[Bioc-devel] Updating for 3.11

[Karl Stamm]

I was notified recently my package has build errors going in to bioc 3.11.
So begins the biannual saga of updating everything to see what's new.
My package has quite a few dependencies, so it's normal for someone to
change their API and break my scripted usage. This time a default parameter
changed in DESeq2::lfcShrink and my fix is simply to specify the previous
method.
However, to get there, we need to update the system to R 4.0.0 release
candidate, and download and compile all of the bioconductor packages
implicated. My primary system is an OSX 10.12, and certain system packages
are out of date routinely on OSX.
I'm sharing this story with the group to report some commands I have found
necessary and may help others fighting through this process.

First was "clang4" a c compiler needed by R devel and not available in the
right spot on OSX 10.12.  A fix was found by reinstalling clang in several
spots lying about the version numbers. these downloads are complete
installation with varied linker names.

To install the R package called XML you need a system library for libxml.
Which is called libxml2 on OSX, and primarily available through Homebrew,
which itself wanted to update. Brew update brings in a Ruby engine and a
Python installation, and finally warns that OSX 10.12 is aged out of
support, and will only make the libxml available "within the keg" which is
apparently their nomenclature for a local installation vs system.
So to get the R library to see it we first need to run
Sys.setenv(XML_CONFIG = "/usr/local/Cellar/libxml2/2.9.10/bin/xml2-config")
Where the 2.9.10 folder name may vary with your system. Had I known,
perhaps I could have avoided updating brew entirely.

Next RCurl didn't want to install/compile, because Apple XCode 9 has
removed the libsystem_darwin.dylib for the x64 architecture. The command to
re-use a previously installed version is simply:
sudo xcode-select -s /Library/Developer/CommandLineTools

With that I was able to install the Bioc Devel versions and finally
reproduce the bug found on the build servers.

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