[Bioc-devel] Updating for 3.11

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Jan 7 21:36:36 CET 2020


On 1/7/20 10:47, Karl Stamm wrote:
> 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 are out of date routinely on OSX.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.

FWIW celaya2 (Mac builder for BioC 3.11) uses clang 8.0.0 (see 
which is available on CRAN here https://cran.r-project.org/bin/macosx/tools/

Note that the page says that this is the version "to be used with El 
Capitan builds of R 3.7.0 and higher" which is a little confusing given 
that there won't be a 3.7.0 release of R. Anyway that's what you should 
use if you use R 4.0.0.

> 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

The lack of Mac binary packages for R-devel on CRAN together with the 
high turnover of Mac OS versions are a major PITA and the reason why 
when R/Bioconductor newbies ask me what OS I recommend for package 
development I always say Linux, without hesitation. Unless they want to 
suffer ;-)


> With that I was able to install the Bioc Devel versions and finally
> reproduce the bug found on the build servers.
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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