GNU bug report logs - #44450
Issues installing Avogadro

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Godefroy Vannoye <godefroy.vannoye <at> gmail.com>
To: bug-guix <at> gnu.org
Subject: Issues installing Avogadro
Date: Wed, 4 Nov 2020 19:17:56 +0100

Hi,

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

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.

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

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

cd /tmp/guix-build-avogadro-1.2.0.drv-0/build && $(MAKE) -f
CMakeFiles/Makefile2 libavogadro/all

This is the first line of the makefile where $(MAKE) appears, but I
could not find where it was defined (I suppose it is defined as make
-j4, but it is not explicit in the makefile or in
environment-variables). This makes me assume that the error comes from
the $(MAKE), but I'm not knowledgeable enough to verify it.

Feel free to ask me anything or to explain me what I could have done wrong.

Thank you for your work and for your time,

Godefroy Vannoye

Message #8 received at 44450 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Godefroy Vannoye <godefroy.vannoye <at> gmail.com>, 44450 <at> debbugs.gnu.org
Subject: Re: bug#44450: Issues installing Avogadro
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 <godefroy.vannoye <at> gmail.com> 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

Message #13 received at 44450-done <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: Godefroy Vannoye <godefroy.vannoye <at> gmail.com>, 44450-done <at> debbugs.gnu.org
Subject: Re: bug#44450: Issues installing Avogadro
Date: Wed, 06 Sep 2023 00:05:09 -0400

Hi,

zimoun <zimon.toutoune <at> gmail.com> writes:

> Dear,
>
> Thank you for the report.
>
> On Wed, 04 Nov 2020 at 19:17, Godefroy Vannoye <godefroy.vannoye <at> gmail.com> 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

We now have avogradro2, which builds correctly.

-- 
Thanks,
Maxim

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