[Bioc-devel] How to move package from workflow to software

On Dec 5, 2019, at 4:39 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Julien,

I've done a basic review of your package, BgeeCall as a software package. 

This is a very basic review of just running BiocCheck. There need to be some improvements in your package to make the switch.

https://gist.github.com/nturaga/189b71ca4e6247747b72d4163a7b2bf1

Please take a look. 

Nitesh 

On Nov 15, 2019, at 12:44 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Julien,

We have decided that it shouldn't go through a deprecation cycle. Instead, I will do a quick review of the package(build + check, and the times for build and check are reasonable) from my end. And if all is acceptable I'll make the switch on my end. 

I'll get back to you once this is complete.

Best,

Nitesh 

On Nov 15, 2019, at 9:30 AM, Julien Wollbrett <julien.wollbrett at unil.ch> wrote:

Hello Nitesh,

Thank you for your answer.

I added some functionalities to the BgeeCall package that are not compatible to a workflow approach.
It is now possible to run some steps outside of the initial workflow, to download files from different locations, to reuse data generated by the user or already processed by the Bgee team, etc.

Furthermore BgeeCall does not only reuse already existing bioconductor packages and combine them to create a workflow. It corresponds to a new approach allowing to generate present/absent gene expression calls from RNA-Seq libraries without using an arbitrary cutoff.

I would be very happy if you can help me moving it to the software section.

Best,

Julien

Le 15.11.19 ? 11:59, Turaga, Nitesh a ?crit :

Hi,

Changing the BiocViews section in the DESCRIPTION file doesn't change your package from a workflow package to a software package.

There are fundamental differences between workflow packages and software packages in the way we handle them within Bioconductor. Could you tell us why you'd like to change it from a workflow to a software package?

The Bioc team, would have to assist in moving it to the software section.

Best,

Nitesh

?On 11/15/19, 4:46 AM, "Bioc-devel on behalf of Julien Wollbrett" <bioc-devel-bounces at r-project.org on behalf of julien.wollbrett at unil.ch> wrote:

  Hello,
       I am the maintainer of the BgeeCall R package.
       In bioconductor 3.9 my package was registered as a workflow package.
  I modified my DESCRIPTION file before the release 3.10 in order to move
  the package to the software section hopping for it to automatically move
  after the new release. Unfortunately it did not work.
       Could you please tell me how to do to move BgeeCall to the software section?
       Thank you,
       Julien

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On Dec 9, 2019, at 10:31 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Julien,

After re-considering how this package should go forward. Please submit your package to the  https://github.com/Bioconductor/Contributions. This will put your package through the Single Package Builder which will help us review your package better.

There have been significant code changes which are better managed and reviewed via that process. 


Best,

Nitesh 

On Dec 5, 2019, at 4:39 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Julien,

I've done a basic review of your package, BgeeCall as a software package. 

This is a very basic review of just running BiocCheck. There need to be some improvements in your package to make the switch.

https://gist.github.com/nturaga/189b71ca4e6247747b72d4163a7b2bf1

Please take a look. 

Nitesh 

On Nov 15, 2019, at 12:44 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Julien,

We have decided that it shouldn't go through a deprecation cycle. Instead, I will do a quick review of the package(build + check, and the times for build and check are reasonable) from my end. And if all is acceptable I'll make the switch on my end. 

I'll get back to you once this is complete.

Best,

Nitesh 

On Nov 15, 2019, at 9:30 AM, Julien Wollbrett <julien.wollbrett at unil.ch> wrote:

Hello Nitesh,

Thank you for your answer.

I added some functionalities to the BgeeCall package that are not compatible to a workflow approach.
It is now possible to run some steps outside of the initial workflow, to download files from different locations, to reuse data generated by the user or already processed by the Bgee team, etc.

Furthermore BgeeCall does not only reuse already existing bioconductor packages and combine them to create a workflow. It corresponds to a new approach allowing to generate present/absent gene expression calls from RNA-Seq libraries without using an arbitrary cutoff.

I would be very happy if you can help me moving it to the software section.

Best,

Julien

Le 15.11.19 ? 11:59, Turaga, Nitesh a ?crit :

Hi,

Changing the BiocViews section in the DESCRIPTION file doesn't change your package from a workflow package to a software package.

There are fundamental differences between workflow packages and software packages in the way we handle them within Bioconductor. Could you tell us why you'd like to change it from a workflow to a software package?

The Bioc team, would have to assist in moving it to the software section.

Best,

Nitesh

?On 11/15/19, 4:46 AM, "Bioc-devel on behalf of Julien Wollbrett" <bioc-devel-bounces at r-project.org on behalf of julien.wollbrett at unil.ch> wrote:

 Hello,
      I am the maintainer of the BgeeCall R package.
      In bioconductor 3.9 my package was registered as a workflow package.
 I modified my DESCRIPTION file before the release 3.10 in order to move
 the package to the software section hopping for it to automatically move
 after the new release. Unfortunately it did not work.
      Could you please tell me how to do to move BgeeCall to the software section?
      Thank you,
      Julien

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.