Install issue #1

juanmayorgahenao · 2024-12-11T22:26:48Z

Hi!

I'm running into an installation error that I can' seem to overcome. Seems like it's an issue trying to find gmp. Any ideas how to fix it? I've reinstall all relevant libraries using homebrew.

Here is the error

`remotes::install_github("prioritizr/prepr")

Using GitHub PAT from the git credential store.
Downloading GitHub repo prioritizr/prepr@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: RcppCGAL (5.6.4 -> 6.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/f2/n6b1dv_12qvc6pyj9cz4lcjm0000gp/T/Rtmp70HL3w/remotesafb978dc6ed2/prioritizr-prepr-c3953e8/DESCRIPTION’ (401ms)
─ preparing ‘prepr’: (1.1s)
✔ checking DESCRIPTION meta-information
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (701ms)
─ checking for empty or unneeded directories
─ building ‘prepr_0.3.0.tar.gz’

installing source package ‘prepr’ ...
** using staged installation
checking if R found... yes
configure: R version: 4.4.2
configure: CC: clang -arch arm64
configure: CPP:
configure: CFLAGS: -falign-functions=64 -Wall -g -O2
configure: CPPFLAGS: -I/opt/R/arm64/include
configure: LDFLAGS: -L/opt/R/arm64/lib
checking for gdal-config... /opt/homebrew/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.10.0
checking GDAL version >= 2.0.1... yes
checking for pkg-config... yes
checking if gmp compiles... no
configure: Configuration failed because gmp was not found. Try installing:
configure: * deb: libgmp3-dev (Debian, Ubuntu)
configure: * rpm: gmp-devel (Fedora, EPEL)
configure: * brew: gmp (Mac OSX)
configure:
configure: If gmp is already installed, check that 'pkg-config' is in
configure: your PATH and PKG_CONFIG_PATH contains a gmpxx.pc file.
configure:
configure: error: ERROR: Installation failed
ERROR: configuration failed for package ‘prepr’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/prepr’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/f2/n6b1dv_12qvc6pyj9cz4lcjm0000gp/T//Rtmp70HL3w/fileafb95b3f91de/prepr_0.3.0.tar.gz’ had non-zero exit status`

And here is the output of my sessionInfo()

`R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Bogota
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] processx_3.8.4 compiler_4.4.2 R6_2.5.1 cli_3.6.3 tools_4.4.2 rstudioapi_0.16.0 curl_5.2.1 remotes_2.5.0
[9] desc_1.4.3 callr_3.7.6 ps_1.7.7 pkgbuild_1.4.4 `

The text was updated successfully, but these errors were encountered:

jeffreyhanson · 2024-12-11T22:31:53Z

Thanks for reaching out! I see that you're using macOS, have you followed the installation instructions on the README (https://github.com/prioritizr/prepr?tab=readme-ov-file#macos) to install system dependencies? Sorry in advance if you've already tried this.

jeffreyhanson · 2024-12-11T22:44:01Z

Oh, sorry, I just reread your post and saw that you said you already installed the homebrew libraries.

jeffreyhanson · 2024-12-11T22:46:39Z

What happens if you run these commands in the terminal?

pkg-config --cflags gmp
pkg-config --libs gmp

juanmayorgahenao · 2024-12-11T23:37:57Z

Thank you, Jeffrey.

The output of those commands is:

-I/opt/homebrew/Cellar/gmp/6.3.0/include

and

-L/opt/homebrew/Cellar/gmp/6.3.0/lib -lgmp

jeffreyhanson · 2024-12-11T23:42:04Z

Interesting - so it seems that pkg-config knows about gmp being installed. What's in the /opt/homebrew/Cellar/gmp/6.3.0/include and /opt/homebrew/Cellar/gmp/6.3.0/lib folders? E.g., what if you do:

ls -la /opt/homebrew/Cellar/gmp/6.3.0/include
ls -la /opt/homebrew/Cellar/gmp/6.3.0/lib

juanmayorgahenao · 2024-12-11T23:47:27Z

the outputs of those are

total 424 drwxr-xr-x 4 marinedatascience admin 128 Jul 29 2023 . drwxr-xr-x 14 marinedatascience admin 448 Dec 11 16:55 .. -rw-r--r-- 1 marinedatascience admin 84266 Jul 29 2023 gmp.h -rw-r--r-- 1 marinedatascience admin 129502 Jul 29 2023 gmpxx.h

and

total 2744 drwxr-xr-x 9 marinedatascience admin 288 Dec 11 16:55 . drwxr-xr-x 14 marinedatascience admin 448 Dec 11 16:55 .. -r--r--r-- 1 marinedatascience admin 452816 Dec 11 16:55 libgmp.10.dylib -r--r--r-- 1 marinedatascience admin 829736 Jul 29 2023 libgmp.a lrwxr-xr-x 1 marinedatascience admin 15 Jul 29 2023 libgmp.dylib -> libgmp.10.dylib -r--r--r-- 1 marinedatascience admin 80992 Dec 11 16:55 libgmpxx.4.dylib -r--r--r-- 1 marinedatascience admin 33096 Jul 29 2023 libgmpxx.a lrwxr-xr-x 1 marinedatascience admin 16 Jul 29 2023 libgmpxx.dylib -> libgmpxx.4.dylib drwxr-xr-x 4 marinedatascience admin 128 Dec 11 16:55 pkgconfig

Any clues?

jeffreyhanson · 2024-12-11T23:56:34Z

So it looks like the files are in this folder - but for some reason it's not working. Could you try adding these folders to your computer's PATH variable, and then installing prepr again?

juanmayorgahenao · 2024-12-12T15:00:57Z

Thank you Jeffrey. I've added those folder (plus the pfgconfig folder where the gmpxx.pc file lives) to the PATH variable but still no luck. I've also added the pkgconfig directory to the PKG_CONFIG_PATH variable. The error remains the same.

Here is some useful output from terminal

❯ echo $PKG_CONFIG_PATH /opt/homebrew/Cellar/gmp/6.3.0/lib/pkgconfig

echo -e ${PATH//:/\\n} /Users/marinedatascience/google-cloud-sdk/bin /opt/homebrew/bin /opt/homebrew/sbin /usr/local/bin /System/Cryptexes/App/usr/bin /usr/bin /bin /usr/sbin /sbin /opt/homebrew/Cellar/gmp/6.3.0/lib /opt/homebrew/Cellar/gmp/6.3.0/include /opt/homebrew/bin/pkg-config /opt/homebrew/Cellar/gmp/6.3.0/lib/pkgconfig /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin /opt/X11/bin /Library/Apple/usr/bin /Library/TeX/texbin /usr/local/sbin /Applications/quarto/bin /Applications/iTerm.app/Contents/Resources/utilities

Thanks again for your help!

Juan

jeffreyhanson · 2024-12-12T19:08:35Z

No worries! I'm sorry about this issue and that it's taking so long to address. I think it might be useful to get more information on what compilation flags are being used on your compuer. So, I've updated the configuration files to provide more information. Could you please try installing the debug-autoconf branch and post the output?

remotes::install_github("prioritizr/prepr@debug-autoconf")

Also, just to check, are you able to install other packages that require compilation from source on your computer? E.g., does running this command work?

install.packages("dplyr", type="source")

juanmayorgahenao · 2024-12-12T21:21:05Z

Hi Jeffrey,

Thanks for your help again. I'm actually not able to install other packages from source :(

This is the output from install.packages("dplyr", type="source")

`

installing source package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.4)’
using SDK: ‘MacOSX15.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chop.cpp -o chop.o
In file included from chop.cpp:1:
In file included from ./dplyr.h:5:
/Library/Frameworks/R.framework/Resources/include/R.h:39:11: fatal error: 'cstdlib' file not found
39 | # include
| ^~~~~~~~~
1 error generated.
make: *** [chop.o] Error 1
ERROR: compilation failed for package ‘dplyr’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dplyr’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/f2/n6b1dv_12qvc6pyj9cz4lcjm0000gp/T/RtmpmfOLCH/downloaded_packages’`

I guess my problem is bigger than I thought.... Any ideas?

juanmayorgahenao · 2024-12-12T21:24:22Z

And the output from remotes::install_github("prioritizr/prepr@debug-autoconf") is below:

`── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/f2/n6b1dv_12qvc6pyj9cz4lcjm0000gp/T/RtmpmfOLCH/remotes7ac930fcb017/prioritizr-prepr-650042b/DESCRIPTION’ (563ms)
─ preparing ‘prepr’: (1.3s)
✔ checking DESCRIPTION meta-information
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (872ms)
─ checking for empty or unneeded directories
─ building ‘prepr_0.3.0.tar.gz’

installing source package ‘prepr’ ...
** using staged installation
checking if R found... yes
configure: R version: 4.4.2
configure: CC: clang -arch arm64
configure: CPP:
configure: CFLAGS: -falign-functions=64 -Wall -g -O2
configure: CPPFLAGS: -I/opt/R/arm64/include
configure: LDFLAGS: -L/opt/R/arm64/lib
checking for gdal-config... /opt/homebrew/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.10.0
checking GDAL version >= 2.0.1... yes
checking for pkg-config... yes
configure: GMP_CFLAGS: -I/opt/homebrew/Cellar/gmp/6.3.0/include
configure: GMP_LIBS: -L/opt/homebrew/Cellar/gmp/6.3.0/lib -lgmpxx -lgmp
configure: MPFR_CFLAGS: -I/opt/homebrew/Cellar/mpfr/4.2.1/include
configure: MPFR_LIBS: -L/opt/homebrew/Cellar/mpfr/4.2.1/lib -lmpfr -lgmp
checking if gmp compiles... no
configure: Configuration failed because gmp was not found. Try installing:
configure: * deb: libgmp3-dev (Debian, Ubuntu)
configure: * rpm: gmp-devel (Fedora, EPEL)
configure: * brew: gmp (Mac OSX)
configure:
configure: If gmp is already installed, check that 'pkg-config' is in
configure: your PATH and PKG_CONFIG_PATH contains a gmpxx.pc file.
configure:
configure: error: ERROR: Installation failed
ERROR: configuration failed for package ‘prepr’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/prepr’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/f2/n6b1dv_12qvc6pyj9cz4lcjm0000gp/T//RtmpmfOLCH/file7ac91d8ccf21/prepr_0.3.0.tar.gz’ had non-zero exit status`

jeffreyhanson · 2024-12-12T21:51:17Z

Thanks for persisting with this. Since you can't install dplyr from source, this would suggest that your computer is missing some general peice of software for installing/building R packages from source. I don't know much about macOS sorry. I checked a book on R package development, and it seems like xcode might be needed. Could you try installing it following these instructions (https://r-pkgs.org/setup.html#macos) and see if it works after that?

juanmayorgahenao · 2024-12-12T23:39:12Z

Thanks, Jeffrey. I've updated xcode and I'm now using version Apple clang version 16.0.0 (clang-1600.0.26.6). Still no luck... I wonder what might have caused this mess in the first place... I tried installing ggplot from source and it worked... As this doesn't seem exclusive to prepr feel free to close the issue. I appreciate your help!!

jeffreyhanson · 2024-12-13T00:03:55Z

No worries! Yeah, both prepr and dplyr have C/C++ source that needs to be compiled during installation (when installing from source) and this requires additional software to be installed (e.g., like xcode). Whereas, ggplot2 doesn't have any C/C++ source code, so it can be installed from source without requiring additional software (beyond a working R installation). Does dplyr still fail to install from source?

Another option we can try is compiling prepr using R-universe so that you can install a precompiled binary of the package (this is the default option when installing packages from CRAN on macOS and Windows). This means that you won't need to compile C/C++ code as part of the installation process on your computer. I'll see if can get that working for you.

jeffreyhanson · 2024-12-13T00:15:28Z

I've updated the r-universe configuration for the prioritizr org, so it will build precompiled binaries for the prepr package. Since there's a bit of a delay, it's not going to do this immediately unfortunately. As I understand it, r-universe automatically updates once each day to see if there's new packages it should build. But hopefully, it should start soon. If you visit here (https://prioritizr.r-universe.dev/builds), this will show the precompiled packages that are available for installation. It currently doesn't show prepr, but hopefully will in the future. Once you see prepr listed there, could you try running this code to install prepr from r-universe?

install.packages(
  "prepr",
  repos = c("https://prioritizr.r-universe.dev", "https://cloud.r-project.org")
)

jeffreyhanson · 2024-12-13T02:24:46Z

Just checked r-universe and it looks like it's finished building prepr, can you try installing it when you get a chance?

juanmayorgahenao · 2024-12-13T14:41:49Z

Hi Jeffrey, thanks again for your help!

I've tried installing prepr in the way you shored above and no luck. Below is the output....

`

Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘prepr’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘prepr’

trying URL 'https://prioritizr.r-universe.dev/src/contrib/prepr_0.3.0.tar.gz'
Content type 'application/gzip' length 224463 bytes (219 KB)

downloaded 219 KB

installing source package ‘prepr’ ...
** using staged installation
checking if R found... yes
configure: R version: 4.4.2
configure: CC: clang -arch arm64
configure: CPP:
configure: CFLAGS: -falign-functions=64 -Wall -g -O2
configure: CPPFLAGS: -I/opt/R/arm64/include
configure: LDFLAGS: -L/opt/R/arm64/lib
checking for gdal-config... /opt/homebrew/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.10.0
checking GDAL version >= 2.0.1... yes
checking for pkg-config... yes
checking if gmp compiles... no
configure: Configuration failed because gmp was not found. Try installing:
configure: * deb: libgmp3-dev (Debian, Ubuntu)
configure: * rpm: gmp-devel (Fedora, EPEL)
configure: * brew: gmp (Mac OSX)
configure:
configure: If gmp is already installed, check that 'pkg-config' is in
configure: your PATH and PKG_CONFIG_PATH contains a gmpxx.pc file.
configure:
configure: error: ERROR: Installation failed
ERROR: configuration failed for package ‘prepr’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/prepr’
Warning in install.packages :
installation of package ‘prepr’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/f2/n6b1dv_12qvc6pyj9cz4lcjm0000gp/T/RtmpofY5e2/downloaded_packages’
`

jeffreyhanson · 2024-12-13T18:39:21Z

Thanks for trying it out! I'm sorry - it looks like the r-universe buids failed for macOS (https://github.com/r-universe/prioritizr/actions/runs/12307931762) (though they worked for Linux and Windows). I'll take another look and see what I can do. I'm a bit busy this weekend, so it might be a few days before I can get to it.

jeffreyhanson added the bug Something isn't working label Dec 11, 2024

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trying URL 'https://prioritizr.r-universe.dev/src/contrib/prepr_0.3.0.tar.gz' Content type 'application/gzip' length 224463 bytes (219 KB)

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trying URL 'https://prioritizr.r-universe.dev/src/contrib/prepr_0.3.0.tar.gz'
Content type 'application/gzip' length 224463 bytes (219 KB)