BioC 3.3: CHECK report for SigCheck on linux2.bioconductor.org

Package: SigCheck

Version: 2.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SigCheck_2.3.0.tar.gz

StartedAt: 2015-10-27 08:05:59 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:07:57 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 117.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: SigCheck.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SigCheck_2.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SigCheck.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SigCheck’ can be installed ... [10s/10s] 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
* 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 ... 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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/SigCheck.Rcheck/00check.log’
for details.

* 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
* DONE (SigCheck)

name	user	system	elapsed
SigCheckObject-class	0.002	0.000	0.003
knownSignatures	0.017	0.003	0.022
nkiResults	0.001	0.000	0.000