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Package 387/444HostnameOS / ArchBUILDCHECKBUILD BIN
segmentSeq 1.3.1
Thomas J. Hardcastle
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq
Last Changed Rev: 51302 / Revision: 53825
Last Changed Date: 2010-12-07 02:41:46 -0800 (Tue, 07 Dec 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ ERROR ] OK 

Summary

Package: segmentSeq
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.3.1.tar.gz
StartedAt: 2011-03-17 17:31:14 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 17:33:34 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 139.9 seconds
RetCode: 1
Status:  ERROR 
CheckDir: segmentSeq.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/segmentSeq.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.3.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'segmentSeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 ... NOTE
getCounts : <anonymous>: no visible binding for global variable 'tag'
lociLikelihoods: no visible binding for global variable 'chr'
* 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 examples ... ERROR
Running examples in 'segmentSeq-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alignmentData-class
> ### Title: Class "alignmentData"
> ### Aliases: alignmentData-class alignmentData [,alignmentData-method
> ###   [,alignmentData,ANY,ANY-method dim,alignmentData-method
> ###   initialize,alignmentData-method show,alignmentData-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> # Define the chromosome lengths for the genome of interest.
> 
> chrlens <- c(2e6, 1e6)
> 
> # Define the files containing sample information.
> 
> datadir <- system.file("data", package = "segmentSeq")
> libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")
> 
> # Establish the library names and replicate structure.
> 
> libnames <- c("SL9", "SL10", "SL26", "SL32")
> replicates <- c(1,1,2,2)
> 
> # Process the files to produce an 'alignmentData' object.
> 
> alignData <- processTags(libfiles, dir = datadir, replicates, libnames, chrlens, chrs = c(">Chr1", ">Chr2"), header = TRUE)
processing...Warning in file(file, "rt") :
  cannot open file '/Users/biocbuild/bbs-2.8-bioc/meat/segmentSeq.Rcheck/segmentSeq/data/SL9.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: processTags -> lapply -> FUN -> read.table -> file
Execution halted

segmentSeq.Rcheck/00install.out:

* installing *source* package 'segmentSeq' ...
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'baySeq'

The following object(s) are masked from 'package:base':

    rbind

Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:baySeq':

    rbind

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (segmentSeq)

segmentSeq.Rcheck/segmentSeq-Ex.timings:

nameusersystemelapsed