[Bioc-devel] Updating for 3.11

McDavid, Andrew Andrew_Mcd@v|d @end|ng |rom URMC@Roche@ter@edu
Wed Jan 8 15:43:33 CET 2020

I agree with Martin that the R administration guide should be frequently consulted on Mac OS and other systems (and would have save me a couple hours of trouble shooting the other week).  However it's not always updated for the most recent Mac OS perversions, as I found:  https://amcdavid.github.io/2019/12/Compiling-R-From-Source. The prebuilt binary didn't work for me this time, in that I was getting segfaults from it last month that went away once I compiled from source.

And I also agree that there is probably a silver lining in that it helps discipline us to avoid unnecessary dependencies, which is of course somewhat in tension with the bioconductor philosophy of reuse of components.

Andrew McDavid
Biostatistics and Computational Biology
Office: SRB 4.206 Ph: 585.275.5983

On Jan 8, 2020, at 6:00 AM, bioc-devel-request using r-project.org<mailto:bioc-devel-request using r-project.org> wrote:

Date: Tue, 7 Jan 2020 19:40:02 +0000
From: Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>
To: Karl Stamm <karl.stamm using gmail.com<mailto:karl.stamm using gmail.com>>, "bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>"
<bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Updating for 3.11
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I'm not an expert on macOS, but generally one wants to follow documented R procedures.

This changes (corrects?) some of the contortions you indicate below, for instance it is not necessary to fiddle with clang4. Also, by using the CRAN-distributed binary (from https://urldefense.proofpoint.com/v2/url?u=http-3A__mac.r-2Dproject.org_&d=DwIGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=YOujD4cGNGWN0ZskTj96dUHU2a4CkraklBd4BndS21sf3_emyYLIG1llnUarWCda&m=qhzUtwVNpidVS2ld_L6Ge6zDl1AOT0itOnwoD4dSkG0&s=qrbZDJn7R1U4XJ9npcLJ0HO7HTEgM2SdHo-uO_6n6ho&e= ) for R-devel one does not need to compile packages (other than your own) from source but rather can install the binaries (see pkgType on ?options and ?install.packages).

I think it's helpful too to ask whether dependencies are all strictly necessary, or only convenient (stringr and stringi useage often seems to fall into this category, where base string manipulation functionality is often sufficient) or providing very marginal functionality that adds minimally to our packages -- perhaps, in general and not necessarily your use of DESeq2, our packages could adopt a New Year's resolution and go on a dependency diet?


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