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new 99fb22110e gnu: openbabel: Fix build and switch to git source.
99fb22110e is described below
commit 99fb22110e9c7c0458d8fe992c75384112e21e07
Author: David Elsing <[email protected]>
AuthorDate: Thu Jul 31 22:27:45 2025 +0200
gnu: openbabel: Fix build and switch to git source.
The git source does not contain the bundled libraries.
* gnu/packages/chemistry.scm (openbabel)[source]: Switch to git-fetch.
[arguments]<#:configure-flags>: Use search-input-file and
search-input-directory.
<#:phases>: Add phase 'fix-time-check.
[inputs]: Add rapidjson.
[home-page]: Update URL.
Signed-off-by: Andreas Enge <[email protected]>
---
gnu/packages/chemistry.scm | 59 ++++++++++++++++++++++++++++------------------
1 file changed, 36 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 9e9f3bf660..d99b817244 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -578,34 +578,47 @@ usual algorithms you expect from a modern molecular
dynamics implementation.")
(package
(name "openbabel")
(version "3.1.1")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/openbabel/openbabel/";
- "releases/download/openbabel-"
- (string-replace-substring version "." "-")
- "/openbabel-" version "-source.tar.bz2"))
- (sha256
- (base32
- "0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openbabel/openbabel";)
+ (commit (string-append
+ "openbabel-"
+ (string-replace-substring version "." "-")))))
+ (sha256
+ (base32 "1ijl4px8nw9824znrsw9nsv4qf9xy0zgd8wrw8hhl15jy1sn02n1"))
+ (file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
- `(;; FIXME: Disable tests on i686 to work around
- ;; https://github.com/openbabel/openbabel/issues/2041.
- #:tests? ,(or (%current-target-system)
- (not (string=? "i686-linux" (%current-system))))
- #:configure-flags
- (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
- (string-append "-DINCHI_LIBRARY="
- (assoc-ref %build-inputs "inchi")
- "/lib/inchi/libinchi.so.1")
- (string-append "-DINCHI_INCLUDE_DIR="
- (assoc-ref %build-inputs "inchi")
"/include/inchi"))
- #:test-target "test"))
+ (list
+ ;; FIXME: Disable tests on i686 to work around
+ ;; https://github.com/openbabel/openbabel/issues/2041.
+ #:tests? (or (%current-target-system)
+ (not (string=? "i686-linux" (%current-system))))
+ #:configure-flags
+ '(list
+ "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
+ (string-append
+ "-DINCHI_LIBRARY="
+ (search-input-file %build-inputs "/lib/inchi/libinchi.so.1"))
+ (string-append "-DINCHI_INCLUDE_DIR="
+ (search-input-directory %build-inputs
"/include/inchi")))
+ #:test-target "test"
+ #:phases
+ '(modify-phases %standard-phases
+ ;; Fixed upstream:
+ ;;
https://github.com/openbabel/openbabel/commit/c0570bfeb2d7e0a6a6de1f257cf28e7f3cac8739
+ (add-after 'unpack 'fix-time-check
+ (lambda _
+ (substitute* "src/config.h.cmake"
+ (("(#ifdef HAVE_(SYS_)?TIME)(.*)$" _ old _ suffix)
+ (string-append old "_H" suffix))))))))
(native-inputs
(list pkg-config))
(inputs
- (list eigen inchi libxml2 zlib))
- (home-page "http://openbabel.org/wiki/Main_Page";)
+ (list eigen inchi libxml2 rapidjson zlib))
+ (home-page "https://openbabel.org/";)
(synopsis "Chemistry data manipulation toolbox")
(description
"Open Babel is a chemical toolbox designed to speak the many languages of
