Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

r Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel <mailto:bioc-devel-boun...@r-project.org>> on behalf of Christian Holland > ma

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

lm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of > Christian Holland > Sent: Tuesday, April 7, 2020 7:22 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Unit tests pass locally but fail on

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

alo, New York 14263 From: Bioc-devel on behalf of Christian Holland Sent: Tuesday, April 7, 2020 7:22 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines Hi there, the unit tests (implemented with test

[Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

Hi there, the unit tests (implemented with testthat) of my package (https://github.com/saezlab/dorothea ) run smoothly on local machines (tested for Linux, Windows and macOS). However, on the Bioconductor machines (both Linux and Window) a particular test fa

Re: [Bioc-devel] Unit Tests & Test Coverage

r all. Best regards, Juan Pablo From: Hervé Pagès Sent: Friday, March 24, 2017 8:29:08 AM To: Romero, Juan Pablo; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Unit Tests & Test Coverage The coverage badge finally got updated: https://biocond

Re: [Bioc-devel] Unit Tests & Test Coverage

The coverage badge finally got updated: https://bioconductor.org/packages/3.5/bioc/html/EventPointer.html I didn't do anything. Looks like for some reason it took a long time for the coverage result on codecov.io to propagate to the package landing page. Cheers, H. On 03/23/2017 01:32 PM, H

Re: [Bioc-devel] Unit tests

ncouraged but not required. > Dan > > > - Original Message - > > From: "张腾" <2573552...@qq.com> > > To: "bioc-devel" > > Sent: Thursday, March 23, 2017 7:33:22 PM > > Subject: [Bioc-devel] Unit tests > > > Hello all, > > >

Re: [Bioc-devel] Unit tests

t; To: "bioc-devel" > Sent: Thursday, March 23, 2017 7:33:22 PM > Subject: [Bioc-devel] Unit tests > Hello all, > > I am not sure whether the Unit tests are necessary to release a package for > Bioconductor. In my package, only one main function to export and oth

[Bioc-devel] Unit tests

Hello all, I am not sure whether the Unit tests are necessary to release a package for Bioconductor. In my package, only one main function to export and other functions are hidden into the main function. In my package, the input data are some files in BAM format and the output is a report in H

Re: [Bioc-devel] Unit Tests & Test Coverage

Hi Juan Pablo, Thanks for adding unit tests to your package. We really encourage developers to do this. I'm sorry that this is not reflected on EventPointer's landing page. I investigated this a bit (I'm not familiar with how the coverage badges are generated on the package landing pages) and he

[Bioc-devel] Unit Tests & Test Coverage

Hi, I'm currently doing the last updates to my package EventPointer before the deadline for next BioC release. I've added unit tests according to the guide lines in http://bioconductor.org/developers/unitTesting-guidelines/ and the package build report shows no problems for both build and ch

Re: [Bioc-devel] Unit tests present/ coverage "unknown"

I do see the same problem for rols. I assume this will clear up at some point, although any suggestion on how to avoid such glitches would be helpful. Laurent On 25 March 2016 16:42, Zach Skidmore wrote: > Hi All, > > Maybe i'm missing something but I don't quite understand why the "test > cov

[Bioc-devel] Unit tests present/ coverage "unknown"

Hi All, Maybe i'm missing something but I don't quite understand why the "test coverage" badge on the GenVisR page displays unknown. I have unit tests set up with testthat, and looking at the R CMD CHECK reports I see that they are running however the badge still reads as "unknown". Any Ideas

Re: [Bioc-devel] unit tests for C code inside a package

Thank you both for your suggestions. Peter: Rcpp attributes seem great but right now I would prefer to avoid changing all the pure C structs of my old codebase in C++ classes and so on. But if in the future we will need to add new features I will definitely add these two ++ :) Dan: yep, that was r

Re: [Bioc-devel] unit tests for C code inside a package

- Original Message - > From: "Elena Grassi" > To: bioc-devel@r-project.org > Sent: Monday, January 26, 2015 1:14:59 AM > Subject: [Bioc-devel] unit tests for C code inside a package > > Hi, > > I'm writing a package that calculates total affini

Re: [Bioc-devel] unit tests for C code inside a package

My favorite solution to this would be to use Rcpp attributes to add R-level functions for each C function. You can use these just for testing and skip the exporting and manual pages. That's not quite what you asked for but it would work. BTW transcription factors are my thing so I'm eager to tr

[Bioc-devel] unit tests for C code inside a package

Hi, I'm writing a package that calculates total affinity (see PMID 21335606 and 16873464 if transcription factors are your thing): up until now in our lab we've used a pure C tool that needs fasta and tabular formatted PFM-PWM files but we are willing to produce something more comfortable that ste