GNU bug report logs - #76079
imp@2.15.0 fails to build

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

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: bug-guix <at> gnu.org 
Cc: rekado <at> elephly.net
Subject: imp <at> 2.15.0 fails to build
Date: Wed, 05 Feb 2025 21:12:02 +0000

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

Hi,

While refreshing python-feature which is in the first level of
dependencies for imp I noticed it has failed to build.


--8<---------------cut here---------------start------------->8---
In file included from /tmp/guix-build-imp-2.15.0.drv-0/imp-2.15.0/modules/kernel/src/Model_evaluate.cpp:21,
                 from /tmp/guix-build-imp-2.15.0.drv-0/build/src/kernel_all.cpp:13:
/gnu/store/wjcwaddsgzibk7vyk3q256bax5yfwsbn-boost-1.83.0/include/boost/timer.hpp:21:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.)
   21 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.)
      |   ^~~~~
In file included from /tmp/guix-build-imp-2.15.0.drv-0/imp-2.15.0/modules/kernel/src/internal/base_static.h:19,
                 from /tmp/guix-build-imp-2.15.0.drv-0/imp-2.15.0/modules/kernel/src/base_utility.cpp:11,
                 from /tmp/guix-build-imp-2.15.0.drv-0/build/src/kernel_all.cpp:33:
/gnu/store/wjcwaddsgzibk7vyk3q256bax5yfwsbn-boost-1.83.0/include/boost/progress.hpp:23:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.)
   23 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.)
      |   ^~~~~
--8<---------------cut here---------------end--------------->8---

--8<---------------cut here---------------start------------->8---
guix describe
Generation 75   Feb 03 2025 21:37:27    (current)
  guix 2574ae3
    repository URL: https://git.savannah.gnu.org/git/guix.git
    branch: master
    commit: 2574ae3733637ead786fb3dc454369590794bc51
--8<---------------cut here---------------end--------------->8---

--
Oleg

[signature.asc (application/pgp-signature, inline)]

Message #8 received at 76079 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 76079 <at> debbugs.gnu.org
Subject: Re: imp <at> 2.15.0 fails to build
Date: Thu, 06 Feb 2025 11:36:12 +0100

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

Here's what I tried:

[0001-gnu-imp-Drop-input-labels.patch (text/x-patch, inline)]

From 475248bfaafcb122676460383705f72ccb050adb Mon Sep 17 00:00:00 2001
Message-ID: <475248bfaafcb122676460383705f72ccb050adb.1738837944.git.rekado <at> elephly.net>
From: Ricardo Wurmus <rekado <at> elephly.net>
Date: Thu, 6 Feb 2025 11:27:17 +0100
Subject: [PATCH 1/2] gnu: imp: Drop input labels.

* gnu/packages/bioinformatics.scm (imp)[native-inputs]: Drop labels.

Change-Id: I3182a4608a88c59ba0de2fa00d74b8d72b72d8bb
---
 gnu/packages/bioinformatics.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4ef4f6788f..16038a7c74 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15768,8 +15768,7 @@ (define-public imp
                   "-E" (format #f "'(~a)'" (string-join disabled-tests "|")))
             ";"))))))
     (native-inputs
-     `(("python" ,python-wrapper)
-       ("swig" ,swig)))
+     (list python-wrapper swig))
     (inputs
      (list boost
            cgal

base-commit: 0c9da3dbcb47840089a0213a59c385e780317bb6
-- 
2.48.1

[0002-gnu-imp-Use-an-older-version-of-boost.patch (text/x-patch, inline)]

From 7786b4e477b888cda42cffd764aacea705631dc1 Mon Sep 17 00:00:00 2001
Message-ID: <7786b4e477b888cda42cffd764aacea705631dc1.1738837944.git.rekado <at> elephly.net>
In-Reply-To: <475248bfaafcb122676460383705f72ccb050adb.1738837944.git.rekado <at> elephly.net>
References: <475248bfaafcb122676460383705f72ccb050adb.1738837944.git.rekado <at> elephly.net>
From: Ricardo Wurmus <rekado <at> elephly.net>
Date: Thu, 6 Feb 2025 11:29:23 +0100
Subject: [PATCH 2/2] gnu: imp: Use an older version of boost.

* gnu/packages/bioinformatics.scm (imp):[inputs]: Replace boost with
boost-for-mysql.

Change-Id: I3d3bec8589972f15770c264f4b2445f4798b7901
---
 gnu/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 16038a7c74..b64baaf463 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15770,7 +15770,7 @@ (define-public imp
     (native-inputs
      (list python-wrapper swig))
     (inputs
-     (list boost
+     (list boost-for-mysql
            cgal
            gsl
            hdf5
-- 
2.48.1

[Message part 4 (text/plain, inline)]

Haven't been able to build it yet, because my laptop runs out of memory,
but it might be enough to fix this.

Merely defining BOOST_TIMER_ENABLE_DEPRECATED=TRUE is not enough to make
it build with the current version of Boost.  I tried this before:

--8<---------------cut here---------------start------------->8---
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'patch-build-system
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("if\\(IMP_STATIC\\)" m)
+                (string-append "add_definitions(-DBOOST_TIMER_ENABLE_DEPRECATED=TRUE)\n" m))))))))
--8<---------------cut here---------------end--------------->8---

-- 
Ricardo

Message #13 received at 76079-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 76079-done <at> debbugs.gnu.org
Subject: Re: imp <at> 2.15.0 fails to build
Date: Thu, 06 Feb 2025 12:32:29 +0100

I pushed my changes to the master branch, because imp built fine with them.

-- 
Ricardo

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