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 |
* 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
* 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)