[Bioc-devel] EXTERNAL: amplican tokay2 i386 error

Marcel Ramos Marcel.Ramos at roswellpark.org
Mon Mar 19 18:45:36 CET 2018

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
* 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 =
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*
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'
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':


  The following objects are masked from 'package:S4Vectors':

      first, second

  > test_check("amplican")
** running tests for arch 'x64' ...
  Running 'testthat.R'
[truncated] ...

## 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



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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