr.adaptthresh text html latex example
pamr.batchadjust text html latex example
pamr.confusion text html latex example
pamr.confusion.survival text html latex example
pamr.cv text html latex example
pamr.decorrelate text html latex example
pamr.fdr text html latex example
pamr.from.excel text html latex
pamr.geneplot text html latex example
pamr.indeterminate text html latex example
pamr.internal text html latex
pamr.knnimpute text html latex
pamr.listgenes text html latex example
pamr.makeclasses text html latex example
pamr.menu text html latex example
pamr.plotcen text html latex example
pamr.plotcv text html latex example
pamr.plotcvprob text html latex example
pamr.plotfdr text html latex example
pamr.plotstrata text html latex example
pamr.plotsurvival text html latex example
pamr.predict text html latex example
pamr.predictmany text html latex example
pamr.surv.to.class2 text html latex example
pamr.test.errors.surv.compute text html latex example
pamr.to.excel text html latex
pamr.train text html latex example
** building package indices ...
* DONE (pamr)