• using R version 2.11.1 (2010-05-31)
• using session charset: ISO8859-1
• checking for file 'pamr/DESCRIPTION' ... OK
• this is package 'pamr' version '1.47'
• 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 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
  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 ... NOTE
  prepare_Rd: khan.Rd:9-10: Dropping empty section \format
  prepare_Rd: khan.Rd:15-16: Dropping empty section \source
  prepare_Rd: khan.Rd:17-18: Dropping empty section \references
  prepare_Rd: pamr.adaptthresh.Rd:63: Dropping empty section \keyword
  prepare_Rd: pamr.batchadjust.Rd:48: Dropping empty section \keyword
  prepare_Rd: pamr.batchadjust.Rd:31: Dropping empty section \references
  prepare_Rd: pamr.confusion.Rd:47: Dropping empty section \keyword
  prepare_Rd: pamr.confusion.Rd:29: Dropping empty section \references
  prepare_Rd: pamr.confusion.survival.Rd:36: Dropping empty section \keyword
  prepare_Rd: pamr.confusion.survival.Rd:23: Dropping empty section \details
  prepare_Rd: pamr.confusion.survival.Rd:27: Dropping empty section \references
  prepare_Rd: pamr.confusion.survival.Rd:34-35: Dropping empty section \examples
  prepare_Rd: pamr.cv.Rd:67: Dropping empty section \keyword
  prepare_Rd: pamr.cv.Rd:50: Dropping empty section \references
  prepare_Rd: pamr.decorrelate.Rd:76: Dropping empty section \keyword
  prepare_Rd: pamr.fdr.Rd:53: Dropping empty section \keyword
  prepare_Rd: pamr.fdr.Rd:36: Dropping empty section \references
  prepare_Rd: pamr.from.excel.Rd:57: Dropping empty section \keyword
  prepare_Rd: pamr.from.excel.Rd:50: Dropping empty section \references
  prepare_Rd: pamr.geneplot.Rd:45: Dropping empty section \keyword
  prepare_Rd: pamr.geneplot.Rd:29: Dropping empty section \references
  prepare_Rd: pamr.indeterminate.Rd:43: Dropping empty section \keyword
  prepare_Rd: pamr.indeterminate.Rd:23-24: Dropping empty section \details
  prepare_Rd: pamr.indeterminate.Rd:27: Dropping empty section \references
  prepare_Rd: pamr.knnimpute.Rd:76: Dropping empty section \keyword
  prepare_Rd: pamr.listgenes.Rd:56: Dropping empty section \keyword
  prepare_Rd: pamr.listgenes.Rd:35: Dropping empty section \references
  prepare_Rd: pamr.makeclasses.Rd:79: Dropping empty section \keyword
  prepare_Rd: pamr.makeclasses.Rd:57: Dropping empty section \references
  prepare_Rd: pamr.menu.Rd:38: Dropping empty section \keyword
  prepare_Rd: pamr.menu.Rd:22-23: Dropping empty section \value
  prepare_Rd: pamr.menu.Rd:25: Dropping empty section \references
  prepare_Rd: pamr.plotcen.Rd:48: Dropping empty section \keyword
  prepare_Rd: pamr.plotcen.Rd:30-31: Dropping empty section \references
  prepare_Rd: pamr.plotcv.Rd:41: Dropping empty section \keyword
  prepare_Rd: pamr.plotcv.Rd:23-24: Dropping empty section \value
  prepare_Rd: pamr.plotcv.Rd:26: Dropping empty section \references
  prepare_Rd: pamr.plotcvprob.Rd:48: Dropping empty section \keyword
  prepare_Rd: pamr.plotcvprob.Rd:27-28: Dropping empty section \value
  prepare_Rd: pamr.plotcvprob.Rd:30: Dropping empty section \references
  prepare_Rd: pamr.plotfdr.Rd:44: Dropping empty section \keyword
  prepare_Rd: pamr.plotfdr.Rd:25-26: Dropping empty section \value
  prepare_Rd: pamr.plotfdr.Rd:28: Dropping empty section \references
  prepare_Rd: pamr.plotstrata.Rd:57: Dropping empty section \keyword
  prepare_Rd: pamr.plotstrata.Rd:17-18: Dropping empty section \details
  prepare_Rd: pamr.plotstrata.Rd:19-20: Dropping empty section \value
  prepare_Rd: pamr.plotstrata.Rd:22: Dropping empty section \references
  prepare_Rd: pamr.plotsurvival.Rd:60: Dropping empty section \keyword
  prepare_Rd: pamr.plotsurvival.Rd:16: Dropping empty section \details
  prepare_Rd: pamr.plotsurvival.Rd:17: Dropping empty section \value
  prepare_Rd: pamr.plotsurvival.Rd:19: Dropping empty section \references
  prepare_Rd: pamr.predict.Rd:55: Dropping empty section \keyword
  prepare_Rd: pamr.predict.Rd:38: Dropping empty section \references
  prepare_Rd: pamr.predictmany.Rd:50: Dropping empty section \keyword
  prepare_Rd: pamr.predictmany.Rd:29-30: Dropping empty section \details
  prepare_Rd: pamr.predictmany.Rd:33: Dropping empty section \references
  prepare_Rd: pamr.surv.to.class2.Rd:83: Dropping empty section \keyword
  prepare_Rd: pamr.test.errors.surv.compute.Rd:77: Dropping empty section \keyword
  prepare_Rd: pamr.test.errors.surv.compute.Rd:26: Dropping empty section \references
  prepare_Rd: pamr.to.excel.Rd:34: Dropping empty section \keyword
  prepare_Rd: pamr.train.Rd:138: Dropping empty section \keyword
• 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