pamr 1.40.1
Rob Tibshirani
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/pamr | | Last Changed Rev: 38931 / Revision: 38965 | | Last Changed Date: 2009-04-17 09:17:15 -0700 (Fri, 17 Apr 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/pamr.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.40.1'
* 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 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
installing R.css in E:/biocbld/bbs-2.3-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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c cox_func.c -o cox_func.o
gfortran -O3 -c knnimpute.f -o knnimpute.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i pamr_res.rc -o pamr_res.o
gcc -std=gnu99 -shared -s -o pamr.dll pamr.def cox_func.o knnimpute.o pamr_res.o -Le:/biocbld/bbs-2.3-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
>>> Building/Updating help pages for package 'pamr'
Formats: text html latex example chm
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Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-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-2.3-bioc\meat\pamr.Rcheck\00_pkg_src\pamr\chm\pamr.chm, 53,795 bytes
Compression decreased file by 55,858 bytes.
adding MD5 sums
* DONE (pamr)