qrqc 1.18.0
Vince Buffalo
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/qrqc | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/qrqc.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ ‘brew’ ‘xtable’
‘Rsamtools’ ‘testthat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘qrqc’ can be installed ... [25s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
‘Rsamtools’ ‘brew’ ‘testthat’ ‘xtable’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generateReads: no visible global function definition for
‘write.XStringSet’
basePlot,SequenceSummary: no visible binding for global variable ‘base’
basePlot,list: no visible binding for global variable ‘base’
gcPlot,SequenceSummary: no visible binding for global variable
‘position’
gcPlot,list: no visible binding for global variable ‘position’
getBase,SequenceSummary: no visible binding for global variable ‘base’
getBaseProp,SequenceSummary: no visible binding for global variable
‘base’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
‘position’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
‘entropy’
kmerEntropyPlot,list: no visible binding for global variable ‘position’
kmerEntropyPlot,list: no visible binding for global variable ‘entropy’
kmerKLPlot,SequenceSummary: no visible binding for global variable
‘kmer’
kmerKLPlot,SequenceSummary: no visible binding for global variable
‘position’
kmerKLPlot,SequenceSummary: no visible binding for global variable ‘kl’
kmerKLPlot,list : <anonymous>: no visible binding for global variable
‘kmer’
kmerKLPlot,list: no visible binding for global variable ‘position’
kmerKLPlot,list: no visible binding for global variable ‘kl’
kmerKLPlot,list: no visible binding for global variable ‘kmer’
qualPlot,FASTQSummary: no visible binding for global variable
‘position’
qualPlot,list: no visible binding for global variable ‘position’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘qrqc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmerKLPlot-methods
> ### Title: Plot K-L Divergence Components for a Subset of k-mers to Inspect
> ### for Contamination
> ### Aliases: kmerKLPlot kmerKLPlot-methods
> ### kmerKLPlot,SequenceSummary-method kmerKLPlot,list-method
> ### Keywords: methods graphics
>
> ### ** Examples
>
> ## Load a somewhat contaminated FASTQ file
> s.fastq <- readSeqFile(system.file('extdata', 'test.fastq',
+ package='qrqc'), hash.prop=1)
Warning in eval(expr, envir, enclos) :
Some k-mer counts are infinite, meaning there was occurence of a k-mer over the maximum double size.
>
> ## Load a really contaminated FASTQ file
> s.contam.fastq <- readSeqFile(system.file('extdata',
+ 'test-contam.fastq', package='qrqc'), hash.prop=1)
>
> ## Load a random (equal base frequency) FASTA file
> s.random.fasta <- readSeqFile(system.file('extdata',
+ 'random.fasta', package='qrqc'), type="fasta", hash.prop=1)
>
> ## Make K-L divergence plot - shows slight 5'-end bias. Note units
> ## (bits)
> suppressWarnings(kmerKLPlot(s.fastq))
>
> ## Plot multiple K-L divergence plots
> suppressWarnings(kmerKLPlot(list("highly contaminated"=s.contam.fastq, "less
+ contaminated"=s.fastq, "random"=s.random.fasta)))
Error in `$<-.data.frame`(`*tmp*`, "sample", value = "less\n contaminated") :
replacement has 1 row, data has 0
Execution halted