Back to the "Multiple platform build/check report"
| Package 123/208 | OS | Arch | BUILD | CHECK | BUILD BIN |
MiPP1.7.0HyungJun Cho | Linux (SUSE 9.2) | x86_64 | OK | ERROR | |
| Linux (SUSE 10.1) | x86_64 | OK | ERROR | ||
| Linux (SUSE 9.2) | i686 | OK | ERROR | ||
| Solaris 2.9 | sparc | OK | ERROR | ||
| Windows Server 2003 | x86_64 | OK | ERROR | OK | |
| Windows Server 2003 | NA | OK | [ ERROR ] | OK | |
| Mac OS X (10.4.6) | i686 | OK | ERROR |
| Package: MiPP |
| Version: 1.7.0 |
| Command: E:\biocbld\2.0d\R\bin\R.exe CMD check MiPP_1.7.0.tar.gz |
| RetCode: 1 |
| Time: 104.5 seconds |
| Status: ERROR |
| CheckDir: MiPP.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory 'E:/biocbld/2.0d/Rpacks/MiPP.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'MiPP/DESCRIPTION' ... OK
* this is package 'MiPP' version '1.7.0'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
MASS
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'MiPP' can be installed ... OK
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating MiPP-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'MiPP-Ex.R' failed.
The error most likely occurred in:
> ### * mipp
>
> flush(stderr()); flush(stdout())
>
> ### Name: mipp
> ### Title: MiPP-based Classification
> ### Aliases: mipp
> ### Keywords: models
>
> ### ** Examples
>
>
> ##########
> #Example 1: When an independent test set is available
>
> data(leukemia)
>
> #Normalize combined data
> leukemia <- cbind(leuk1, leuk2)
> leukemia <- mipp.preproc(leukemia, data.type="MAS4")
>
> #Train set
> x.train <- leukemia[,1:38]
> y.train <- factor(c(rep("ALL",27),rep("AML",11)))
>
> #Test set
> x.test <- leukemia[,39:72]
> y.test <- factor(c(rep("ALL",20),rep("AML",14)))
>
> #Compute MiPP
> out <- mipp(x=x.train, y=y.train, x.test=x.test, y.test=y.test, probe.ID = 1:nrow(x.train), n.fold=5, percent.cut=0.05, rule="lda")
Loading required package: MASS
Please wait. Done.
>
> #Print candidate models
> out$model
Order Gene Tr.ER Tr.MiPP Tr.sMiPP Te.ER Te.MiPP Te.sMiPP Select
1 1 571 0.0526 30.86 0.8122 0.1176 23.92 0.7035
2 2 436 0.0000 36.89 0.9707 0.0294 30.41 0.8945
3 3 366 0.0000 37.95 0.9988 0.0294 31.35 0.9222
4 4 457 0.0000 38.00 0.9999 0.0294 32.14 0.9453
5 5 413 0.0000 38.00 1.0000 0.0294 32.18 0.9464
6 6 635 0.0000 38.00 1.0000 0.0000 33.75 0.9927 **
7 7 648 0.0000 38.00 1.0000 0.0000 33.60 0.9883
8 8 181 0.0000 38.00 1.0000 0.0294 31.95 0.9397
9 9 309 0.0000 38.00 1.0000 0.0000 33.37 0.9816
10 10 99 0.0000 38.00 1.0000 0.0588 29.82 0.8772
>
>
> ##########
> #Example 2: When an independent test set is not available
>
> data(colon)
>
> #Normalize data
> x <- mipp.preproc(colon)
> y <- factor(c("T", "N", "T", "N", "T", "N", "T", "N", "T", "N",
+ "T", "N", "T", "N", "T", "N", "T", "N", "T", "N",
+ "T", "N", "T", "N", "T", "T", "T", "T", "T", "T",
+ "T", "T", "T", "T", "T", "T", "T", "T", "N", "T",
+ "T", "N", "N", "T", "T", "T", "T", "N", "T", "N",
+ "N", "T", "T", "N", "N", "T", "T", "T", "T", "N",
+ "T", "N"))
>
> #Deleting comtaminated chips
> x <- x[,-c(51,55,45,49,56)]
> y <- y[ -c(51,55,45,49,56)]
>
> #Compute MiPP
> out <- mipp(x=x, y=y, probe.ID = 1:nrow(x), n.fold=5, p.test=1/3, n.split=5, n.split.eval=100,
+ percent.cut= 0.1, rule="lda")
Please wait.....Error in as.double.default(gene.list[jj, 1:k]) :
(list) object cannot be coerced to 'double'
Execution halted
MiPP.Rcheck/00install.out:
installing R.css in E:/biocbld/2.0d/Rpacks/MiPP.Rcheck
---------- Making package MiPP ------------
adding build stamp to DESCRIPTION
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'MiPP'
Formats: text html latex example chm
colon text html latex chm
cv.mipp.rule text html latex chm
get.mipp text html latex chm
get.mipp.lda text html latex chm
get.mipp.logistic text html latex chm
get.mipp.qda text html latex chm
get.mipp.svm.linear text html latex chm
get.mipp.svm.rbf text html latex chm
leuk1 text html latex chm
leuk2 text html latex chm
leukemia text html latex chm
linearkernel.decision.function text html latex chm
mipp text html latex example chm
mipp.preproc text html latex example chm
mipp.rule text html latex chm
mipp.seq text html latex example chm
pre.select text html latex chm
quant.normal text html latex chm
quant.normal2 text html latex chm
rbfkernel.decision.function text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\2.0d\Rpacks\MiPP.Rcheck\00_pkg_src\MiPP\chm\MiPP.chm
Compile time: 0 minutes, 0 seconds
21 Topics
41 Local links
0 Internet links
1 Graphic
Created e:\biocbld\2.0d\Rpacks\MiPP.Rcheck\00_pkg_src\MiPP\chm\MiPP.chm, 25,093 bytes
Compression decreased file by 13,209 bytes.
preparing package MiPP for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: e1071
Loading required package: class
adding MD5 sums
* DONE (MiPP)