BioSeqClass 1.11.0
Li Hong
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BioSeqClass | | Last Changed Rev: 56578 / Revision: 56603 | | Last Changed Date: 2011-07-05 17:51:53 -0700 (Tue, 05 Jul 2011) |
| wilson2 | Linux (openSUSE 11.4) / 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 |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | ERROR |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/BioSeqClass.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioSeqClass/DESCRIPTION' ... OK
* this is package 'BioSeqClass' version '1.11.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BioSeqClass' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
data 5.1Mb
scripts 3.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: selectWeka.Rd:49-51: Dropping empty section \examples
* 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 ... NOTE
'library' or 'require' call not declared from: 'scatterplot3d'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
Note: significantly better compression could be obtained
by using tools::resaveRdaFiles() or R CMD build --resave-data
old_size new_size compress
DiProDB.rda 15Kb 12Kb xz
aa.index.rda 127Kb 71Kb bzip2
dssp.ss.rda 5.0Mb 2.8Mb xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... ERROR
Running examples in 'BioSeqClass-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: classify
> ### Title: Classification with Specific Features and Cross-Validation
> ### Aliases: classify
>
> ### ** Examples
>
> ## read positive/negative sequence from files.
> tmpfile1 = file.path(.path.package("BioSeqClass"), "example", "acetylation_K.pos40.pep")
> tmpfile2 = file.path(.path.package("BioSeqClass"), "example", "acetylation_K.neg40.pep")
> posSeq = as.matrix(read.csv(tmpfile1,header=FALSE,sep="\t",row.names=1))[,1]
> negSeq = as.matrix(read.csv(tmpfile2,header=FALSE,sep="\t",row.names=1))[,1]
> seq=c(posSeq,negSeq)
> classLable=c(rep("+1",length(posSeq)),rep("-1",length(negSeq)) )
> data = data.frame(featureBinary(seq),classLable)
>
> ## Use LibSVM and 5-cross-validation to classify.
> LIBSVM_CV5 = classify(data,classifyMethod="libsvm",cv=5,
+ svm.kernel="linear",svm.scale=FALSE)
> ## Features selection is done by envoking "CfsSubsetEval" method in WEKA.
> FS_LIBSVM_CV5 = classify(data,classifyMethod="libsvm",cv=5,evaluator="CfsSubsetEval",
+ search="BestFirst",svm.kernel="linear",svm.scale=FALSE)
Error in system(command, intern = TRUE) : 'java' not found
Calls: classify -> selectWeka -> system
Execution halted
install for i386
* installing *source* package 'BioSeqClass' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: rpart
Loading required package: MASS
Loading required package: mlbench
Loading required package: survival
Loading required package: splines
Loading required package: class
Loading required package: nnet
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'BioSeqClass.Rnw'
** testing if installed package can be loaded
add DLL for x64
* installing *source* package 'BioSeqClass' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioSeqClass' as BioSeqClass_1.11.0.zip
* DONE (BioSeqClass)