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Package 154/234HostnameOSArchBUILDCHECKBUILD 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check pamr_1.36.0.tar.gz
RetCode: 0
Time: 58.5 seconds
Status: WARNINGS
CheckDir: pamr.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/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)
  Warning: Unused variable jj declared at (1)
See '/Users/biocbuild/bbs-2.1-bioc/meat/pamr.Rcheck/00install.out' for details.
* 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.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
  /Users/biocbuild/bbs-2.1-bioc/meat/pamr.Rcheck/00check.log
for details

pamr.Rcheck/00install.out:

* Installing *source* package 'pamr' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c cox_func.c -o cox_func.o
gfortran-4.0 -arch i386  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   -fPIC  -g -O2 -Wall -march=nocona -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
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o  -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.1 -lgfortran -lgcc_s.10.4 -F/Library/Frameworks/R.framework/.. -framework R 
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c cox_func.c -o cox_func.o
gfortran-4.0 -arch ppc  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   -fPIC  -g -O2 -Wall -c knnimpute.f -o knnimpute.o
Warning: Nonconforming tab character in column 1 of line 89
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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
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pamr.so cox_func.o knnimpute.o  -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.1 -lgfortran -lgcc_s.10.4 -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R 
** R
** data
** inst
** help
Note: unmatched right brace in 'pamr.confusion.survival' on or after line 24
Note: unmatched right brace in 'pamr.listgenes' on or after line 8
Note: unmatched right brace in 'pamr.plotcen' on or after line 7
Note: unmatched right brace in 'pamr.predict' on or after line 8
Note: unmatched right brace in 'pamr.predictmany' on or after line 8
 >>> Building/Updating help pages for package 'pamr'
     Formats: text html latex example 
  khan                              text    html    latex
  pamr.adaptthresh                  text    html    latex   example
  pamr.batchadjust                  text    html    latex   example
  pamr.confusion                    text    html    latex   example
  pamr.confusion.survival           text    html    latex   example
  pamr.cv                           text    html    latex   example
  pamr.decorrelate                  text    html    latex   example
  pamr.fdr                          text    html    latex   example
  pamr.from.excel                   text    html    latex
  pamr.geneplot                     text    html    latex   example
  pamr.indeterminate                text    html    latex   example
  pamr.internal                     text    html    latex
  pamr.knnimpute                    text    html    latex
  pamr.listgenes                    text    html    latex   example
  pamr.makeclasses                  text    html    latex   example
  pamr.menu                         text    html    latex   example
  pamr.plotcen                      text    html    latex   example
  pamr.plotcv                       text    html    latex   example
  pamr.plotcvprob                   text    html    latex   example
  pamr.plotfdr                      text    html    latex   example
  pamr.plotstrata                   text    html    latex   example
  pamr.plotsurvival                 text    html    latex   example
  pamr.predict                      text    html    latex   example
  pamr.predictmany                  text    html    latex   example
  pamr.surv.to.class2               text    html    latex   example
  pamr.test.errors.surv.compute     text    html    latex   example
  pamr.to.excel                     text    html    latex
  pamr.train                        text    html    latex   example
** building package indices ...
* DONE (pamr)