Use bioconductor-anndatar v1.0.0

[lazappi]

We now have a GitHub v0.1.0 release of {anndataR}. It would make sense to pin to this version for consistency. I couldn't find the Docker file where this should be done so currently this just has some minor script changes.

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[github-actions]

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[fmalmeida]

Hi @lazappi ,
Thanks for sharing. I believe the Dockerfile had been generated privately before since the tools is not available in conda.
On that note, do you think it would be possible to pack it in conda so module can be easier mantained via the seqera containers?

[grst]

A bioconductor release is planned, isn't it @lazappi?
I think conda recipes are built for all bioconductor packages, so we'll get it "for free" then.

So for now, I'd be pragmatic and just rebuild the container with the latest version.

[lazappi]

Yep, we are planning to submit to Bioconductor soon and then it should get automatically added to conda. I don't want to do it manually before then to avoid having two conda packages.

FYI we should have a fairly major 0.2.0 this week or so, so it might be worth waiting for that.

[lazappi]

There is now a 0.2.0 release on GitHub https://github.com/scverse/anndataR/releases/tag/v0.2.0. Note that we have changed the HDF5 backend so you will need to have {rhdf5} instead of {hdf5r} to read/write H5AD files.

[grst]

anndataR is now officially part of bioconductor. @lazappi do you know why the corresponding bioconductor-anndatar package does not exist yet on bioconda?

[lazappi]

Not exactly. I'm guessing the conda packages for the latest release haven't been published yet. I don't know what the process for that is but it's handled centrally somewhere.

[grst]

bioconductor-anndatar is now available from bioconda.

[fmalmeida]

Hi @grst ,
Awesome :)

[fmalmeida]

This PR is going to master.

Should I create a new work for the issue where we create the seqera container and then update the module?

[grst]

Sure, whatever is easiest for you!

[fmalmeida]

Hi @grst ,
unfortunately, the required packages have a dependency problem.
The conda package references to R base version are mutually exclusive :/

---

Could not solve for environment specs
The following packages are incompatible
├─ bioconductor-anndatar =* * is installable and it requires
│  └─ r-base >=4.5,<4.6.0a0 *, which can be installed;
├─ bioconductor-singlecellexperiment =* * is not installable because there are no viable options
│  ├─ bioconductor-singlecellexperiment 1.0.0 would require
│  │  └─ r-base [=3.4.1 *|>=3.4.1,<3.4.2.0a0 *] but there are no viable options
│  │     ├─ r-base 3.4.1 conflicts with any installable versions previously reported;
│  │     └─ r-base 3.4.1 would require
│  │        └─ icu =54 *, which does not exist (perhaps a missing channel);
│  ├─ bioconductor-singlecellexperiment [1.0.0|1.2.0|1.4.0] would require
│  │  ├─ bioconductor-summarizedexperiment >=1.12.0,<1.13.0 *, which requires
│  │  │  └─ bioconductor-genomicranges >=1.34.0,<1.35.0 *, which requires
│  │  │     └─ bioconductor-xvector >=0.22.0,<0.23.0 *, which requires
│  │  │        └─ bioconductor-zlibbioc >=1.28.0,<1.29.0 *, which requires
│  │  │           └─ r-base >=3.5.1,<3.5.2.0a0 *, which conflicts with any installable versions previously reported;
│  │  └─ r-base >=3.5.1,<3.5.2.0a0 *, which conflicts with any installable versions previously reported;
│  ├─ bioconductor-singlecellexperiment [1.10.1|1.12.0] would require
│  │  ├─ bioconductor-summarizedexperiment >=1.18.0,<1.19.0 *, which requires
│  │  │  └─ bioconductor-genomicranges >=1.40.0,<1.41.0 *, which requires
│  │  │     └─ bioconductor-xvector >=0.28.0,<0.29.0 *, which requires
│  │  │        └─ bioconductor-zlibbioc >=1.34.0,<1.35.0 *, which requires
│  │  │           └─ r-base >=4.0,<4.1.0a0 *, which conflicts with any installable versions previously reported;
│  │  └─ r-base >=4.0,<4.1.0a0 *, which conflicts with any installable versions previously reported;
│  ├─ bioconductor-singlecellexperiment [1.14.1|1.16.0] would require
│  │  ├─ bioconductor-genomicranges >=1.44.0,<1.45.0 *, which requires
│  │  │  └─ bioconductor-xvector >=0.32.0,<0.33.0 *, which requires
│  │  │     └─ bioconductor-zlibbioc >=1.38.0,<1.39.0 *, which requires
│  │  │        └─ r-base >=4.1,<4.2.0a0 *, which conflicts with any installable versions previously reported;
│  │  └─ bioconductor-summarizedexperiment >=1.24.0,<1.25.0 *, which requires
│  │     └─ bioconductor-matrixgenerics >=1.6.0,<1.7.0 *, which requires
│  │        └─ r-base >=4.1,<4.2.0a0 *, which conflicts with any installable versions previously reported;
│  ├─ bioconductor-singlecellexperiment 1.20.0 would require
│  │  └─ bioconductor-summarizedexperiment >=1.28.0,<1.29.0 *, which requires
│  │     └─ bioconductor-matrixgenerics >=1.10.0,<1.11.0 *, which requires
│  │        └─ r-base >=4.2,<4.3.0a0 *, which conflicts with any installable versions previously reported;
│  ├─ bioconductor-singlecellexperiment [1.22.0|1.24.0] would require
│  │  ├─ bioconductor-genomicranges >=1.52.0,<1.53.0 *, which requires
│  │  │  └─ bioconductor-xvector >=0.40.0,<0.41.0 *, which requires
│  │  │     └─ bioconductor-zlibbioc >=1.46.0,<1.47.0 *, which requires
│  │  │        └─ r-base >=4.3,<4.4.0a0 *, which conflicts with any installable versions previously reported;
│  │  └─ bioconductor-summarizedexperiment >=1.32.0,<1.33.0 *, which requires
│  │     └─ r-base >=4.3,<4.4.0a0 *, which conflicts with any installable versions previously reported;
│  ├─ bioconductor-singlecellexperiment 1.28.0 would require
│  │  └─ bioconductor-summarizedexperiment >=1.36.0,<1.37.0 *, which requires
│  │     └─ bioconductor-matrixgenerics >=1.18.0,<1.19.0 *, which requires
│  │        └─ r-base >=4.4,<4.5.0a0 *, which conflicts with any installable versions previously reported;
│  └─ bioconductor-singlecellexperiment [1.6.0|1.8.0] would require
│     └─ bioconductor-summarizedexperiment [>=1.14.0,<1.15.0 *|>=1.16.0,<1.17.0 *], which requires
│        └─ bioconductor-genomicranges [>=1.36.0,<1.37.0 *|>=1.38.0,<1.39.0 *], which requires
│           └─ bioconductor-xvector [>=0.24.0,<0.25.0 *|>=0.26.0,<0.27.0 *], which requires
│              ├─ bioconductor-zlibbioc >=1.32.0,<1.33.0 *, which requires
│              │  └─ r-base >=3.6,<3.7.0a0 *, which conflicts with any installable versions previously reported;
│              └─ r-base >=3.6,<3.7.0a0 *, which conflicts with any installable versions previously reported;
└─ r-base =4.5 * is requested and can be installed.

[grst]

which packages are you trying to install?
Since this is now on conda, I think we can build an image with seqera containers and don't need a custom dockerfile anymore.

[fmalmeida]

The anndataR package does not add seuratobject and singlecellexperiment packages as dependencies.

So, using seqera containers, when trying to install the three of them, the incompatibilities arise.

And they I understand are not R incompatibilities but rather conda meta yml definitions mismatches

[grst]

Ok, so I believe the reason is that bioconductor-singlecellexperiment==1.18.1 is not on bioconda which is the release required for Bioconductor version 3.20. I'll check if I can bump it on bioconda

[grst]

Let's see how that goes:
bioconda/bioconda-recipes#61865

[grst]

There are still a bunch of bioconductor packages not updated yet to the 3.22 release. See bioconda/bioconda-recipes#61776.

So unfortunately, we'll have to wait a little longer, or build or own container.

See also related discussion: scverse/anndataR#405