* using log directory 'd:/Rcompile/CRANpkg/local/2.9/pamr.Rcheck'
* using R version 2.9.2 Patched (2009-09-02 r49531)
* using session charset: ISO8859-1
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.44.0'
* 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 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