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| Package 154/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
| pamr 1.36.0 Rob Tibshirani Last Changed Date: 2007-10-02 17:41:09 -0700 Last Changed Rev: 27709 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
| wellington | Linux (SUSE 9.2) | i686 | OK | OK | ||
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | [ WARNINGS ] | OK | |
| pitt | Mac OS X (10.4.10) | i386 | OK | WARNINGS | OK |
| Package: pamr |
| Version: 1.36.0 |
| Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check pamr_1.36.0.tar.gz |
| RetCode: 0 |
| Time: 54.3 seconds |
| Status: WARNINGS |
| CheckDir: pamr.Rcheck |
| Warnings: 1 |
* checking for working latex ... OK * using log directory 'E:/biocbld/bbs-2.1-bioc/meat/pamr.Rcheck' * using R version 2.6.0 (2007-10-03) * checking for file 'pamr/DESCRIPTION' ... OK * this is package 'pamr' version '1.36.0' * 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 ... WARNING Found the following significant warnings: Warning: Unused variable jj declared at (1) See 'E:/biocbld/bbs-2.1-bioc/meat/pamr.Rcheck/00install.out' for details. * 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 WARNING: There was 1 warning, see E:/biocbld/bbs-2.1-bioc/meat/pamr.Rcheck/00check.log for details
pamr.Rcheck/00install.out:
installing R.css in E:/biocbld/bbs-2.1-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-2.1-bioc/R/include -Wall -O3 -c cox_func.c -o cox_func.o
gfortran-sjlj -O3 -Wall -c knnimpute.f -o knnimpute.o
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knnimpute.f:6.37:
integer iworkp(p),iworkn(n), jj
1
Warning: Unused variable jj declared at (1)
knnimpute.f: In function 'twomis':
knnimpute.f:132: warning: 'dold' may be used uninitialized in this function
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.1-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-2.1-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: unmatched right brace in 'pamr.confusion.survival' on or after line 24
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Note: unmatched right brace in 'pamr.predictmany' on or after line 8
Note: unmatched right brace in 'pamr.predictmany.Rd' on or after line 8
>>> 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 example 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-2.1-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-2.1-bioc\meat\pamr.Rcheck\00_pkg_src\pamr\chm\pamr.chm, 53,613 bytes
Compression decreased file by 56,572 bytes.
adding MD5 sums
* DONE (pamr)