[Bioc-devel] Bioconductor package update

[Martin Morgan]

For RELEASE 3.7 you need to push changes to the git.bioconductor.org 
repository RELEASE_3_7 branch with a version bump to 1.0.1. See

 
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/#optional-merge-changes-to-the-current-release-branch

remember that changes to the release branch should be 'bug fixes', not 
new features.

Martin

On 07/10/2018 01:08 PM, Ahrim Youn wrote:
> Dear Martin,
> 
> The updates that I made to man files are not reflected in the manual of
> the package (release 3.7) :
> 
> https://bioconductor.org/packages/release/bioc/manuals/BiFET/man/BiFET.pdf
> 
> In fact, I found that all files in the release_3_7 are old files that were
> not updated since January and not in sync with the files in GitHub
> repository.
> 
> How can I update the files in the release_3_7?
> 
> Thank you very much for your help,
> Ahrim
> 
> On 7/3/18, 11:09 AM, "Nathan Lawlor" <Nathan.Lawlor using jax.org> wrote:
> 
>> Apologies, I meant to say July 2nd, not June 2nd.
>>
>> On 7/3/18, 11:03 AM, "Nathan Lawlor" <Nathan.Lawlor using jax.org> wrote:
>>
>>> Hi Ahrim,
>>>
>>> I forget exactly when the nightly build/check reports occur for
>>> Bioconductor packages but looking at the BiFET report: (BiFET:
>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/BiFET/) it looks
>>> like the build for June 2nd has not yet been updated? So any changes you
>>> made on June 2nd won’t be reflected just yet
>>>
>>> Best,
>>> Nathan
>>>
>>> On 7/3/18, 10:28 AM, "Ahrim Youn" <Ahrim.Youn using jax.org> wrote:
>>>
>>>> Dear Martin,
>>>>
>>>> Thank you for your answer. I updated the man/ files and bumped the
>>>> version
>>>> in the DESCRIPTION file yesterday, but the change is not reflected in
>>>> the
>>>> manual of the package.
>>>>
>>>> Ahrim
>>>>
>>>> On 6/30/18, 11:32 AM, "Martin Morgan" <martin.morgan using roswellpark.org>
>>>> wrote:
>>>>
>>>>> (cc'ing bioc-devel, where questions like this should be posted so other
>>>>> developers can benefit / contribute)
>>>>>
>>>>> I see
>>>>>
>>>>> commit 5fea2c1f2e0f3407cb6804db638b565e0a2ea5dd
>>>>> Author: Ahrim Youn <youna using mlg-jgm164.local.jax.org>
>>>>> Date:   Fri Jun 22 16:34:02 2018 -0400
>>>>>
>>>>>      update version number
>>>>>
>>>>>   DESCRIPTION          |  2 +-
>>>>>   R/library_function.r | 12 ++++++------
>>>>>   2 files changed, 7 insertions(+), 7 deletions(-)
>>>>>
>>>>> where you changed the R/ file roxygen comment but did not regenerate
>>>>> the
>>>>> documentation, I guess with
>>>>>
>>>>>    devtools::document()
>>>>>
>>>>> The build system does not do this for you. So Update the man/ files and
>>>>> bump the version.
>>>>>
>>>>> Martin
>>>>>
>>>>> On 06/30/2018 10:55 AM, Ahrim Youn wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I¹m a maintainer of the package BiFET and I¹m having a problem in
>>>>>> changing the manual of the package :
>>>>>>
>>>>>>
>>>>>> http://bioconductor.org/packages/devel/bioc/manuals/BiFET/man/BiFET.pd
>>>>>> f
>>>>>>
>>>>>> I changed the comments in the main R function which is linked to the
>>>>>> manual, and updated it to both github and biocondutor, but the manual
>>>>>> pdf file does not change.
>>>>>>    What is interesting is that the Vignette which I also updated is
>>>>>> updating according to my change :
>>>>>>
>>>>>>
>>>>>> http://bioconductor.org/packages/devel/bioc/vignettes/BiFET/inst/doc/B
>>>>>> i
>>>>>> F
>>>>>> E
>>>>>> T.html
>>>>>>
>>>>>>
>>>>>> Do you know why the manual pdf file does not update?
>>>>>>
>>>>>> Thanks for your help!
>>>>>>
>>>>>> Best,
>>>>>> Ahrim
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