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acorg / Racmacs

Racmacs R package for performing antigenic cartography
https://acorg.github.io/Racmacs/
GNU Affero General Public License v3.0
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Racmacs install #149

Closed Nicolaaht closed 1 year ago

Nicolaaht commented 1 year ago

I'm trying to re-install Racmacs. Gcc and Makevars updated

devtools::install_github("acorg/Racmacs") Downloading GitHub repo acorg/Racmacs@HEAD Error: Failed to install 'Racmacs' from GitHub: Could not find tools necessary to compile a package Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

pkgbuild::check_build_tools(debug = TRUE) Trying to compile a simple C file Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c gcc-13.1.0 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -O3 -c foo.c -o foo.o /bin/sh: gcc-13.1.0: command not found make: *** [foo.o] Error 127 Error: Could not find tools necessary to compile a package Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

Thoughts?

Thanks, Nic

shwilks commented 1 year ago

Sounds like maybe you need to fix your compiler toolchain. There are some updated instructions on it you can try following here and see if it fixes it: https://shwilks.github.io/Racmacs/index.html

Nicolaaht commented 1 year ago

I think its still invoking clang version

(base) nicolalewis@Nicolas-MBP-2 .R % open Makevars (base) nicolalewis@Nicolas-MBP-2 .R % gcc --version Apple clang version 14.0.0 (clang-1400.0.29.202) Target: x86_64-apple-darwin21.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin (base) nicolalewis@Nicolas-MBP-2 .R %

shwilks commented 1 year ago

What does your current ~/.R/Makevars file look like?

Nicolaaht commented 1 year ago

I'm just changing the version to align with the fxcoudert ....

CC=gcc-12.2.0 CXX=/usr/local/bin/g++-12.2.0 CXX1X=/usr/local/bin/g++-12.2.0 CXX13.1.0=/usr/local/bin/g++-12.2.0 SHLIB_CXXLD=/usr/local/bin/g++-12.2.0 FC=/usr/local/bin/gfortran-12.2.0 F77=/usr/local/bin/gfortran-12.2.0 MAKE=make -j8 CFLAGS = -O3 CXXFLAGS = -O3

SHLIB_OPENMP_CFLAGS=-fopenmp SHLIB_OPENMP_CXXFLAGS=-fopenmp SHLIB_OPENMP_FCFLAGS=-fopenmp SHLIB_OPENMP_FFLAGS=-fopenmp

shwilks commented 1 year ago

You need to match the paths to the compilers that come with the gfortran version for me (on an M2 Mac) it ends up being:

CC=/usr/local/gfortran/bin/gcc
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
SHLIB_CXXLD=/usr/local/gfortran/bin/g++
FC=/usr/local/gfortran/bin/gfortran
F77=/usr/local/gfortran/bin/gfortran
MAKE=make -j8

SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp
SHLIB_OPENMP_FFLAGS=-fopenmp

But I needed to find the right installer that gave me all these executables in /usr/local/gfortran/bin/

Nicolaaht commented 1 year ago

Is the next step to delete my Makevars and start again. I'm on an intel, Monterey 12.6.2

shwilks commented 1 year ago

What do you get it you run which gfortran | xargs ls -l?

Nicolaaht commented 1 year ago

Last login: Tue Jun 6 11:09:12 on ttys000 (base) nicolalewis@Nicolas-MBP-2 ~ % which gfortran | xargs ls -l lrwxr-xr-x 1 root admin 32 6 Jun 12:45 /usr/local/bin/gfortran -> /usr/local/gfortran/bin/gfortran (base) nicolalewis@Nicolas-MBP-2 ~ %

shwilks commented 1 year ago

Ok, it looks like it should work if you copy and paste my Makevars file instead. Although you may want to double check that all the other executables in it like /usr/local/gfortran/bin/gcc also exist in that location on your system

Nicolaaht commented 1 year ago

All good. Thanks Sam.

From: Sam Wilks @.> Sent: 06 June 2023 13:35 To: acorg/Racmacs @.> Cc: Lewis, Nicola @.>; Author @.> Subject: Re: [acorg/Racmacs] Racmacs install (Issue #149)

Ok, it looks like it should work if you copy and paste my Makevars file instead. Although you may want to double check that all the other executables in it like /usr/local/gfortran/bin/gcc also exist in that location on your system

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shwilks commented 1 year ago

No problem, glad we could fix it! :)

Nicolaaht commented 1 year ago

One query: what's the number next to the map stress? - bottom left of viewer window?

BW Nicola

From: Sam Wilks @.> Sent: 06 June 2023 15:33 To: acorg/Racmacs @.> Cc: Lewis, Nicola @.>; Author @.> Subject: Re: [acorg/Racmacs] Racmacs install (Issue #149)

No problem, glad we could fix it! :)

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shwilks commented 1 year ago

It's a calculation of the stress per titer to try and make map stress a bit more comparable between maps

Nicolaaht commented 1 year ago

Very helpful. So I don't need to try calculating this myself after all this time 😉

From: Sam Wilks @.> Sent: 08 June 2023 10:07 To: acorg/Racmacs @.> Cc: Lewis, Nicola @.>; Author @.> Subject: Re: [acorg/Racmacs] Racmacs install (Issue #149)

It's a calculation of the stress per titer to try and make map stress a bit more comparable between maps

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