R version update for DiMSum compatibility with ARM64 architectures

[MaximilianStammnitz]

Hola again @ajfaure,

Thanks again for checking the recent cutadapt version upgrade (#23)!

Now another challenge has come up during our efforts to build DiMSum containers: ARM64 processor architectures like e.g. the Mac M1/M2/M3 series require substantially newer R versions than 4.0.0. We are able to compile DiMSum singularity images with R v4.4.3, but have started running into what looks like a general R environment incompatibility on our small scale test data (which works perfectly fine with the default DiMSum + R v4.0.0).

Note that the same error had already been observed by @roserao some time ago (#16):

  ******* DiMSum STAGE 4 (STEAM): PROCESS VARIANT SEQUENCES *******
  
  Loading variant count files:
  counts_merged.tsv
  Processing...
        counts_merged.tsv
  Processing merged variants...
  Done
  Saving merged variant data...
  Done
  There were problems while running 'dimsum__merge_report'
  There were problems while running 'dimsum__diagnostics_report'
  Error in dimsum_stage_merge(dimsum_meta = pipeline[["3_tally"]], merge_outpath = pipeline[["3_tally"]][["project_path"]],  : 
    object 'dimsum_meta_new_report' not found
  Calls: dimsum -> dimsum_stage_merge
  Execution halted

Do you have a feel for what it could be that is triggering this? I'd be happy to get involved with any debugging efforts, though am finding it a bit challenging to identify the right starting point and main underlying source.

Note that our test is only from stage 4 onwards, hence not sure if there may be other potential R >4.0.0 warnings upstream. Sharing our toy data files and run details here:

counts_merged.tsv
experimentalDesign.tsv
2025-09-30_run_DiMSum_test.sh

@BenjaminWehnert1008 @tlmighell @wtsi-hgi @ewels

[andrefaure]

Hi, I'm not sure how you're building your containers but if with conda you could try this: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#specifying-a-different-target-platform-for-an-environment

This allows me to run DiMSum with R v4.0 on my Mac M3 with no problems.

[MaximilianStammnitz]

Thanks for checking! Did you specify osx-arm as the platform here?

To make the DiMSum docker and singularity images compatible with ARM64, we are building the containers via wave CLI which imports directly from bioconda as well (https://nf-co.re/docs/contributing/software_packaging/arm64_builds). For the docker image of DiMSum 1.4 (bump 2), this looks like:

wave --conda-package bioconda::r-dimsum=1.4=r40hdfd78af_2 --await --freeze --platform linux/arm64

And results in these clashes with R v4.0.0 (https://wave.seqera.io/view/builds/bd-e952e5d2234f34b5_2):

#10 [3/3] RUN micromamba install -y -n base -f /tmp/conda.yml     && micromamba install -y -n base conda-forge::procps-ng     && micromamba env export --name base --explicit > environment.lock     && echo ">> CONDA_LOCK_START"     && cat environment.lock     && echo "<< CONDA_LOCK_END"     && micromamba clean -a -y
#10 23.08 error    libmamba Could not solve for environment specs
#10 23.08     The following package could not be installed
#10 23.08     └─ r-dimsum 1.4 r40hdfd78af_2 is not installable because it requires
#10 23.08        ├─ bioconductor-shortread with the potential options
#10 23.08        │  ├─ bioconductor-shortread 1.60.0 would require
#10 23.08        │  │  ├─ bioconductor-biostrings >=2.70.0,<2.71.0 , which requires
#10 23.08        │  │  │  └─ r-base >=4.3,<4.4.0a0  with the potential options
#10 23.08        │  │  │     ├─ r-base [4.3.0|4.3.1|4.3.2|4.3.3], which can be installed;
#10 23.08        │  │  │     ├─ r-base 4.3.1 would require
#10 23.08        │  │  │     │  └─ krb5 >=1.21.2,<1.22.0a0 , which can be installed;
#10 23.08        │  │  │     ├─ r-base 4.3.1 would require
#10 23.08        │  │  │     │  └─ krb5 >=1.21.1,<1.22.0a0 , which can be installed;
#10 23.08        │  │  │     ├─ r-base [4.3.3|4.4.1|4.4.2|4.4.3] would require
#10 23.08        │  │  │     │  └─ icu >=75.1,<76.0a0 , which can be installed;
#10 23.08        │  │  │     └─ r-base [4.3.3|4.4.3] would require
#10 23.08        │  │  │        └─ libjpeg-turbo >=3.1.0,<4.0a0 , which requires
#10 23.08        │  │  │           └─ jpeg <0.0.0a , which can be installed;
#10 23.08        │  │  ├─ bioconductor-genomicalignments >=1.38.0,<1.39.0 , which requires
#10 23.08        │  │  │  └─ bioconductor-summarizedexperiment >=1.32.0,<1.33.0 , which requires
#10 23.08        │  │  │     └─ bioconductor-delayedarray >=0.28.0,<0.29.0 , which requires
#10 23.08        │  │  │        └─ bioconductor-sparsearray >=1.2.0,<1.3.0 , which requires
#10 23.08        │  │  │           └─ r-base >=4.3,<4.4.0a0  with the potential options
#10 23.08        │  │  │              ├─ r-base [4.3.0|4.3.1|4.3.2|4.3.3], which can be installed;
#10 23.08        │  │  │              ├─ r-base 4.3.1, which can be installed (as previously explained);
#10 23.08        │  │  │              ├─ r-base 4.3.1, which can be installed (as previously explained);
#10 23.08        │  │  │              ├─ r-base [4.3.3|4.4.1|4.4.2|4.4.3], which can be installed (as previously explained);
#10 23.08        │  │  │              └─ r-base [4.3.3|4.4.3], which can be installed (as previously explained);
#10 23.08        │  │  ├─ bioconductor-s4vectors >=0.40.0,<0.41.0 , which requires
#10 23.08        │  │  │  └─ r-base >=4.3,<4.4.0a0  with the potential options
#10 23.08        │  │  │     ├─ r-base [4.3.0|4.3.1|4.3.2|4.3.3], which can be installed;
#10 23.08        │  │  │     ├─ r-base 4.3.1, which can be installed (as previously explained);
#10 23.08        │  │  │     ├─ r-base 4.3.1, which can be installed (as previously explained);
#10 23.08        │  │  │     ├─ r-base [4.3.3|4.4.1|4.4.2|4.4.3], which can be installed (as previously explained);
#10 23.08        │  │  │     └─ r-base [4.3.3|4.4.3], which can be installed (as previously explained);
#10 23.08        │  │  └─ r-base >=4.3,<4.4.0a0  with the potential options
#10 23.08        │  │     ├─ r-base [4.3.0|4.3.1|4.3.2|4.3.3], which can be installed;
#10 23.08        │  │     ├─ r-base 4.3.1, which can be installed (as previously explained);
#10 23.08        │  │     ├─ r-base 4.3.1, which can be installed (as previously explained);
#10 23.08        │  │     ├─ r-base [4.3.3|4.4.1|4.4.2|4.4.3], which can be installed (as previously explained);
#10 23.08        │  │     └─ r-base [4.3.3|4.4.3], which can be installed (as previously explained);
#10 23.08        │  └─ bioconductor-shortread 1.64.0 would require
#10 23.08        │     ├─ bioconductor-pwalign >=1.2.0,<1.3.0 , which requires
#10 23.08        │     │  └─ r-base >=4.4,<4.5.0a0  with the potential options
#10 23.08        │     │     ├─ r-base [4.3.3|4.4.1|4.4.2|4.4.3], which can be installed (as previously explained);
#10 23.08        │     │     ├─ r-base [4.3.3|4.4.3], which can be installed (as previously explained);
#10 23.08        │     │     └─ r-base [4.4.0|4.4.1], which can be installed;
#10 23.08        │     └─ r-base >=4.4,<4.5.0a0  with the potential options
#10 23.08        │        ├─ r-base [4.3.3|4.4.1|4.4.2|4.4.3], which can be installed (as previously explained);
#10 23.08        │        ├─ r-base [4.3.3|4.4.3], which can be installed (as previously explained);
#10 23.08        │        └─ r-base [4.4.0|4.4.1], which can be installed;
#10 23.08        └─ r-base >=4.0,<4.1.0a0  but there are no viable options
#10 23.08           ├─ r-base 4.0.0 would require
#10 23.08           │  ├─ icu >=64.2,<65.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  ├─ jpeg >=9c,<10a , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ krb5 >=1.17.1,<1.18.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base [4.0.1|4.0.2] would require
#10 23.08           │  ├─ icu >=64.2,<65.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  ├─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ krb5 >=1.17.1,<1.18.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base [4.0.2|4.0.3] would require
#10 23.08           │  ├─ icu >=67.1,<68.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  ├─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ krb5 >=1.17.1,<1.18.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base [4.0.3|4.0.5] would require
#10 23.08           │  ├─ icu >=68.1,<69.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  ├─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ krb5 >=1.17.1,<1.18.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base 4.0.5 would require
#10 23.08           │  ├─ icu >=69.1,<70.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ jpeg >=9e,<10a , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base 4.0.5 would require
#10 23.08           │  ├─ icu >=68.1,<69.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  ├─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ krb5 >=1.19.1,<1.20.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base 4.0.5 would require
#10 23.08           │  ├─ icu >=69.1,<70.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base 4.0.5 conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base 4.0.5 would require
#10 23.08           │  ├─ icu >=68.1,<69.0a0 , which conflicts with any installable versions previously reported;
#10 23.08           │  └─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported;
#10 23.08           ├─ r-base 4.0.5 would require
#10 23.08           │  └─ jpeg >=9e,<10a , which conflicts with any installable versions previously reported;
#10 23.08           └─ r-base 4.0.5 would require
#10 23.08              ├─ icu >=70.1,<71.0a0 , which conflicts with any installable versions previously reported;
#10 23.08              └─ jpeg >=9e,<10a , which conflicts with any installable versions previously reported.
#10 23.12 critical libmamba Could not solve for environment specs