• using R version 2.9.0 Under development (unstable) (2008-11-19 r46992)
• using session charset: UTF-8
• checking for file 'pamr/DESCRIPTION' ... OK
• this is package 'pamr' version '1.31'
• 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 ... WARNING
  Found the following directory(s) with names of check directories:
  man/pamr.Rcheck
  Most likely, these were included erroneously.
• 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 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 using pdflatex ... OK