[Bioc-devel] Updating for 3.11
Hi,
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 My primary system is an OSX 10.12, and certain system packages are out of date routinely on OSX.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 http://bioconductor.org/checkResults/devel/bioc-LATEST/celaya2-NodeInfo.html) 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 ;-) Cheers, H.
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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