Re: [Bioc-devel] Unit tests

There are multiple examples of unit tests for parsers. In your case I would include a small BAM file in /inst/extdata and make a test which parses this file and asserts a number of things about the output. Depending on philosophy, this may not be considered a pure unit test, but it is very

Re: [Bioc-devel] Unit tests

Here's what BiocCheck says: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/ So, unit tests are encouraged but not required. Dan - Original Message - > From: "张腾" <2573552...@qq.com> > To: "bioc-devel"

[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

Re: [Bioc-devel] xps build problem on veracruz2

- Original Message - > From: "Hervé Pagès" > To: "cstrato" , "bioc-devel" > Sent: Thursday, March 23, 2017 12:14:38 PM > Subject: Re: [Bioc-devel] xps build problem on veracruz2 > On 03/23/2017 11:09 AM, cstrato wrote: >>

Re: [Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis

Hi Alexey, Based on the Travis build report, it looks like Travis used install.packages() to install reactome.db. What makes you think it used biocLite()? The problem seems to be related to the fact that reactome.db deps are divided in 2 groups: binary packages on one side and source packages

[Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis

Hello all, I'm using travis for checking my project build and found something that looks like a bug in how biocLite installs package dependencies. It appears that at some point biocLite started to install them in an alphabet order, not topological, and specifically on OS X. I've made a small

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

Re: [Bioc-devel] xps build problem on veracruz2

On 03/23/2017 11:09 AM, cstrato wrote: Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was

Re: [Bioc-devel] Bioconductor 3.5 release: deprecated packages

Sorry, xcms was a mistake on my part. This package is not deprecated. Valerie On 03/23/2017 10:06 AM, Obenchain, Valerie wrote: > Just a heads up about deprecated packages. > > These have been 'deprecated' in Biocondcutor 3.4 and will be 'defunct' > in Bioconductor 3.5. The 'defunct' status

Re: [Bioc-devel] xps build problem on veracruz2

Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay

Re: [Bioc-devel] xps build problem on veracruz2

Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT

Re: [Bioc-devel] xps build problem on veracruz2

Hi, veracruz2 is in testing / setup stage and is not the official Mac devel builder. See my post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010629.html Currently there are more pressing issues than the ROOT system dependency. Rest assured that ROOT will be correctly installed

Re: [Bioc-devel] questions about windows build execute permissions and R version dependency

You can also test your package on R Travis against R 3.4 as shown at https://travis-ci.org/leekgroup/recount#L518. Just use this on your .travis.yml file https://github.com/leekgroup/recount/blob/master/.travis.yml#L3 On Thu, Mar 23, 2017 at 4:26 AM, Martin Morgan

[Bioc-devel] xps build problem on veracruz2

Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So

[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

Re: [Bioc-devel] questions about windows build execute permissions and R version dependency

On 03/22/2017 11:08 PM, Alicia Schep wrote: Hi, I have a two questions about the bioconductor build and BiocCheck process when submitting packages. 1) My submitted package ('motifmatchr') returns the following warning on the Windows computer: Warning: file 'motifmatchr/cleanup' did not have