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Package 303/444HostnameOS / ArchBUILDCHECKBUILD BIN
pamr 1.49.0
Rob Tibshirani
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pamr
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: pamr
Version: 1.49.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pamr_1.49.0.tar.gz
StartedAt: 2011-03-17 17:02:45 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 17:03:22 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 36.9 seconds
RetCode: 0
Status:  OK 
CheckDir: pamr.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/pamr.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.49.0'
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
prepare_Rd: khan.Rd:9-10: Dropping empty section \format
prepare_Rd: khan.Rd:15-16: Dropping empty section \source
prepare_Rd: khan.Rd:17-18: Dropping empty section \references
prepare_Rd: pamr.adaptthresh.Rd:63: Dropping empty section \keyword
prepare_Rd: pamr.batchadjust.Rd:48: Dropping empty section \keyword
prepare_Rd: pamr.batchadjust.Rd:31: Dropping empty section \references
prepare_Rd: pamr.confusion.Rd:47: Dropping empty section \keyword
prepare_Rd: pamr.confusion.Rd:29: Dropping empty section \references
prepare_Rd: pamr.confusion.survival.Rd:36: Dropping empty section \keyword
prepare_Rd: pamr.confusion.survival.Rd:23: Dropping empty section \details
prepare_Rd: pamr.confusion.survival.Rd:27: Dropping empty section \references
prepare_Rd: pamr.confusion.survival.Rd:34-35: Dropping empty section \examples
prepare_Rd: pamr.cv.Rd:67: Dropping empty section \keyword
prepare_Rd: pamr.cv.Rd:50: Dropping empty section \references
prepare_Rd: pamr.decorrelate.Rd:76: Dropping empty section \keyword
prepare_Rd: pamr.fdr.Rd:53: Dropping empty section \keyword
prepare_Rd: pamr.fdr.Rd:36: Dropping empty section \references
prepare_Rd: pamr.from.excel.Rd:57: Dropping empty section \keyword
prepare_Rd: pamr.from.excel.Rd:50: Dropping empty section \references
prepare_Rd: pamr.geneplot.Rd:45: Dropping empty section \keyword
prepare_Rd: pamr.geneplot.Rd:29: Dropping empty section \references
prepare_Rd: pamr.indeterminate.Rd:43: Dropping empty section \keyword
prepare_Rd: pamr.indeterminate.Rd:23-24: Dropping empty section \details
prepare_Rd: pamr.indeterminate.Rd:27: Dropping empty section \references
prepare_Rd: pamr.knnimpute.Rd:76: Dropping empty section \keyword
prepare_Rd: pamr.listgenes.Rd:56: Dropping empty section \keyword
prepare_Rd: pamr.listgenes.Rd:35: Dropping empty section \references
prepare_Rd: pamr.makeclasses.Rd:79: Dropping empty section \keyword
prepare_Rd: pamr.makeclasses.Rd:57: Dropping empty section \references
prepare_Rd: pamr.menu.Rd:38: Dropping empty section \keyword
prepare_Rd: pamr.menu.Rd:22-23: Dropping empty section \value
prepare_Rd: pamr.menu.Rd:25: Dropping empty section \references
prepare_Rd: pamr.plotcen.Rd:48: Dropping empty section \keyword
prepare_Rd: pamr.plotcen.Rd:30-31: Dropping empty section \references
prepare_Rd: pamr.plotcv.Rd:41: Dropping empty section \keyword
prepare_Rd: pamr.plotcv.Rd:23-24: Dropping empty section \value
prepare_Rd: pamr.plotcv.Rd:26: Dropping empty section \references
prepare_Rd: pamr.plotcvprob.Rd:48: Dropping empty section \keyword
prepare_Rd: pamr.plotcvprob.Rd:27-28: Dropping empty section \value
prepare_Rd: pamr.plotcvprob.Rd:30: Dropping empty section \references
prepare_Rd: pamr.plotfdr.Rd:44: Dropping empty section \keyword
prepare_Rd: pamr.plotfdr.Rd:25-26: Dropping empty section \value
prepare_Rd: pamr.plotfdr.Rd:28: Dropping empty section \references
prepare_Rd: pamr.plotstrata.Rd:57: Dropping empty section \keyword
prepare_Rd: pamr.plotstrata.Rd:17-18: Dropping empty section \details
prepare_Rd: pamr.plotstrata.Rd:19-20: Dropping empty section \value
prepare_Rd: pamr.plotstrata.Rd:22: Dropping empty section \references
prepare_Rd: pamr.plotsurvival.Rd:60: Dropping empty section \keyword
prepare_Rd: pamr.plotsurvival.Rd:16: Dropping empty section \details
prepare_Rd: pamr.plotsurvival.Rd:17: Dropping empty section \value
prepare_Rd: pamr.plotsurvival.Rd:19: Dropping empty section \references
prepare_Rd: pamr.predict.Rd:55: Dropping empty section \keyword
prepare_Rd: pamr.predict.Rd:38: Dropping empty section \references
prepare_Rd: pamr.predictmany.Rd:50: Dropping empty section \keyword
prepare_Rd: pamr.predictmany.Rd:29-30: Dropping empty section \details
prepare_Rd: pamr.predictmany.Rd:33: Dropping empty section \references
prepare_Rd: pamr.surv.to.class2.Rd:83: Dropping empty section \keyword
prepare_Rd: pamr.test.errors.surv.compute.Rd:77: Dropping empty section \keyword
prepare_Rd: pamr.test.errors.surv.compute.Rd:26: Dropping empty section \references
prepare_Rd: pamr.to.excel.Rd:34: Dropping empty section \keyword
prepare_Rd: pamr.train.Rd:138: Dropping empty section \keyword
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

pamr.Rcheck/00install.out:

* installing *source* package 'pamr' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c cox_func.c -o cox_func.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic -c knnimpute.f -o knnimpute.o
knnimpute.f: In function 'twomis':
knnimpute.f:132: warning: 'dold' may be used uninitialized in this function
gcc -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
installing to /Users/biocbuild/bbs-2.8-bioc/meat/pamr.Rcheck/pamr/libs/i386
** R
** data
** inst
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (pamr)

pamr.Rcheck/pamr-Ex.timings:

nameusersystemelapsed
pamr.adaptthresh0.8580.0240.882
pamr.batchadjust0.0100.0010.010
pamr.confusion0.3740.0050.379
pamr.cv0.3740.0050.380
pamr.decorrelate0.2080.0100.218
pamr.fdr1.8890.0871.977
pamr.geneplot0.1560.0130.168
pamr.indeterminate0.0840.0120.097
pamr.listgenes0.0890.0060.094
pamr.makeclasses0.1130.0150.127
pamr.menu0.0050.0010.006
pamr.plotcen0.3580.0340.396
pamr.plotcv0.4100.0260.436
pamr.plotcvprob0.3560.0160.443
pamr.plotfdr1.3580.1511.575
pamr.plotstrata0.4440.0120.455
pamr.plotsurvival0.4380.0070.445
pamr.predict0.3420.0230.366
pamr.predictmany0.2370.0370.273
pamr.surv.to.class20.7140.0400.754
pamr.test.errors.surv.compute0.7290.0620.792
pamr.train0.2030.0220.224