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 are out of date routinely on OSX.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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8XBFBXfZmFNax6cb7EqQvhtsWvEbY9Jn7RZGOvO51EY&s=jkDO8EHGdj91KKbcHHxkkQAsloNYDV1U3aGwieRP9Ro&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
