Subject: bug#76079: [email-masked] fails to build

From: Ricardo Wurmus <[email-masked]>
Date: Thu, 06 Feb 2025 11:36:12 +0100

Here's what I tried:

>From 475248bfaafcb122676460383705f72ccb050adb Mon Sep 17 00:00:00 2001
Message-ID: <[email-masked]>
From: Ricardo Wurmus <[email-masked]>
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

>From 7786b4e477b888cda42cffd764aacea705631dc1 Mon Sep 17 00:00:00 2001
Message-ID: <[email-masked]>
In-Reply-To: <[email-masked]>
References: <[email-masked]>
From: Ricardo Wurmus <[email-masked]>
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

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