BioC 3.1: CHECK report for jmosaics on morelia

Package: jmosaics

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings jmosaics_1.8.0.tar.gz

StartedAt: 2015-10-09 03:16:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:18:45 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 106.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: jmosaics.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings jmosaics_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/jmosaics.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘jmosaics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘jmosaics’ version ‘1.8.0’
* 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 ‘jmosaics’ can be installed ... [6s/6s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘mosaics:::.margDist_2S’
  See the note in ?`:::` about the use of this operator.
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘jmosaics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jmosaics-package
> ### Title: Joint analysis of multiple ChIP-seq data sets
> ### Aliases: jmosaics-package jmosaics
> 
> ### ** Examples
> 
> 
> ## step by step not run
> ## Not run: 
> ##D bin1 <- readBins(type = c("chip", "M", "GC", "N","input"), 
> ##D  fileName = c("h3k27me3_chip_chr10.txt",
> ##D  "./M_chr10.txt", "./GC_chr10.txt", "./N_chr10.txt",
> ##D "h3k27me3_input_chr10.txt"))
> ##D bin2 <- readBins(type = c("chip", "M", "GC", "N","input"), 
> ##D  fileName = c("h3k4me1_chip_chr10.txt",
> ##D  "./M_chr1.txt", "./GC_chr10.txt", "./N_chr10.txt",
> ##D  "h3k4me1_input_chr10.txt"))
> ##D origin_bin <- list(bin1, bin2)
> ## End(Not run)
> 
> data("jmosaics_example_data")
> bin <- readBinsMultiple(origin_bin)
> fit1 <- mosaicsFit(bin[[1]], analysisType = "IO")
Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Info: done!
> fit2 <- mosaicsFit(bin[[2]], analysisType = "IO")
Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Info: done!
> fit <- list(fit1,fit2)
> result <- jmosaicsPattern(fit, region_length=1, FDR=0.01, thres=c(10,10), type=c('B','E','Pattern'), patternInfo='FALSE')
Error in while (max(abs(L)) > eps & iter < 100) { : 
  missing value where TRUE/FALSE needed
Calls: jmosaicsPattern -> .EM
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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/jmosaics.Rcheck/00check.log’
for details.

* installing *source* package ‘jmosaics’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (jmosaics)

name	user	system	elapsed