[Bioc-devel] Build issues under macOS

Stone, Matt m@tone @end|ng |rom |redhutch@org
Wed Sep 9 03:03:10 CEST 2020


I've begun the submission of a new package [1], but I'm encountering some errors in the automated build under macOS on merida1 and would greatly appreciate any assistance.

I've currently tried to build twice, once upon initial submission and once after updating the DESCRIPTION to remove a redundant Maintainer field. I'm a bit confused that each build failed with different errors, as the only difference between the two was the removal of the Maintainer field.

In the first build [2], the binary build failed because the installer could not link to the fortran libraries. I have previously encountered a similar issue on my own macbook and was able to work around it by installing gfortran directly [3] rather than through homebrew. I have this noted in the package's README, but is there a better solution to ensure compatibility in more environments, including merida1?

In the second build [4], the check failed because the package was uninstallable, and the binary build failed because edgeR could not be found. I'm assuming the latter is the cause of the former error. edgeR is an indirect dependency via scran; is it necessary to make it an explicit import?

Before submission, I set up the BiocCheck github action supported by r-lib [5], and was able to build the package and run a mostly clean (minus a few NOTEs) check/BiocCheck under Ubuntu, Windows, and macOS. Is anyone familiar with the distinction between the environments on merida1 and the docker image in this workflow? I'd be happy to help update the latter to be consistent with merida1.

Thank you!


[1] https://github.com/Bioconductor/Contributions/issues/1624
[2] http://bioconductor.org/spb_reports/BayesSpace_buildreport_20200908155859.html
[3] https://github.com/fxcoudert/gfortran-for-macOS/releases
[4] http://bioconductor.org/spb_reports/BayesSpace_buildreport_20200908162457.html
[5] https://github.com/r-lib/actions/issues/84

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