pamr 1.37.0
Rob Tibshirani
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pamr | | Last Changed Rev: 27716 / Revision: 29143 | | Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/pamr.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-14 r43455)
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.37.0'
* 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.makeclasses: no visible global function definition for
'plot.hclust'
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 ... OK
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/pamr.Rcheck
---------- Making package pamr ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making cox_func.d from cox_func.c
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c cox_func.c -o cox_func.o
gfortran-sjlj -O3 -c knnimpute.f -o knnimpute.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i pamr_res.rc -o pamr_res.o
gcc-sjlj -std=gnu99 -shared -s -o pamr.dll pamr.def cox_func.o knnimpute.o pamr_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lgfortran -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
Note: removing empty section \source
Note: removing empty section \format
Note: removing empty section \references
Note: removing empty section \source
Note: removing empty section \format
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: unmatched right brace in 'pamr.confusion.survival' on or after line 24
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \references
Note: removing empty section \examples
Note: unmatched right brace in 'pamr.confusion.survival.Rd' on or after line 24
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \references
Note: removing empty section \examples
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: unmatched right brace in 'pamr.listgenes' on or after line 8
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: unmatched right brace in 'pamr.listgenes.Rd' on or after line 8
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: unmatched right brace in 'pamr.plotcen' on or after line 7
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: unmatched right brace in 'pamr.plotcen.Rd' on or after line 7
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \references
Note: unmatched right brace in 'pamr.predict' on or after line 8
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: unmatched right brace in 'pamr.predict.Rd' on or after line 8
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: unmatched right brace in 'pamr.predictmany' on or after line 8
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \references
Note: unmatched right brace in 'pamr.predictmany.Rd' on or after line 8
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: removing empty section \references
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
>>> Building/Updating help pages for package 'pamr'
Formats: text html latex example chm
khan text html latex chm
pamr.adaptthresh text html latex example chm
pamr.batchadjust text html latex example chm
pamr.confusion text html latex example chm
pamr.confusion.survival text html latex chm
pamr.cv text html latex example chm
pamr.decorrelate text html latex example chm
pamr.fdr text html latex example chm
pamr.from.excel text html latex chm
pamr.geneplot text html latex example chm
pamr.indeterminate text html latex example chm
pamr.internal text html latex chm
pamr.knnimpute text html latex chm
pamr.listgenes text html latex example chm
pamr.makeclasses text html latex example chm
pamr.menu text html latex example chm
pamr.plotcen text html latex example chm
pamr.plotcv text html latex example chm
pamr.plotcvprob text html latex example chm
pamr.plotfdr text html latex example chm
pamr.plotstrata text html latex example chm
pamr.plotsurvival text html latex example chm
pamr.predict text html latex example chm
pamr.predictmany text html latex example chm
pamr.surv.to.class2 text html latex example chm
pamr.test.errors.surv.compute text html latex example chm
pamr.to.excel text html latex chm
pamr.train text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\pamr.Rcheck\00_pkg_src\pamr\chm\pamr.chm
Compile time: 0 minutes, 0 seconds
29 Topics
55 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\pamr.Rcheck\00_pkg_src\pamr\chm\pamr.chm, 53,619 bytes
Compression decreased file by 55,617 bytes.
adding MD5 sums
* DONE (pamr)