[Bioc-devel] no more commits allowed before release ?
Alright, I'll do one more final round of manual testing, just in case. At the moment, I can see the reports for 2014-10-08 16:20:09 -0700 (Wed, 08 Oct 2014) , so I'll just wait to see the next one, which should include my recent changes. I was confusing myself between the time difference, the time when the build server runs, and the time when the corresponding report becomes available. I'll take the time to introduce unit tests when things cool down after the release. I was using man page examples as a sort of unit tests, but for some lengthy functions (~1 min), I didn't cover multiple scenarios to respect a reasonable CMD check time. But this bug fix probably proved me wrong. Thanks for your time Kevin
On 10 October 2014 16:15, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
----- Original Message -----
From: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie> To: "Dan Tenenbaum" <dtenenba at fhcrc.org> Cc: bioc-devel at r-project.org Sent: Friday, October 10, 2014 8:03:25 AM Subject: Re: [Bioc-devel] no more commits allowed before release ? Hi Dan, Ok good, you have just given me the most recent commit that I did today, so the ones I was most concerned about (from yesterday) should be there too, that's good for me. The changes should show up in the next build report.
I do see a commit with the commit message "Bug fix...".
Maybe the build system just started the checks just before I pushed those changes yesterday morning (10am, Irish time.. so around 2am Seattle time, I believe), which could have left them out of the build report.
Changes need to be committed by 4:20 PM Seattle time in order to show up in the following day's build report.
I always run CMD check locally before submitting. That wasn't the
problem, it was just a scenario that I hadn't tested in a while. I
am considering throwing some unit tests in the package soon, but I
won't have time before the release.. I'll have to spend some time to
do it correctly as it'd be my first time writing unit tests for an R
package (did it in other languages before).
* Are the unit tests run by the BiocCheck ? In which case, I
would need to add another testing dataset corresponding to the
scenario that I fixed yesterday.
Yes, unit tests are run by BiocCheck, our howto page shows you how to make this happen: http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/ Dan
Cheers Kevin On 10 October 2014 15:40, Dan Tenenbaum < dtenenba at fhcrc.org > wrote: ----- Original Message -----
From: "Kevin Rue-Albrecht" < kevin.rue at ucdconnect.ie > To: bioc-devel at r-project.org Sent: Friday, October 10, 2014 7:31:36 AM Subject: [Bioc-devel] no more commits allowed before release ? Dear all, I fixed a bug affecting one particular situation in my package (GOexpress) yesterday, and pushed the changes to GitHub. However, the webhook did not trigger to update the page, due to the feature freeze if I understand the schedule correctly ( http://www.bioconductor.org/developers/release-schedule/ ).
I see a commit at 2014-10-10 13:13:54 +0100 (your time) / 2014-10-10 05:11:29 -0700 (Seattle time). Is that the one? The commit message is " Little addition of details to the description of DAM and NCN participation in the project." We do not disable commits to trunk. We have disabled commits to the current release branch (Bioconductor 2.14) because 2.14 builds have stopped.
I suppose I need to wait the release is out to push these changes again to update the SVN ? Or is it still possible to include those changes in the release? From the schedule, it still sounds possible "Package maintainers should limit changes to "show-stopper" bugs and documentation improvements."
It is possible, but there are very few build cycles left till the release, so please build and check your package locally before committing changes and then keep an eye on the build report to make sure that the package built ok. Dan
Sincerely, Kevin -- K?vin RUE-ALBRECHT Wellcome Trust Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en [[alternative HTML version deleted]]
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-- K?vin RUE-ALBRECHT Wellcome Trust Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
K?vin RUE-ALBRECHT Wellcome Trust Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en [[alternative HTML version deleted]]