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
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"
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
- 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:
>>
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
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
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
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
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
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
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
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
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
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
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
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
16 matches
Mail list logo