GNU bug report logs - #74672
Package hypre build failure for output "doc"

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

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: bug-guix <at> gnu.org
Subject: Package hypre build failure for output "doc"
Date: Tue, 3 Dec 2024 19:13:53 +0100 (CET)

[Message part 1 (text/plain, inline)]

Hello, 

I am getting failures for the package "hypre", during the building of its "doc" output. I have last tested it on 32d1dfb5545bb01c9d8d7a2465f13f2f379dd96e, and the error I get is of the form: 

error: Problems running gs. Check your installation! 

(repeated many several times) 
It seems to be related to doxygen, and I can reproduce it if I keep the build directory (as in [ https://guix.gnu.org/manual/devel/en/html_node/Debugging-Build-Failures.html | https://guix.gnu.org/manual/devel/en/html_node/Debugging-Build-Failures.html ] ) and I manually try to build the ref-manual. 
That said, I have not been able to fix the problem, so I ask for help in case the original package authors have a hint. 

P.S. When the package does build on certain machines, I get errors if I pass the --check option: 

guix build: error: derivation `/gnu/store/1i8b07ll0m5j2p2m7z0wcxqgp407b5qc-hypre-2.20.0.drv' may not be deterministic: output `/gnu/store/g8ci2qjbz49aq2zwn8hbl3dl44d30rfg-hypre-2.20.0-doc' differs 


Thanks, 
Luca 

[Message part 2 (text/html, inline)]

Message #8 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludovic.courtes <at> inria.fr>
To: Luca Cirrottola <luca.cirrottola <at> inria.fr>
Cc: 74672 <at> debbugs.gnu.org
Subject: Re: bug#74672: Package hypre build failure for output "doc"
Date: Fri, 21 Mar 2025 14:46:03 +0100

Hi Luca,

Apologies for not noticing earlier.

Luca Cirrottola <luca.cirrottola <at> inria.fr> skribis:

> I am getting failures for the package "hypre", during the building of its "doc" output. I have last tested it on 32d1dfb5545bb01c9d8d7a2465f13f2f379dd96e, and the error I get is of the form: 
>
> error: Problems running gs. Check your installation! 

I was hoping to find a complete log with that error on the build farm to
try and investigate, but apparently it has been building find since
November:

  https://ci.guix.gnu.org/build/9433751/details

I rebuilt it 5 times in a row to see if I could reproduce it, but I
cannot:

  guix build -c64 -v1 -K /gnu/store/cc591030mmnz23iiqfn0l6czdjlnn78d-hypre-openmpi-2.20.0.drv --check

Do you still experience it?  If so, do you have a longer log excerpt and
commit ID I could use to reproduce it?

> P.S. When the package does build on certain machines, I get errors if I pass the --check option: 
>
> guix build: error: derivation `/gnu/store/1i8b07ll0m5j2p2m7z0wcxqgp407b5qc-hypre-2.20.0.drv' may not be deterministic: output `/gnu/store/g8ci2qjbz49aq2zwn8hbl3dl44d30rfg-hypre-2.20.0-doc' differs 

That I can reproduce; reported at <https://issues.guix.gnu.org/77152>.

Thanks,
Ludo’.

Message #11 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: 74672 <at> debbugs.gnu.org
Date: Fri, 21 Mar 2025 15:07:45 +0100 (CET)

[Message part 1 (text/plain, inline)]

Hello, 
I can confirm that the above is still of interest today (2025-03-21) on master (efac1498c15198afc4f9a2bc700408bde1b3b3ed). I can build on my machine, although I get the message: 

error: Problems running gs. Check your installation! 

and, if I pass the --no-grafts --check options: 

guix build: error: derivation `/gnu/store/q0klgx1zgwkck2dkiz619sj059bmq98w-hypre-2.20.0.drv' may not be deterministic: output `/gnu/store/21zjskysh9az39nby24jr8ps46zsm4wq-hypre-2.20.0-doc' differs 

[Message part 2 (text/html, inline)]

Message #14 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: 74672 <74672 <at> debbugs.gnu.org>
Date: Fri, 21 Mar 2025 15:09:56 +0100 (CET)

[Message part 1 (text/plain, inline)]

Sorry I sent the message before reading your reply. I will check with the very same options as you and provide a log. 

[Message part 2 (text/html, inline)]

Message #17 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: Ludovic Courtès <ludovic.courtes <at> inria.fr>
Cc: 74672 <74672 <at> debbugs.gnu.org>
Subject: Re: bug#74672: Package hypre build failure for output "doc"
Date: Fri, 21 Mar 2025 15:29:46 +0100 (CET)

[Message part 1 (text/plain, inline)]

Hello,
Thanks for investigating it! Please find a log attached to the email. gs error at line 2898, still the package build formally succeed.

What I cannot reproduce is the fact that the error does not cause a build failure on my machine, while it does on some of my coworkers' machines...

[log_hypre (text/plain, attachment)]

Message #20 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludovic.courtes <at> inria.fr>
To: Luca Cirrottola <luca.cirrottola <at> inria.fr>
Cc: andreas <at> enge.fr, sharlatanus <at> gmail.com, 74672 <74672 <at> debbugs.gnu.org>,
 bavier <at> posteo.net
Subject: Re: bug#74672: Package hypre build failure for output "doc"
Date: Fri, 21 Mar 2025 16:32:28 +0100

Hi Luca,

(Cc’in the “science” team.)

Luca Cirrottola <luca.cirrottola <at> inria.fr> skribis:

> Thanks for investigating it! Please find a log attached to the email. gs error at line 2898, still the package build formally succeed.

Oh, so it could be that I overlooked them too since the files are being
generated anyway.  Perhaps those PDFs are actually broken?

For those following along, the relevant log excerpt is:

--8<---------------cut here---------------start------------->8---
starting phase `build-docs'
make: Entering directory '/tmp/guix-build-hypre-openmpi-2.20.0.drv-0/source/src/docs'
make[1]: Entering directory '/tmp/guix-build-hypre-openmpi-2.20.0.drv-0/source/src/docs/ref-manual'
doxygen conf.doxygen
warning: Tag 'TCL_SUBST' at line 227 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'COLS_IN_ALPHA_INDEX' at line 984 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'HTML_TIMESTAMP' at line 1117 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'FORMULA_TRANSPARENT' at line 1397 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'LATEX_SOURCE_CODE' at line 1669 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'XML_SCHEMA' at line 1794 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'XML_DTD' at line 1800 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'PERL_PATH' at line 2006 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'CLASS_DIAGRAMS' at line 2019 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'MSCGEN_PATH' at line 2028 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'DOT_FONTNAME' at line 2063 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'DOT_FONTSIZE' at line 2070 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'DOT_TRANSPARENT' at line 2264 of file 'conf.doxygen' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Changing CLASS_GRAPH option to TEXT because obsolete option CLASS_DIAGRAM was found and set to NO.
/tmp/guix-build-hypre-openmpi-2.20.0.drv-0/source/src/parcsr_ls/HYPRE_parcsr_ls.h:4319: warning: end of file with unbalanced grouping commands
/tmp/guix-build-hypre-openmpi-2.20.0.drv-0/source/src/krylov/HYPRE_krylov.h:1249: warning: end of file with unbalanced grouping commands
error: Problems running gs. Check your installation!
error: Problems running gs. Check your installation!
error: Problems running gs. Check your installation!
error: Problems running gs. Check your installation!
error: Problems running gs. Check your installation!
error: Problems running gs. Check your installation!
error: Problems running gs. Check your installation!
Doxygen version used: 1.9.8
Searching for include files...
Searching for example files...
--8<---------------cut here---------------end--------------->8---

Anyway, let’s investigate some more; we can get rid of the ‘build-docs’
phase if we cannot fix it.

Thanks,
Ludo’.

Message #23 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Ludovic Courtès <ludovic.courtes <at> inria.fr>
Cc: bavier <at> posteo.net, sharlatanus <at> gmail.com,
 Luca Cirrottola <luca.cirrottola <at> inria.fr>, 74672 <74672 <at> debbugs.gnu.org>
Subject: Re: bug#74672: Package hypre build failure for output "doc"
Date: Fri, 21 Mar 2025 18:58:06 +0100

Hello,

our hypre package is very old, version 2.20 of 2020 (yes, the regexp
matches!), while the most recent one is 2.32 from last October.

Maybe you could try updating the package first, assuming that more
recent versions are still compatible with its dependents?

Apart from that, it could be enough to add ghostscript as a native
input.

Andreas

Message #26 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: 74672 <at> debbugs.gnu.org
Cc: Luca Cirrottola <luca.cirrottola <at> inria.fr>
Subject: [PATCH 0/2] *** Hypre update ***
Date: Mon, 24 Mar 2025 18:03:28 +0100

Hello Andreas,

New version, old problems!

I have added ghostscript, and it reminds me that I already tried to do it in the past, but the errors just change into (a lot of):

   Fontconfig error: No writable cache directories


Luca Cirrottola (2):
  Hypre: switch to v2.32.0.
  Add ghostscript as native input.

 gnu/packages/maths.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)


base-commit: cb19f54b429c82c77b7602a240d8a78ff8063cc0
-- 
2.34.1

Message #29 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: 74672 <at> debbugs.gnu.org
Cc: Luca Cirrottola <luca.cirrottola <at> inria.fr>
Subject: [PATCH 1/2] Hypre: switch to v2.32.0.
Date: Mon, 24 Mar 2025 18:03:29 +0100

---
 gnu/packages/maths.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8baf3a0a7f..3e44cc6ede 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7697,7 +7697,7 @@ (define-public xaos
 (define-public hypre
   (package
     (name "hypre")
-    (version "2.20.0")
+    (version "2.32.0")
     (source
      (origin
        (method git-fetch)
@@ -7706,7 +7706,7 @@ (define-public hypre
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14iqjwg5sv1qjn7c2cfv0xxmn9rwamjrhh9hgs8fjbywcbvrkjdi"))))
+        (base32 "1hlydh15wz0yv5bgry7yyx4pvrl656mifhqjgifzf6dyksfvwpl7"))))
     (build-system gnu-build-system)
     (outputs '("out"                    ;5.3 MiB of headers and libraries
                "doc"))                  ;12 MiB of documentation
@@ -7716,6 +7716,7 @@ (define-public hypre
            python
            python-breathe
            python-sphinx
+           python-sphinx-rtd-theme
            (texlive-updmap.cfg
             (list texlive-adjustbox
                   texlive-alphalph
-- 
2.34.1

Message #32 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: 74672 <at> debbugs.gnu.org
Cc: Luca Cirrottola <luca.cirrottola <at> inria.fr>
Subject: [PATCH 2/2] Add ghostscript as native input.
Date: Mon, 24 Mar 2025 18:03:30 +0100

---
 gnu/packages/maths.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 3e44cc6ede..5823047300 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7713,6 +7713,7 @@ (define-public hypre
     (native-inputs
      (list doc++
            doxygen
+           ghostscript
            python
            python-breathe
            python-sphinx
-- 
2.34.1

Message #35 received at 74672 <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: 74672 <74672 <at> debbugs.gnu.org>
Subject: Re: [PATCH 2/2] Add ghostscript as native input.
Date: Mon, 24 Mar 2025 18:13:43 +0100 (CET)

When adding ghostscript, nonewithstanding the fontconfig error, I do not get the reproducibility error anymore when building with `--no-grafts --check` (on my machine). Can you check it please?

Still, I notice that building the doc in the 2.32.0 version takes much much longer than before.

Luca

Message #40 received at 74672-done <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Luca Cirrottola <luca.cirrottola <at> inria.fr>
Cc: 74672-done <at> debbugs.gnu.org
Subject: Re: [PATCH 2/2] Add ghostscript as native input.
Date: Fri, 28 Mar 2025 22:43:09 +0100

Hello Luca,

Am Mon, Mar 24, 2025 at 06:13:43PM +0100 schrieb Luca Cirrottola:
> When adding ghostscript, nonewithstanding the fontconfig error, I do not get the reproducibility error anymore when building with `--no-grafts --check` (on my machine). Can you check it please?
> Still, I notice that building the doc in the 2.32.0 version takes much much longer than before.

thanks for the patches! I have pushed them, after adapting the commit
messages to the GNU standards, to master as commits
   aedbde9052a0de2689b3bbc030bee957d3e9061b and
   c31662f7294b194663bc521358b01c3a7d7e4e27

The fontconfig error was a bit tricky, since it appeared inside an execution
of doxygen through make. A little Internet search revealed that fontconfig
uses the home directory to write a cache, which is set to
/homeless-shelter in the builder. So I added a line setting it to the
current directory. Hopefully it works, at least the error message has
disappeared.

Building the doc takes some time, but not shockingly so.

I am closing the bug, as my impression is that everything is fixed.

If you notice a problem, please do not hesitate to open a new issue.

Andreas

Message #43 received at 74672-done <at> debbugs.gnu.org (full text, mbox):

From: Luca Cirrottola <luca.cirrottola <at> inria.fr>
To: Andreas Enge <andreas <at> enge.fr>
Cc: 74672-done <at> debbugs.gnu.org
Subject: Re: [PATCH 2/2] Add ghostscript as native input.
Date: Mon, 31 Mar 2025 14:41:40 +0200 (CEST)

Thank you Andreas!

Luca

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