* using log directory 'd:/Rcompile/CRANpkg/local/2.10/pamr.Rcheck' * using R version 2.10.1 (2009-12-14) * 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 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 ... 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 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