BioC experimental data: CHECK report for EatonEtAlChIPseq on linux2.bioconductor.org

Package: EatonEtAlChIPseq

Version: 0.9.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings EatonEtAlChIPseq_0.9.0.tar.gz

StartedAt: 2015-10-24 12:06:04 -0400 (Sat, 24 Oct 2015)

EndedAt: 2015-10-24 12:07:47 -0400 (Sat, 24 Oct 2015)

EllapsedTime: 103.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: EatonEtAlChIPseq.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 EatonEtAlChIPseq_0.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.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 ‘EatonEtAlChIPseq/DESCRIPTION’ ... OK
* this is package ‘EatonEtAlChIPseq’ version ‘0.9.0’
* 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 ‘EatonEtAlChIPseq’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is 20.6Mb
  sub-directories of 1Mb or more:
    extdata  20.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 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 ... NOTE
  Error: Input/Output
    'readAligned' failed to parse files
    dirPath: '/home/biocbuild/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.Rcheck/EatonEtAlChIPseq/extdata/GSM424494_wt_G2_orc_chip_rep1_S288C_14.mapview.txt.gz'
    pattern: ''
    type: 'MAQMapview'
    error: invalid class "IntegerQuality" object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
  Call sequence:
  13: .throw(SRError("Input/Output", msg))
  12: .throw(SRError("Input/Output", msg))
  11: value[[3L]](cond)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatch({
         switch(type, SolexaExport = .readAligned_SolexaExport(dirPath, 
             pattern = pattern, ...), SolexaPrealign = , SolexaAlign = , 
             SolexaRealign = .readAligned_SolexaAlign(dirPath, pattern = pattern, 
                 ...), SolexaResult = .readAligned_SolexaResult(dirPath, 
                 pattern = pattern, ...), 
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘EatonEtAlChIPseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: orcAligns
> ### Title: Alignments of ChIP-seq data to yeast chromosome XIV
> ### Aliases: orcAlignsRep1 orcAlignsRep2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(orcAlignsRep1)
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist
Error: Input/Output
  'readAligned' failed to parse files
  dirPath: '/home/biocbuild/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.Rcheck/EatonEtAlChIPseq/extdata/GSM424494_wt_G2_orc_chip_rep1_S288C_14.mapview.txt.gz'
  pattern: ''
  type: 'MAQMapview'
  error: invalid class “IntegerQuality” object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.Rcheck/00check.log’
for details.

* installing *source* package ‘EatonEtAlChIPseq’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (EatonEtAlChIPseq)

name	user	system	elapsed