[Bioc-devel] EXTERNAL: amplican tokay2 i386 error

[Martin Morgan]

On 03/19/2018 01:45 PM, Marcel Ramos wrote:
> Hi Kornel,
> 
> I downloaded your package from our git repo and ran check locally on
> Windows 7.
> It seems like there are some issues with the `data.table` (version
> 1.10.4-3) package.
> Here is my result for the `i386` architecture:
> 
>>>> R CMD check --force-multiarch --no-vignettes amplican_1.1.6.tar.gz
> [truncated]...
> * checking examples ...
> ** running examples for arch 'i386' ... ERROR
> Running examples in 'amplican-Ex.R' failed
> The error most likely occurred in:
> 
>> ### Name: amplicanPipeline
>> ### Title: Wraps main package functionality into one function.
>> ### Aliases: amplicanPipeline
>>
>> ### ** Examples
>>
>> # path to example config file
>> config <- system.file("extdata", "config.csv", package = "amplican")
>> # path to example fastq files
>> fastq_folder <- system.file("extdata", package = "amplican")
>> # output folder
>> results_folder <- tempdir()
>>
>> #full analysis, not knitting files automatically
>> amplicanPipeline(config, fastq_folder, results_folder, knit_reports =
> FALSE)
> Checking write access...
> Checking configuration file...
> Making alignments...
> Aligning reads for barcode_1
> Aligning reads for barcode_2
> Saving alignments...
> Saving parameters...
> Saving unassigned sequences...
> Saving barcode statistics...
> Translating alignments into events...
> Saving complete events - unfiltered...
> *Error in data.table::foverlaps(aln_fwd, aln_rve, type = "any", which =
> TRUE,  :**
> **  negative length vectors are not allowed*

Thanks Marcel; FWIW 'negative length vectors' typically occurs with 
integer overflow, which on 32-bit platforms are limited to 2^31 - 1

If this is the cause then maybe amplican should anticipate this, failing 
  more gracefully or working around the issue (e.g., by processing in 
batches...)

Martin


> Calls: amplicanPipeline -> amplicanConsensus -> <Anonymous>
> Execution halted
> ** running examples for arch 'x64' ... OK
> * checking for unstated dependencies in 'tests' ... OK
> * checking tests ...
> ** running tests for arch 'i386' ...
>    Running 'testthat.R'
>   *ERROR*
> Running the tests in 'tests/testthat.R' failed.
> Last 13 lines of output:
> 
>    Loading required package: data.table
> 
>    Attaching package: 'data.table'
> 
>    The following object is masked from 'package:IRanges':
> 
>        shift
> 
>    The following objects are masked from 'package:S4Vectors':
> 
>        first, second
> 
>    >
>    > test_check("amplican")
> ** running tests for arch 'x64' ...
>    Running 'testthat.R'
>   OK
> [truncated] ...
> 
> ## R.version
> R.version
>                 _
> platform       x86_64-w64-mingw32
> arch           x86_64
> os             mingw32
> system         x86_64, mingw32
> status         Under development (unstable)
> major          3
> minor          5.0
> year           2018
> month          03
> day            18
> svn rev        74422
> language       R
> version.string R Under development (unstable) (2018-03-18 r74422)
> nickname       Unsuffered Consequences
> 
> ## sessionInfo() header
> R Under development (unstable) (2018-03-18 r74422)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> 
> Regards,
> 
> Marcel
> 
> 
> On 03/16/2018 05:55 AM, Kornel Labun wrote:
>> Hi,
>>
>> Could you help me diagnose what is wrong with my package, amplican, that
>> fails to pass check on tokay2 i386?
>>
>> I fail to understand what might be wrong from the report
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/amplican/tokay2-checksrc.html
>> .
>> It is long standing problem, since the first moment we moved into devel
>> 3.7. I think it might be related to my data.table package which I import as
>> I have tried to comment out some tests and examples, but it seems I am
>> running in circle.
>>
>> Best,
>> Kornel Labun
>>
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
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