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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: /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 |
* 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 Warning: Nonconforming tab character in column 1 of line 89 Warning: Nonconforming tab character in column 1 of line 91 Warning: Nonconforming tab character in column 1 of line 92 Warning: Nonconforming tab character in column 1 of line 93 Warning: Nonconforming tab character in column 1 of line 94 Warning: Nonconforming tab character in column 1 of line 95 Warning: Nonconforming tab character in column 1 of line 96 Warning: Nonconforming tab character in column 1 of line 97 Warning: Nonconforming tab character in column 1 of line 98 Warning: Nonconforming tab character in column 1 of line 99 Warning: Nonconforming tab character in column 1 of line 100 Warning: Nonconforming tab character in column 1 of line 101 Warning: Nonconforming tab character in column 1 of line 102 Warning: Nonconforming tab character in column 1 of line 103 Warning: Nonconforming tab character in column 1 of line 104 Warning: Nonconforming tab character in column 1 of line 105 Warning: Nonconforming tab character in column 1 of line 106 Warning: Nonconforming tab character in column 1 of line 107 Warning: Nonconforming tab character in column 1 of line 108 Warning: Nonconforming tab character in column 1 of line 109 Warning: Nonconforming tab character in column 1 of line 110 Warning: Nonconforming tab character in column 1 of line 111 Warning: Nonconforming tab character in column 1 of line 112 Warning: Nonconforming tab character in column 1 of line 113 Warning: Nonconforming tab character in column 1 of line 114 Warning: Nonconforming tab character in column 1 of line 115 Warning: Nonconforming tab character in column 1 of line 116 Warning: Nonconforming tab character in column 1 of line 117 Warning: Nonconforming tab character in column 1 of line 118 Warning: Nonconforming tab character in column 1 of line 119 Warning: Nonconforming tab character in column 1 of line 120 Warning: Nonconforming tab character in column 1 of line 121 Warning: Nonconforming tab character in column 1 of line 122 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 Warning: Nonconforming tab character in column 1 of line 91 Warning: Nonconforming tab character in column 1 of line 92 Warning: Nonconforming tab character in column 1 of line 93 Warning: Nonconforming tab character in column 1 of line 94 Warning: Nonconforming tab character in column 1 of line 95 Warning: Nonconforming tab character in column 1 of line 96 Warning: Nonconforming tab character in column 1 of line 97 Warning: Nonconforming tab character in column 1 of line 98 Warning: Nonconforming tab character in column 1 of line 99 Warning: Nonconforming tab character in column 1 of line 100 Warning: Nonconforming tab character in column 1 of line 101 Warning: Nonconforming tab character in column 1 of line 102 Warning: Nonconforming tab character in column 1 of line 103 Warning: Nonconforming tab character in column 1 of line 104 Warning: Nonconforming tab character in column 1 of line 105 Warning: Nonconforming tab character in column 1 of line 106 Warning: Nonconforming tab character in column 1 of line 107 Warning: Nonconforming tab character in column 1 of line 108 Warning: Nonconforming tab character in column 1 of line 109 Warning: Nonconforming tab character in column 1 of line 110 Warning: Nonconforming tab character in column 1 of line 111 Warning: Nonconforming tab character in column 1 of line 112 Warning: Nonconforming tab character in column 1 of line 113 Warning: Nonconforming tab character in column 1 of line 114 Warning: Nonconforming tab character in column 1 of line 115 Warning: Nonconforming tab character in column 1 of line 116 Warning: Nonconforming tab character in column 1 of line 117 Warning: Nonconforming tab character in column 1 of line 118 Warning: Nonconforming tab character in column 1 of line 119 Warning: Nonconforming tab character in column 1 of line 120 Warning: Nonconforming tab character in column 1 of line 121 Warning: Nonconforming tab character in column 1 of line 122 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)