Bioconductor / BBS

The Bioconductor Build System
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Update packages to install via Homebrew #374

Closed jwokaty closed 9 months ago

jwokaty commented 9 months ago

A few difficult packages that aren't available in Simon's binaries should be installed via Homebrew. Two that work after Homebrew installation are hiredis and mariadb-connector-c; however, a few others don't seem to work, even after making symlinks from the pkg-config files in the Cellar to /opt/homebrew/lib/pkgconfig on arm64. (We didn't do this on x86_64, so maybe the arm64 binaries are behind the x86_64 or the paths are different?)

After attempting to install difficult packages and also brew installing dependencies, we fail to install archive, av, proj4, rsvg, units, lwgeom,sf`.

(Note: Also unable to install Rmpfr, 'terra' -- these seem to have a link issue)

hpages commented 9 months ago

Can you provide some details on the problems/errors you get when trying to install the difficult packages using the trick documented here?

FWIW using this trick seems to work fine for archive on kjohnson3:

contriburl <- "https://cran.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3"

install.packages("archive", contriburl=contriburl)
# trying URL 'https://cran.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/archive_1.1.5.tgz'
# Content type 'application/x-gzip' length 1531678 bytes (1.5 MB)
# ==================================================
# downloaded 1.5 MB
# 
# The downloaded binary packages are in
#   /var/folders/kj/tw9rgy0j1nv62ttkz2z2wqcm0000gt/T//RtmpsHMQzC/downloaded_packages

library(archive)  # successful load

Note that the advantage of using this trick is that we still install package binaries so we don't need Simon's binaries or additional Homebrew installs.

jwokaty commented 9 months ago

I see in looking back on my most recent attempt, I had an error in my code when I tried to install it before I wrote this since I was just testing it individually. They seem to be installing fine. I'll close this after I finish installing everything.