pamr 1.51.0
Rob Tibshirani
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pamr | | Last Changed Rev: 54802 / Revision: 56603 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/pamr.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pamr/DESCRIPTION’ ... OK
* this is package ‘pamr’ version ‘1.51.0’
* 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 installed package size ... 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 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 for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* installing *source* package ‘pamr’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran -fpic -g -O2 -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In function ‘twomis’:
knnimpute.f:132:0: 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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/pamr.Rcheck/pamr/libs
** R
** data
** inst
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (pamr)