SigCheck 2.3.0
Rory Stark
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SigCheck | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### rm -rf SigCheck.buildbin-libdir SigCheck.Rcheck && mkdir SigCheck.buildbin-libdir SigCheck.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigCheck.buildbin-libdir SigCheck_2.3.0.tar.gz >SigCheck.Rcheck\00install.out 2>&1 && cp SigCheck.Rcheck\00install.out SigCheck-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SigCheck.buildbin-libdir --install="check:SigCheck-install.out" --force-multiarch --no-vignettes --timings SigCheck_2.3.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/SigCheck.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SigCheck/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SigCheck' version '2.3.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SigCheck' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking 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
sigCheckKnown: no visible binding for global variable 'knownSignatures'
Undefined global functions or variables:
knownSignatures
* checking Rd files ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'SigCheck-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sigCheck
> ### Title: Create a 'SigCheckObject' and establish baseline performance.
> ### Aliases: sigCheck
>
> ### ** Examples
>
> library(breastCancerNKI)
> data(nki)
> nki <- nki[,!is.na(nki$e.dmfs)]
> data(knownSignatures)
>
> ## survival analysis
> check <- sigCheck(nki, classes="e.dmfs", survival="t.dmfs",
+ signature=knownSignatures$cancer$VANTVEER,
+ annotation="HUGO.gene.symbol")
Warning: NOTE: 10152 features with NA values removed
Warning: NOTE: 23 unmatched features in signature
> check@survivalPval
[1] 5.437319e-11
>
> ## survival analysis with separate training and validation using SVM
> check <- sigCheck(nki, classes="e.dmfs", survival="t.dmfs",
+ signature=knownSignatures$cancer$VANTVEER,
+ annotation="HUGO.gene.symbol",
+ validationSamples=150:319,
+ scoreMethod="classifier")
Warning: NOTE: 10152 features with NA values removed
Warning: NOTE: 23 unmatched features in signature
Error in checkAtAssignment("SigCheckObject", "confusion", "table") :
assignment of an object of class "table" is not valid for @'confusion' in an object of class "SigCheckObject"; is(value, "matrix") is not TRUE
Calls: sigCheck -> sigCheckClassifier -> checkAtAssignment
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'SigCheck-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sigCheck
> ### Title: Create a 'SigCheckObject' and establish baseline performance.
> ### Aliases: sigCheck
>
> ### ** Examples
>
> library(breastCancerNKI)
> data(nki)
> nki <- nki[,!is.na(nki$e.dmfs)]
> data(knownSignatures)
>
> ## survival analysis
> check <- sigCheck(nki, classes="e.dmfs", survival="t.dmfs",
+ signature=knownSignatures$cancer$VANTVEER,
+ annotation="HUGO.gene.symbol")
Warning: NOTE: 10152 features with NA values removed
Warning: NOTE: 23 unmatched features in signature
> check@survivalPval
[1] 5.437319e-11
>
> ## survival analysis with separate training and validation using SVM
> check <- sigCheck(nki, classes="e.dmfs", survival="t.dmfs",
+ signature=knownSignatures$cancer$VANTVEER,
+ annotation="HUGO.gene.symbol",
+ validationSamples=150:319,
+ scoreMethod="classifier")
Warning: NOTE: 10152 features with NA values removed
Warning: NOTE: 23 unmatched features in signature
Error in checkAtAssignment("SigCheckObject", "confusion", "table") :
assignment of an object of class "table" is not valid for @'confusion' in an object of class "SigCheckObject"; is(value, "matrix") is not TRUE
Calls: sigCheck -> sigCheckClassifier -> checkAtAssignment
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/SigCheck.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SigCheck' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'signature' in package 'SigCheck'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'SigCheck' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SigCheck' as SigCheck_2.3.0.zip
* DONE (SigCheck)