Install problem with M1 Mac

[jaseeverett]

Hi @dickoa
Thanks so much for this package!
I am having some trouble installing prepr on an M1 Max Mac. I am trying to use it with the wdpar package (https://github.com/prioritizr/wdpar). The main error seems to be: checking for __gmpz_init in -lgmp... no configure: error: GNU MP not found!

I have installed all the prepr dependencies successfully via homebrew

brew install pkg-config
brew install gmp
brew install mpfr
brew install gdal

and checked homebrew is on the $PATH

/opt/homebrew/bin:/opt/homebrew/sbin

When running remotes::install_github("dickoa/prepr") I get the output:

Downloading GitLab repo dickoa/prepr@HEAD
from URL https://gitlab.com/api/v4/projects/18598906/repository/archive.tar.gz?sha=HEAD
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/_r/mcmw_qtn0m7cd23cbdqfszl40000gp/T/Rtmp9tM69Z/remotes786e211d1c5e/prepr-HEAD-5eae64f2b6b2f37970318a351fbb2d3050752212/DESCRIPTION’ ...
─ preparing ‘prepr’: (497ms)
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (486ms)
─ checking for empty or unneeded directories (511ms)
─ building ‘prepr_0.1.9000.tar.gz’

• installing source package ‘prepr’ ...
  ** using staged installation
  configure: CC: clang -arch arm64
  configure: CXX: clang++ -arch arm64 -std=gnu++14
  checking for gdal-config... /opt/homebrew/bin/gdal-config
  checking gdal-config usability... yes
  configure: GDAL: 3.6.3
  checking GDAL version >= 2.0.1... yes
  checking for gcc... clang -arch arm64
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether the compiler supports GNU C... yes
  checking whether clang -arch arm64 accepts -g... yes
  checking for clang -arch arm64 option to enable C11 features... none needed
  checking for __gmpz_init in -lgmp... no
  configure: error: GNU MP not found!
  ERROR: configuration failed for package ‘prepr’
• removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/prepr’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/_r/mcmw_qtn0m7cd23cbdqfszl40000gp/T//Rtmp9tM69Z/file786e59b0e0bb/prepr_0.1.9000.tar.gz’ had non-zero exit status

The output of R.version is

R.version
_
platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 2.3
year 2023
month 03
day 15
svn rev 83980
language R
version.string R version 4.2.3 (2023-03-15)
nickname Shortstop Beagle

I have spoken to two other colleagues, also on an M1 Mac, and they have the exact same install error. I wonder if you can help with this?
Many thanks in advance

[tungxphung]

I am also experiencing this issue, I hope there are updates!

[mdsumner]

can probably use sfdct to do the same fwiw, got a reprex I can try?

[tungxphung]

I am simply running
remotes::install_github("dickoa/prepr") on a Mac M1
This is part of installing some packages for extra functionality for the aoh package (https://prioritizr.github.io/aoh/)

[jeffreyhanson]

Hi @dickoa, thank you very much for developing this package. I find it extremely useful in my own work for fixing spatial vector data, and it's a great option when other methods don't work (e.g., sf::st_make_valid())! I would be interested in trying to find a way to resolve this issue so that M1 Mac users can install the package, would you be open to reviewing and potentially accepting a PR that resolve this issue? No worries if you're busy with other projects and don't have the time availability, I just wanted to ask?

[jeffreyhanson]

I've been trying to get prepr compatible with M1 Mac's this afternoon, and I think I might have got it working. If you have a moment, @jaseeverett or @tungxphung, could you please try installing my fork and see if works for you? You can install it with:

remotes::install_github("jeffreyhanson/prepr")

[jaseeverett]

Thanks so much @jeffreyhanson. This now works! Installation was successful and I ran the following from the prepr from the README and it runs successfully.

library(sf)
#> Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
library(prepr)
p3 <- st_as_sfc("POLYGON((0 0, 10 0, 10 10, 0 10, 0 0),(5 2, 5 7, 10 7, 10 2, 5 2))")
st_is_valid(p3, reason = TRUE)
#> [1] "Self-intersection[10 2]"

p33 <- st_prepair(p3)
st_is_valid(p33)
#> [1] TRUE

st_as_text(p33)
#> [1] "POLYGON ((0 0, 10 0, 10 2, 5 2, 5 7, 10 7, 10 10, 0 10, 0 0))"

par(mfrow = c(1, 2))
plot(p3, main = "RAW", col = "#D7722C")
plot(p33, main = "Repaired", col = "#D7722C")

^{Created on 2024-04-19 with reprex v2.1.0}

[mdsumner]

Just a note, you can do this with RTriangle still. The lib does the hard work but decomposing polygon paths to edges, and recomposing triangles to paths is pure R tidy work 🙏

[jeffreyhanson]

Brilliant - thanks for testing it out @jaseeverett!

@mdsumner, oh I see - thanks for raising this point! I don't really know much about topology/paths/mesh/triangle stuff, so that's good to know.

[jeffreyhanson]

@dickoa, if I put togeather a PR and explained all the changes, would you be interested in reviewing it?

[jeffreyhanson]

Due to lack of activity, I'll create a fork of this package (https://github.com/prioritizr/prepr2) and update my packages (i.e., aoh and wdpar) that currently depend on prepr to use prepr2 instead. Although I would prefer to avoid creating an entirely new seperate/fork, I think it's important to make progress on resolving the M1 Mac and boost compaiiblity issues.

To help recognize your contributions, @dickoa, I would like to list you as a copyright holder and contributor to the prepr2 package (similar to how prepr recognizes contributions of the prepair library). How does that sound? If I don't hear from you, I will assume this is how you would prefer your contributions to be recognized.

[dickoa]

Hi @jeffreyhanson,

I hope all is good. Thank you for all your work on prepr.
I'm sorry for not being that active. I'm a humanitarian worker and I travel a lot lately in places with low connectivity.
You can fork it and keep the same name, I can archive the repository after. I won't really mind if you want to take over maintenance, if it's OK with you of course. I can still be a contributor, and we could aim for a CRAN release, let me know what you think ?

Best,
Ahmadou

[jeffreyhanson]

No worries at all!

Yeah that sounds great. Ok - I'll use the prepr name for the fork. Yeah, if you like, you could be listed as an author (instead of contributor)? I think it's important to recognize all your brilliant work on this package. A CRAN release down the line would be awesome! That said, it might be a while before this happens and it might be a bit difficult given that prepr has some complicated system dependencies (i.e., gdal) which might cause some unforeseen issues and headaches on certain CRAN check platforms (e.g., fedora, debian). I know we can get gmp and mpfr system dependnecies on all CRAN check platforms (see https://cran.r-project.org/web/packages/surveyvoi/index.html) How does that sound?

[dickoa]

Sounds great @jeffreyhanson!
Let's start, and happy to have a look as soon as I have more time home.

[jeffreyhanson]

Awesome! I've just invited you to join the dev team for the repo.