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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:4}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
