bug#67416: Error when installing package, CMAKE_Fortran_COMPILER could be found

bug#67416: Error when installing package, CMAKE_Fortran_COMPILER could be found

[Pierre Clouzet]

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Hello, 
I'm trying to install a package with the command: 

guix package --install-from-file=gmsh-try.scm 

the gmsh-try.csm looks like this: 

(use-modules (guix packages) 
(guix download) 
(guix licenses) 
(guix build-system cmake)) 
(package 
(name "mygmsh") 
(version "3.0.6") 
(source (origin 
(method url-fetch) 
(uri (string-append "https://gmsh.info/src/gmsh-3.0.6-source.tgz")) 
(sha256 
(base32 
"0ywqhr0zmdhn8dvi6l8z1vkfycyv67fdrz6b95mb39np832bq04p")))) 
(build-system cmake-build-system) 
(arguments 
`(#:configure-flags '("-DENABLE_BUILD_LIB=1" 
"-DCMAKE_INSTALL_PREFIX=/opt/nextsim_gnu/gmsh-3.0.6" 
"-DENABLE_MMG3D=FALSE"))) 
(synopsis "3D finite element grid generator") 
(description "Gmsh is a 3D finite element grid generator with a built-in 
CAD engine and post-processor. Its design goal is to provide a fast, light 
and user-friendly meshing tool with parametric input and advanced 
visualization capabilities. Gmsh is built around four modules: geometry, 
mesh, solver and post-processing. The specification of any input to these 
modules is done either interactively using the graphical user interface or in 
ASCII text files using Gmsh's own scripting language.") 
(home-page "http://gmsh.info//") 
(license gpl2+)) 

When at some point, cmake tests things, this is what I get: 

-- The CXX compiler identification is GNU 11.3.0 
-- The C compiler identification is GNU 11.3.0 
-- Detecting CXX compiler ABI info 
-- Detecting CXX compiler ABI info - done 
-- Check for working CXX compiler: /gnu/store/5lqhcv91ijy82p92ac6g5xw48l0lwwz4-gcc-11.3.0/bin/c++ - skipped 
-- Detecting CXX compile features 
-- Detecting CXX compile features - done 
-- Detecting C compiler ABI info 
-- Detecting C compiler ABI info - done 
-- Check for working C compiler: /gnu/store/5lqhcv91ijy82p92ac6g5xw48l0lwwz4-gcc-11.3.0/bin/gcc - skipped 
-- Detecting C compile features 
-- Detecting C compile features - done 
-- Looking for sys/types.h 
-- Looking for sys/types.h - found 
-- Looking for stdint.h 
-- Looking for stdint.h - found 
-- Looking for stddef.h 
-- Looking for stddef.h - found 
-- Check size of void* 
-- Check size of void* - done 
-- Found 64Bit 
-- Performing Test STDCXX11 
-- Performing Test STDCXX11 - Success 
-- Found C++11 
-- The Fortran compiler identification is unknown 
CMake Error at CMakeLists.txt:421 (enable_language): 
No CMAKE_Fortran_COMPILER could be found. 

Tell CMake where to find the compiler by setting either the environment 
variable "FC" or the CMake cache entry CMAKE_Fortran_COMPILER to the full 
path to the compiler, or to the compiler name if it is in the PATH. 


-- Configuring incomplete, errors occurred! 
See also "/tmp/guix-build-mygmsh-3.0.6.drv-0/build/CMakeFiles/CMakeOutput.log". 
See also "/tmp/guix-build-mygmsh-3.0.6.drv-0/build/CMakeFiles/CMakeError.log". 
error: in phase 'configure': uncaught exception: 
%exception #<&invoke-error program: "cmake" arguments: ("../gmsh-3.0.6-source" "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DCMAKE_INSTALL_PREFIX=/gnu/store/kvx8rfsa457xz9723zsyk8x41zscs63l-mygmsh-3.0.6" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" "-DCMAKE_INSTALL_RPATH=/gnu/store/kvx8rfsa457xz9723zsyk8x41zscs63l-mygmsh-3.0.6/lib" "-DCMAKE_VERBOSE_MAKEFILE=ON" "-DENABLE_BUILD_LIB=1" "-DCMAKE_INSTALL_PREFIX=/opt/nextsim_gnu/gmsh-3.0.6" "-DENABLE_MMG3D=FALSE") exit-status: 1 term-signal: #f stop-signal: #f> 
phase `configure' failed after 0.8 seconds 
command "cmake" "../gmsh-3.0.6-source" "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DCMAKE_INSTALL_PREFIX=/gnu/store/kvx8rfsa457xz9723zsyk8x41zscs63l-mygmsh-3.0.6" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" "-DCMAKE_INSTALL_RPATH=/gnu/store/kvx8rfsa457xz9723zsyk8x41zscs63l-mygmsh-3.0.6/lib" "-DCMAKE_VERBOSE_MAKEFILE=ON" "-DENABLE_BUILD_LIB=1" "-DCMAKE_INSTALL_PREFIX=/opt/nextsim_gnu/gmsh-3.0.6" "-DENABLE_MMG3D=FALSE" failed with status 1 

It looks like cmake cant find fortran compiler. I'm very new to guix universe so I may have missed a step. 

Thanks in advance, 
Pierre 

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Error when installing package, CMAKE_Fortran_COMPILER could be found

[Tobias Geerinckx-Rice]

close 67416
thanks

(The above is for the Debbugs control bot.  The bug-guix@ address is for reporting shortcomings in Guix.  For general support, please use help-guix@.  I've moved this discussion there.)

Hi Pierre,

It appears that you haven't given the package a FORTRAN compiler to find.  Try

  (native-inputs (list gfortran))

to add one to the build environment.  Do not waste time 'guix install'ing anything, this will have 0 effect.

If the build system still won't find gfortran, try

  (arguments
    `(
      ...
      #:phases
      (modify-phases %standard-phases
        (add-before 'configure 'find-gfortran
          (lambda _
            (setenv "FC" (which "gfortran"))))))

or so.  Untested example, assuming the compiler binary is also named 'gfortran'.

Kind regards,

T G-R

Sent on the go.  Excuse or enjoy my brevity.

Re: Error when installing package, CMAKE_Fortran_COMPILER could be found

[Simon Tournier]

Hi Pierre,

On Fri, 24 Nov 2023 at 16:53, Tobias Geerinckx-Rice <me@tobias.gr> wrote:

> It appears that you haven't given the package a FORTRAN compiler to find.  Try
>
>   (native-inputs (list gfortran))

In addition to Tobias’s words, the recipe will fail at the tests:

--8<---------------cut here---------------start------------->8---
The following tests FAILED:
	  1 - ../gmsh-3.0.6-source/demos/post_processing/lowmem-anim.geo (Failed)
	  4 - ../gmsh-3.0.6-source/demos/simple_geo/antenna.geo (Timeout)
	  8 - ../gmsh-3.0.6-source/demos/simple_geo/filter.geo (Failed)
	  9 - ../gmsh-3.0.6-source/demos/simple_geo/hex.geo (Failed)
	 11 - ../gmsh-3.0.6-source/demos/simple_geo/indheat.geo (Failed)
	 12 - ../gmsh-3.0.6-source/demos/simple_geo/machine.geo (Timeout)
	 13 - ../gmsh-3.0.6-source/demos/simple_geo/piece-extr-rec.geo (Failed)
	 14 - ../gmsh-3.0.6-source/demos/simple_geo/piece-extr.geo (Failed)
	 16 - ../gmsh-3.0.6-source/demos/simple_geo/pripyrtet.geo (Failed)
	 18 - ../gmsh-3.0.6-source/demos/simple_geo/sphere.geo (Failed)
	 29 - ../gmsh-3.0.6-source/tutorial/t13.geo (SEGFAULT)
	 32 - ../gmsh-3.0.6-source/tutorial/t16.geo (Failed)
	 33 - ../gmsh-3.0.6-source/tutorial/t17.geo (Failed)
	 35 - ../gmsh-3.0.6-source/tutorial/t3.geo (Failed)
--8<---------------cut here---------------end--------------->8---

Well, IIRC, gmsh has some dependencies, depending on the default options
selected at configure time.  For instance, see the current Gmsh from the
module (gnu packages maths), e.g., guix edit gmsh or [1] lists all the
dependencies:

    (propagated-inputs
     (list fltk
           gfortran
           glu
           gmp
           hdf5
           lapack
           libx11
           libxext
           mesa
           metis
           opencascade-occt))
    (inputs
     (list fontconfig
           libxft
           python))

Moreover, I am not sure for this flag you set in your recipe:

                         "-DCMAKE_INSTALL_PREFIX=/opt/nextsim_gnu/gmsh-3.0.6"

Hope that helps.

Cheers,
simon


1: https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/maths.scm#n3233

Re: Error when installing package, CMAKE_Fortran_COMPILER could be found

[Pierre Clouzet]

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Hi Simon, 
Thanks for your reply! I managed to make it work finally. I'm working with an old code that need this specific version of the package.

Also, this code does not use configure/make/make install of cmake/make/make install way of installing.
Instead I need to run a script exporting variables with a . ./script.sh command
I was wondering if you could give me a hint about how to say in a manifest how to run such script (if possible).
You can find such script attached.

Thanks, 
Pierre
----- Mail original -----
> De: "Simon Tournier" <zimon.toutoune@gmail.com>
> À: "Tobias Geerinckx-Rice" <me@tobias.gr>, "Pierre Clouzet" <pierre.clouzet@inria.fr>, help-guix@gnu.org
> Envoyé: Mardi 28 Novembre 2023 16:42:46
> Objet: Re: Error when installing package, CMAKE_Fortran_COMPILER could be found

> Hi Pierre,
> 
> On Fri, 24 Nov 2023 at 16:53, Tobias Geerinckx-Rice <me@tobias.gr> wrote:
> 
>> It appears that you haven't given the package a FORTRAN compiler to find.  Try
>>
>>   (native-inputs (list gfortran))
> 
> In addition to Tobias’s words, the recipe will fail at the tests:
> 
> --8<---------------cut here---------------start------------->8---
> The following tests FAILED:
>	  1 - ../gmsh-3.0.6-source/demos/post_processing/lowmem-anim.geo (Failed)
>	  4 - ../gmsh-3.0.6-source/demos/simple_geo/antenna.geo (Timeout)
>	  8 - ../gmsh-3.0.6-source/demos/simple_geo/filter.geo (Failed)
>	  9 - ../gmsh-3.0.6-source/demos/simple_geo/hex.geo (Failed)
>	 11 - ../gmsh-3.0.6-source/demos/simple_geo/indheat.geo (Failed)
>	 12 - ../gmsh-3.0.6-source/demos/simple_geo/machine.geo (Timeout)
>	 13 - ../gmsh-3.0.6-source/demos/simple_geo/piece-extr-rec.geo (Failed)
>	 14 - ../gmsh-3.0.6-source/demos/simple_geo/piece-extr.geo (Failed)
>	 16 - ../gmsh-3.0.6-source/demos/simple_geo/pripyrtet.geo (Failed)
>	 18 - ../gmsh-3.0.6-source/demos/simple_geo/sphere.geo (Failed)
>	 29 - ../gmsh-3.0.6-source/tutorial/t13.geo (SEGFAULT)
>	 32 - ../gmsh-3.0.6-source/tutorial/t16.geo (Failed)
>	 33 - ../gmsh-3.0.6-source/tutorial/t17.geo (Failed)
>	 35 - ../gmsh-3.0.6-source/tutorial/t3.geo (Failed)
> --8<---------------cut here---------------end--------------->8---
> 
> Well, IIRC, gmsh has some dependencies, depending on the default options
> selected at configure time.  For instance, see the current Gmsh from the
> module (gnu packages maths), e.g., guix edit gmsh or [1] lists all the
> dependencies:
> 
>    (propagated-inputs
>     (list fltk
>           gfortran
>           glu
>           gmp
>           hdf5
>           lapack
>           libx11
>           libxext
>           mesa
>           metis
>           opencascade-occt))
>    (inputs
>     (list fontconfig
>           libxft
>           python))
> 
> Moreover, I am not sure for this flag you set in your recipe:
> 
>                         "-DCMAKE_INSTALL_PREFIX=/opt/nextsim_gnu/gmsh-3.0.6"
> 
> Hope that helps.
> 
> Cheers,
> simon
> 
> 
> 1: https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/maths.scm#n3233

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Re: Error when installing package, CMAKE_Fortran_COMPILER could be found

[Simon Tournier]

Hi Pierre,

Sorry for the late reply.

On Thu, 30 Nov 2023 at 10:44, Pierre Clouzet <pierre.clouzet@inria.fr> wrote:

> Also, this code does not use configure/make/make install of cmake/make/make install way of installing.
> Instead I need to run a script exporting variables with a . ./script.sh command
> I was wondering if you could give me a hint about how to say in a manifest how to run such script (if possible).
> You can find such script attached.

If you have not found a way in the mean time, I do not have an answer
because I am a bit confused by your question. :-)

Do you mean run the script with some manifest.scm file as with “guix
shell -m manifest.scm” or do you mean include such script with the Guix
recipe of your package variant?

If I understand correctly, you are trying to package nextsim that needs
one specific version of Gmsh, right?

The script set_env_linux.sh reads,

--8<---------------cut here---------------start------------->8---
# 1. Before compiling, install:
# - necdf, necdfcxx, boost, openmpi, gcc11:
# sudo apt install libnetcdf-c++4 libnetcdf-dev libblas-dev liblapack-dev libboost-dev \
#	libboost-chrono-dev \ libboost-date-time-dev \ libboost-filesystem-dev \
#	libboost-iostreams-dev \ libboost-log-dev \ libboost-locale-dev \
#	libboost-math-dev \ libboost-mpi-dev \ libboost-program-options-dev \
#	libboost-regex-dev \ libboost-serialization-dev \ libboost-system-dev \ libboost-timer-dev
# - also go to dependencies/gmsh-3.0.6-source
# and run the install_gmsh_for_nextsim.sh WITHOUT changing the CMAKE_PREFIX_INSTALL variable.
# 2. Compiling:
# -check that paths listed below, fit your configuration.
# - run this script to set the environement: ". ./set_env_linux.sh" (NOT ./set_env_linux.sh)
# - run make -j${nproc}
--8<---------------cut here---------------end--------------->8---

and it is not clear:

 1. if you want or not keep the dependencies from APT or replace them by
    the ones from Guix?
 2. if you want to only build Gmsh with Guix and all the rest not?
 3. how you would like to build nextsim?

What would make sense to me would to build all using Guix; it would
mean:

 a) package the patched version of Gmsh (somehow replace
    install_gmsh_for_nextsim.sh)
 b) tweak set_env_linux.sh for making it Guix-friendly (substitute the
    various hard coded PATH by Guix ones, etc.)
 c) replace the ’build’ phase of cmake build-system by calling this
    modified script by step b.

Well, maybe I misread the question. :-)

Cheers,
simon