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Package 215/319HostnameOS / ArchBUILDCHECKBUILD BIN
pamr 1.42.0
Rob Tibshirani
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/pamr
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 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 (10.5.8) / i386  OK [ OK ] OK 
Package: pamr
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes pamr_1.42.0.tar.gz
StartedAt: 2009-10-20 18:23:30 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 18:24:25 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 55.5 seconds
RetCode: 0
Status: OK
CheckDir: pamr.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/pamr.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.42.0'
* 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 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 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 files against version 2 parser ... 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

pamr.Rcheck/00install.out:

* Installing *source* package ‘pamr’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In function ‘twomis’:
knnimpute.f:132: warning: ‘dold’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In function ‘twomis’:
knnimpute.f:132: warning: ‘dold’ may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran-4.2 -arch ppc64   -fPIC  -g -O2 -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In function ‘twomis’:
knnimpute.f:132: warning: ‘dold’ may be used uninitialized in this function
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In function ‘twomis’:
knnimpute.f:132: warning: ‘dold’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** help
*** installing help indices
 >>> Building/Updating help pages for package 'pamr'
     Formats: text html latex example 
Note: removing empty section \source in file 'khan.Rd'
Note: removing empty section \format in file 'khan.Rd'
Note: removing empty section \references in file 'khan.Rd'
  khan                              text    html    latex
Note: ignoring empty \keyword entries in file 'pamr.adaptthresh.Rd'
  pamr.adaptthresh                  text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.batchadjust.Rd'
Note: removing empty section \references in file 'pamr.batchadjust.Rd'
  pamr.batchadjust                  text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.confusion.Rd'
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  pamr.confusion                    text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.confusion.survival.Rd'
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  pamr.confusion.survival           text    html    latex
Note: ignoring empty \keyword entries in file 'pamr.cv.Rd'
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  pamr.cv                           text    html    latex   example
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  pamr.decorrelate                  text    html    latex   example
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  pamr.fdr                          text    html    latex   example
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  pamr.from.excel                   text    html    latex
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  pamr.geneplot                     text    html    latex   example
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  pamr.indeterminate                text    html    latex   example
  pamr.internal                     text    html    latex
Note: ignoring empty \keyword entries in file 'pamr.knnimpute.Rd'
  pamr.knnimpute                    text    html    latex
Note: ignoring empty \keyword entries in file 'pamr.listgenes.Rd'
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  pamr.listgenes                    text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.makeclasses.Rd'
Note: removing empty section \references in file 'pamr.makeclasses.Rd'
  pamr.makeclasses                  text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.menu.Rd'
Note: removing empty section \value in file 'pamr.menu.Rd'
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  pamr.menu                         text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.plotcen.Rd'
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  pamr.plotcen                      text    html    latex   example
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  pamr.plotcv                       text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.plotcvprob.Rd'
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  pamr.plotcvprob                   text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.plotfdr.Rd'
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  pamr.plotfdr                      text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.plotstrata.Rd'
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  pamr.plotstrata                   text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.plotsurvival.Rd'
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  pamr.plotsurvival                 text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.predict.Rd'
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  pamr.predict                      text    html    latex   example
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  pamr.predictmany                  text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.surv.to.class2.Rd'
  pamr.surv.to.class2               text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.test.errors.surv.compute.Rd'
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  pamr.test.errors.surv.compute     text    html    latex   example
Note: ignoring empty \keyword entries in file 'pamr.to.excel.Rd'
  pamr.to.excel                     text    html    latex
Note: ignoring empty \keyword entries in file 'pamr.train.Rd'
  pamr.train                        text    html    latex   example
** building package indices ...
* DONE (pamr)