Re: BioConductor seems to have replaced MOFA by MOFA2

Hi Steffen, Andreas,

Thanks for your efforts, Steffen. Looks like Andreas uploaded, this still did not seem to fix the problem.

Looks like it still uses api-bioc 3.12, as seen in the build log (https://buildd.debian.org/status/fetch.php?pkg=r-bioc-mofa&arch=all&ver=1.6.1%2Bdfsg-2&stamp=1631512871&raw=0)

and also:

$ apt show ./r-bioc-mofa_1.6.1+dfsg-2_all.deb | grep api-bioc 2>/dev/null

Depends: r-base-core (>= 4.1.1-2), r-api-4.0, r-api-bioc-3.12, r-bioc-rhdf5, r-cran-dplyr, r-cran-reshape2, r-cran-pheatmap, r-cran-corrplot, r-cran-ggplot2, r-cran-ggbeeswarm, r-cran-scales, r-cran-ggally, r-cran-rcolorbrewer, r-cran-cowplot, r-cran-ggrepel, r-bioc-multiassayexperiment, r-bioc-biobase, r-cran-doparallel, r-cran-foreach, r-cran-reticulate, python3-mofapy

I just uploaded it by forcing it to build with api 3.13, hopefully that is fine. Can I ask you to give it a quick look?

And let me know if this is somehow wrong as well? I admit, I do not understand bioconductor well.

Also, I don't see why mofa should be there in the archive, it has no reverse-dep/reverse-build-dep

$ reverse-depends python3-mofapy
Reverse-Depends
* r-bioc-mofa

$ reverse-depends python3-mofapy -b
No reverse dependencies found

$ reverse-depends r-bioc-mofa
Reverse-Recommends
* med-bio

$ reverse-depends r-bioc-mofa -b
No reverse dependencies found

I really think we can replace this with mofa2, since this is a leaf package. What do you say?

On Mon, 13 Sept 2021 at 05:09, Steffen Möller <steffen_moeller@gmx.de> wrote:

Hello,

https://salsa.debian.org/r-pkg-team/r-bioc-mofa/-/blob/master/debian/control

I took the opportunity to reword the description again. From my side it
can be uploaded. Builds in cowbuilder for me.

Best,
Steffen

On 12.09.21 22:14, Andreas Tille wrote:
> Hi Steffen,
>
> ping? Migration is at level 7 with mofa now.
>
> Kind regards
>
> Andreas.
>
> On Wed, Sep 08, 2021 at 09:13:55AM +0200, Andreas Tille wrote:
>> On Mon, Sep 06, 2021 at 09:01:45PM +0200, Andreas Tille wrote:
>>> Hi Steffen,
>>>
>>> please commit a patch that includes your suggestions.
>> ... and ping me once ready since I do not have any means to
>> automatically get commits.
>>
>> Thank you
>> Andreas.
>>
>>> Kind regards
>>>
>>> Andreas.
>>>
>>> On Mon, Sep 06, 2021 at 08:57:32PM +0200, Steffen Möller wrote:
>>>> Hi Andreas,
>>>>
>>>> On 06.09.21 20:48, Andreas Tille wrote:
>>>>> should we drop MOFA in favour of MOFA2?
>>>> Since it still builds, I suggest to keep it in. We should possibly add a
>>>> comment that this package was substitute with MOFA2 (MOFA+) and should
>>>> no longer be used for new projects.
>>>>
>>>> I am saying this since we want to support older projects that still work
>>>> with MOFA and there is this BioConductor transition happening, so it
>>>> cannot be installed from snapshot.
>>>>
>>>> Best,
>>>>
>>>> Steffen
>>>>
>>>>
>>> --
>>> http://fam-tille.de
>> --
>> http://fam-tille.de
>>
>>