Subject: Re: bug#44450: Issues installing Avogadro

From: zimoun <[email-masked]>
Date: Tue, 10 Nov 2020 00:27:06 +0100

Dear,

Thank you for the report.

On Wed, 04 Nov 2020 at 19:17, Godefroy Vannoye <[email-masked]> wrote:

> First let me apologize if I have missed something, I'm a new user of
> guix and know only the basics about compilation processes.

Welcome! :-)

> I am using guix on the Arch distribution, and installed it using the
> shell installer script. My first tests seem to indicate that guix is
> installed properly.

The Guix Data Service indicates that the package avogrado is broken.

https://data.guix.gnu.org/repository/1/branch/master/package/avogadro/output-history

> I then tried to install Avogadro, but met the following error when
> building it:
>
> make[1]: Leaving directory '/tmp/guix-build-avogadro-1.2.0.drv-0/build'
> make: *** [Makefile:155: all] Error 2
> command "make" "-j" "4" failed with status 2
> note: keeping build directory `/tmp/guix-build-avogadro-1.2.0.drv-0'
> builder for
> `/gnu/store/pc3pdcpm0mwbfvymwizfs14mdfb6qa5x-avogadro-1.2.0.drv' failed
> with exit code 1
> build of /gnu/store/pc3pdcpm0mwbfvymwizfs14mdfb6qa5x-avogadro-1.2.0.drv
> failed

Before that, I get:

--8<---------------cut here---------------start------------->8---
[..]
-- Setting new boost python libraries
CMake Error: failed to create symbolic link '/tmp/guix-build-avogadro-1.2.0.drv-0/build/libavogadro/include/avogadro//tmp/guix-build-avogadro-1.2.0.drv-0/build/libavogadro/src/config.h': no such file or directory
-- Enabled python terminal
CMake Warning at libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt:44 (export):
  Cannot create package registry file:

    /homeless-shelter/.cmake/packages/libmsym/0734694d5c49e2816b4ae48943d7700a

  No such file or directory
[..]
--8<---------------cut here---------------end--------------->8---

then:

--8<---------------cut here---------------start------------->8---
[..]
/tmp/guix-build-avogadro-1.2.0.drv-0/avogadro-1.2.0-checkout/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c: In function ‘orbitalFromQuantumNumbers’:
/tmp/guix-build-avogadro-1.2.0.drv-0/avogadro-1.2.0-checkout/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c:70:24: error: non-floating-point argument in call to function ‘__builtin_signbit’
             char *d = (signbit(m) == 1 ? "-" : "+");
                        ^~~~~~~
/tmp/guix-build-avogadro-1.2.0.drv-0/avogadro-1.2.0-checkout/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c:76:24: error: non-floating-point argument in call to function ‘__builtin_signbit’
             char *d = (signbit(m) == 1 ? "-" : "+");
                        ^~~~~~~
make[2]: *** [libavogadro/src/extensions/symmetry/libmsym/CMakeFiles/msym.dir/build.make:170: libavogadro/src/extensions/symmetry/libmsym/CMakeFiles/msym.dir/src/orbital.c.o] Error 1
make[2]: Leaving directory '/tmp/guix-build-avogadro-1.2.0.drv-0/build'
make[1]: *** [CMakeFiles/Makefile2:2069: libavogadro/src/extensions/symmetry/libmsym/CMakeFiles/msym.dir/all] Error 2
make[2]: Leaving directory '/tmp/guix-build-avogadro-1.2.0.drv-0/build'
make[1]: *** [CMakeFiles/Makefile2:2069: libavogadro/src/extensions/symmetry/libmsym/CMakeFiles/msym.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  1%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o
[..]
--8<---------------cut here---------------end--------------->8---

> I retried to build it by running guix build avogadro -K to look at the
> makefile and found at line 155

I get the same thing.  But I think the error comes from an early step.

Well, then I am running:

  cd /tmp/guix-build-avogadro-1.2.0.drv-0
  mkdir mine && cd mine
  guix environmment avogadro
  cmake ../avogadro-1.2.0-checkout/

--8<---------------cut here---------------start------------->8---
[..]
CMake Error: failed to create symbolic link '/tmp/guix-build-avogadro-1.2.0.drv-0/my/libavogadro/include/avogadro//tmp/guix-build-avogadro-1.2.0.drv-0/my/libavogadro/src/config.h': no such file or directory
[..]
--8<---------------cut here---------------end--------------->8---

So I would try to address this first error by examining the folder avogadro-1.2.0-checkout/.

All the best,
simon