pamr 1.42.0
Rob Tibshirani
| 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/pamr | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 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 '/loc/home/biocbuild/bbs-2.4-bioc/meat/pamr.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.42.0'
* 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.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 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 'pamr' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran -fpic -g -O -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In function 'twomis':
knnimpute.f:132: warning: 'dold' may be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o pamr.so cox_func.o knnimpute.o -lgfortran -lm -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** data
** inst
** help
*** installing help indices
>>> Building/Updating help pages for package 'pamr'
Formats: text html latex example
Note: removing empty section \source in file 'khan.Rd'
Note: removing empty section \format in file 'khan.Rd'
Note: removing empty section \references in file 'khan.Rd'
khan text html latex
Note: ignoring empty \keyword entries in file 'pamr.adaptthresh.Rd'
pamr.adaptthresh text html latex example
Note: ignoring empty \keyword entries in file 'pamr.batchadjust.Rd'
Note: removing empty section \references in file 'pamr.batchadjust.Rd'
pamr.batchadjust text html latex example
Note: ignoring empty \keyword entries in file 'pamr.confusion.Rd'
Note: removing empty section \references in file 'pamr.confusion.Rd'
pamr.confusion text html latex example
Note: ignoring empty \keyword entries in file 'pamr.confusion.survival.Rd'
Note: removing empty section \details in file 'pamr.confusion.survival.Rd'
Note: removing empty section \references in file 'pamr.confusion.survival.Rd'
Note: removing empty section \examples in file 'pamr.confusion.survival.Rd'
pamr.confusion.survival text html latex
Note: ignoring empty \keyword entries in file 'pamr.cv.Rd'
Note: removing empty section \references in file 'pamr.cv.Rd'
pamr.cv text html latex example
Note: ignoring empty \keyword entries in file 'pamr.decorrelate.Rd'
pamr.decorrelate text html latex example
Note: ignoring empty \keyword entries in file 'pamr.fdr.Rd'
Note: removing empty section \references in file 'pamr.fdr.Rd'
pamr.fdr text html latex example
Note: ignoring empty \keyword entries in file 'pamr.from.excel.Rd'
Note: removing empty section \references in file 'pamr.from.excel.Rd'
pamr.from.excel text html latex
Note: ignoring empty \keyword entries in file 'pamr.geneplot.Rd'
Note: removing empty section \references in file 'pamr.geneplot.Rd'
pamr.geneplot text html latex example
Note: ignoring empty \keyword entries in file 'pamr.indeterminate.Rd'
Note: removing empty section \details in file 'pamr.indeterminate.Rd'
Note: removing empty section \references in file 'pamr.indeterminate.Rd'
pamr.indeterminate text html latex example
pamr.internal text html latex
Note: ignoring empty \keyword entries in file 'pamr.knnimpute.Rd'
pamr.knnimpute text html latex
Note: ignoring empty \keyword entries in file 'pamr.listgenes.Rd'
Note: removing empty section \references in file 'pamr.listgenes.Rd'
pamr.listgenes text html latex example
Note: ignoring empty \keyword entries in file 'pamr.makeclasses.Rd'
Note: removing empty section \references in file 'pamr.makeclasses.Rd'
pamr.makeclasses text html latex example
Note: ignoring empty \keyword entries in file 'pamr.menu.Rd'
Note: removing empty section \value in file 'pamr.menu.Rd'
Note: removing empty section \references in file 'pamr.menu.Rd'
pamr.menu text html latex example
Note: ignoring empty \keyword entries in file 'pamr.plotcen.Rd'
Note: removing empty section \references in file 'pamr.plotcen.Rd'
pamr.plotcen text html latex example
Note: ignoring empty \keyword entries in file 'pamr.plotcv.Rd'
Note: removing empty section \value in file 'pamr.plotcv.Rd'
Note: removing empty section \references in file 'pamr.plotcv.Rd'
pamr.plotcv text html latex example
Note: ignoring empty \keyword entries in file 'pamr.plotcvprob.Rd'
Note: removing empty section \value in file 'pamr.plotcvprob.Rd'
Note: removing empty section \references in file 'pamr.plotcvprob.Rd'
pamr.plotcvprob text html latex example
Note: ignoring empty \keyword entries in file 'pamr.plotfdr.Rd'
Note: removing empty section \value in file 'pamr.plotfdr.Rd'
Note: removing empty section \references in file 'pamr.plotfdr.Rd'
pamr.plotfdr text html latex example
Note: ignoring empty \keyword entries in file 'pamr.plotstrata.Rd'
Note: removing empty section \value in file 'pamr.plotstrata.Rd'
Note: removing empty section \details in file 'pamr.plotstrata.Rd'
Note: removing empty section \references in file 'pamr.plotstrata.Rd'
pamr.plotstrata text html latex example
Note: ignoring empty \keyword entries in file 'pamr.plotsurvival.Rd'
Note: removing empty section \value in file 'pamr.plotsurvival.Rd'
Note: removing empty section \details in file 'pamr.plotsurvival.Rd'
Note: removing empty section \references in file 'pamr.plotsurvival.Rd'
pamr.plotsurvival text html latex example
Note: ignoring empty \keyword entries in file 'pamr.predict.Rd'
Note: removing empty section \references in file 'pamr.predict.Rd'
pamr.predict text html latex example
Note: ignoring empty \keyword entries in file 'pamr.predictmany.Rd'
Note: removing empty section \details in file 'pamr.predictmany.Rd'
Note: removing empty section \references in file 'pamr.predictmany.Rd'
pamr.predictmany text html latex example
Note: ignoring empty \keyword entries in file 'pamr.surv.to.class2.Rd'
pamr.surv.to.class2 text html latex example
Note: ignoring empty \keyword entries in file 'pamr.test.errors.surv.compute.Rd'
Note: removing empty section \references in file 'pamr.test.errors.surv.compute.Rd'
pamr.test.errors.surv.compute text html latex example
Note: ignoring empty \keyword entries in file 'pamr.to.excel.Rd'
pamr.to.excel text html latex
Note: ignoring empty \keyword entries in file 'pamr.train.Rd'
pamr.train text html latex example
** building package indices ...
* DONE (pamr)