* [bug#68790] [PATCH 0/9] Update rdkit and its dependencies
@ 2024-01-28 22:59 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6 David Elsing
` (9 more replies)
0 siblings, 10 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 22:59 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
This patch series updates rdkit and some of its dependencies.
I incorporated the patch from [1], which was addressed upstream, but is
not in a new release yet.
It seems like RDKit is only tested on 64 bit systems upstream and
several tests fail on i686 (including one due to a known bug in
Boost.Python [2]), therefore I set supported-systems to
%64bit-supported-systems.
Avalon Toolkit moved to a new repository [3], which was forked for RDKit
[4]. As the changes in the fork are small and only fixes, I put them in
a patch and use [3] as upstream.
[1] https://issues.guix.gnu.org/64559
[2] https://github.com/boostorg/python/issues/312
[3] https://github.com/rohdebe1/ava-formake
[4] https://github.com/rdkit/ava-formake
David Elsing (9):
gnu: tinydir: Update to 1.2.6.
gnu: fast-float: Update to 6.0.0.
gnu: gemmi: Update to 0.6.4.
gnu: maeparser: Update to 1.3.1.
gnu: coordgenlibs: Update to 3.0.2.
gnu: yaehmop: Update to 2023.03.1.
gnu: avalon-toolkit: Update to 2.0.5a.
gnu: freesasa: Fix memerr tests.
gnu: rdkit: Update to 2023.09.4.
gnu/local.mk | 2 +
gnu/packages/c.scm | 6 +-
gnu/packages/chemistry.scm | 175 +++++++--------
gnu/packages/cpp.scm | 10 +-
.../patches/avalon-toolkit-rdkit-fixes.patch | 110 +++++++++
...rdkit-unbundle-external-dependencies.patch | 208 ++++++++++--------
.../patches/tinydir-fix-cbehave-test.patch | 16 +-
7 files changed, 330 insertions(+), 197 deletions(-)
create mode 100644 gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch
--
2.41.0
^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
@ 2024-01-28 23:01 ` David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 2/9] gnu: fast-float: Update to 6.0.0 David Elsing
` (8 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:01 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/c.scm (tinydir): Update to 1.2.6.
* gnu/packages/patches/tinydir-fix-cbehave-test.patch: Adjust patch.
---
gnu/packages/c.scm | 6 +++---
.../patches/tinydir-fix-cbehave-test.patch | 16 ++++++++++++++--
2 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index 1346605c71..b558145ea0 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -20,7 +20,7 @@
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
-;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2023, 2024 David Elsing <david.elsing@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1349,7 +1349,7 @@ (define target-machine #$(and=> (%current-target-system)
(define-public tinydir
(package
(name "tinydir")
- (version "1.2.5")
+ (version "1.2.6")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1358,7 +1358,7 @@ (define-public tinydir
(file-name (git-file-name name version))
(sha256
(base32
- "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
+ "143n6yabznxk032gv5g2k8glf0kzicarg9cx0714zsbfmzj8lr07"))
(patches (search-patches "tinydir-fix-cbehave-test.patch"))
(modules '((guix build utils)))
(snippet '(delete-file-recursively "tests/cbehave"))))
diff --git a/gnu/packages/patches/tinydir-fix-cbehave-test.patch b/gnu/packages/patches/tinydir-fix-cbehave-test.patch
index 84ecee12c2..1cad42c7a0 100644
--- a/gnu/packages/patches/tinydir-fix-cbehave-test.patch
+++ b/gnu/packages/patches/tinydir-fix-cbehave-test.patch
@@ -2,10 +2,22 @@ Make test work with upstream cbehave
(tinydir bundles a modified version)
diff --git a/tests/file_open_test.c b/tests/file_open_test.c
-index 3e659bc..9f6f88d 100644
+index 09b856e..92b13ca 100644
--- a/tests/file_open_test.c
+++ b/tests/file_open_test.c
-@@ -19,4 +19,7 @@ FEATURE(file_open, "File open")
+@@ -4,6 +4,11 @@
+ #include "cbehave.h"
+ #include "util.h"
+
++#define ASSERT(cond, ret) \
++if (!(cond)) {\
++ cbehave_feature_return(__FILE__, __LINE__, ret, _state); \
++ goto _feature_over; \
++}\
+
+ FEATURE(file_open, "File open")
+ SCENARIO("Open file in current directory")
+@@ -34,4 +39,7 @@ FEATURE(file_open, "File open")
SCENARIO_END
FEATURE_END
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 2/9] gnu: fast-float: Update to 6.0.0.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6 David Elsing
@ 2024-01-28 23:01 ` David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4 David Elsing
` (7 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:01 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/cpp.scm (fast-float): Update to 6.0.0.
[arguments]: Adjust path to test files.
---
gnu/packages/cpp.scm | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 44175231af..71c170a48b 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -29,7 +29,7 @@
;;; Copyright © 2022 muradm <mail@muradm.net>
;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com>
;;; Copyright © 2022, 2023, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
@@ -2449,7 +2449,7 @@ (define fast-float-test-files
(define-public fast-float
(package
(name "fast-float")
- (version "3.5.1")
+ (version "6.0.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2458,7 +2458,7 @@ (define-public fast-float
(file-name (git-file-name name version))
(sha256
(base32
- "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
+ "1xf4gbllha760cr0ri53zsja46dypj45lj070ijb5f78xavfd8f8"))))
(build-system cmake-build-system)
(arguments
(list
@@ -2474,9 +2474,7 @@ (define-public fast-float
(("if\\(NOT supplemental_test_files_POPULATED.*")
(string-append
"set(supplemental_test_files_BINARY_DIR "
- (search-input-directory (or native-inputs inputs)
- "data")
- ")\nif(0)\n"))))))))
+ #$fast-float-test-files ")\nif(0)\n"))))))))
(native-inputs (list doctest fast-float-test-files))
(home-page "https://github.com/fastfloat/fast_float")
(synopsis "Floating point number parser for C++")
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 2/9] gnu: fast-float: Update to 6.0.0 David Elsing
@ 2024-01-28 23:01 ` David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 4/9] gnu: maeparser: Update to 1.3.1 David Elsing
` (6 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:01 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/chemistry.scm (gemmi): Update to 0.6.4.
[arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp.
(freesasa)[arguments]: Link to gemmi_cpp explicitly.
---
gnu/packages/chemistry.scm | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index df96a2f5c1..5129470e1e 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -589,7 +589,7 @@ (define-public python-pymol
(define-public gemmi
(package
(name "gemmi")
- (version "0.5.7")
+ (version "0.6.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -598,7 +598,7 @@ (define-public gemmi
(file-name (git-file-name name version))
(sha256
(base32
- "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
+ "0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y"))
(patches
(search-patches "gemmi-fix-sajson-types.patch"
"gemmi-fix-pegtl-usage.patch"))
@@ -625,7 +625,7 @@ (define-public gemmi
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-includes
(lambda _
- (substitute* (list "include/gemmi/sprintf.hpp"
+ (substitute* (list "src/sprintf.cpp"
"include/gemmi/dirwalk.hpp"
"include/gemmi/cif.hpp"
"include/gemmi/json.hpp"
@@ -722,7 +722,7 @@ (define-public freesasa
(("libfreesasa\\.a") "libfreesasa.la")
(("freesasa_LDADD \\+= libfreesasa\\.la" prev)
(string-append prev "\nlibfreesasa_la_LIBADD"
- " = -ljson-c ${libxml2_LIBS}\n"))
+ " = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n"))
(("_a_SOURCES") "_la_SOURCES"))
(substitute* "configure.ac"
(("AC_PROG_INSTALL" inst)
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 4/9] gnu: maeparser: Update to 1.3.1.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (2 preceding siblings ...)
2024-01-28 23:01 ` [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4 David Elsing
@ 2024-01-28 23:01 ` David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 5/9] gnu: coordgenlibs: Update to 3.0.2 David Elsing
` (5 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:01 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/chemistry.scm (maeparser): Update to 1.3.1.
---
gnu/packages/chemistry.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 5129470e1e..9086d659cc 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -765,7 +765,7 @@ (define-public freesasa
(define-public maeparser
(package
(name "maeparser")
- (version "1.3.0")
+ (version "1.3.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -774,7 +774,7 @@ (define-public maeparser
(file-name (git-file-name name version))
(sha256
(base32
- "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
+ "0mr5glg4br04ql5grby8yqni9fqq1l1cc75wyc159a1b9lwr7q7r"))))
(build-system cmake-build-system)
(inputs (list boost zlib))
(home-page "https://github.com/schrodinger/maeparser")
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 5/9] gnu: coordgenlibs: Update to 3.0.2.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (3 preceding siblings ...)
2024-01-28 23:01 ` [bug#68790] [PATCH 4/9] gnu: maeparser: Update to 1.3.1 David Elsing
@ 2024-01-28 23:01 ` David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 6/9] gnu: yaehmop: Update to 2023.03.1 David Elsing
` (4 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:01 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2.
---
gnu/packages/chemistry.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 9086d659cc..44833d9c3f 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -6,7 +6,7 @@
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -785,7 +785,7 @@ (define-public maeparser
(define-public coordgenlibs
(package
(name "coordgenlibs")
- (version "3.0.1")
+ (version "3.0.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -794,7 +794,7 @@ (define-public coordgenlibs
(file-name (git-file-name name version))
(sha256
(base32
- "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
+ "1wjaxwaihjy9xm5ys23f5abl50zcar1h9pww5ajdkgygsqy0bavi"))))
(build-system cmake-build-system)
(arguments
(list
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 6/9] gnu: yaehmop: Update to 2023.03.1.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (4 preceding siblings ...)
2024-01-28 23:01 ` [bug#68790] [PATCH 5/9] gnu: coordgenlibs: Update to 3.0.2 David Elsing
@ 2024-01-28 23:01 ` David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 7/9] gnu: avalon-toolkit: Update to 2.0.5a David Elsing
` (3 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:01 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1.
---
gnu/packages/chemistry.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 44833d9c3f..4a9dd97c5b 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -812,7 +812,7 @@ (define-public coordgenlibs
(define-public yaehmop
(package
(name "yaehmop")
- (version "2022.09.1")
+ (version "2023.03.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -821,7 +821,7 @@ (define-public yaehmop
(file-name (git-file-name name version))
(sha256
(base32
- "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
+ "18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb"))
(modules '((guix build utils)))
(snippet
'(begin
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 7/9] gnu: avalon-toolkit: Update to 2.0.5a.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (5 preceding siblings ...)
2024-01-28 23:01 ` [bug#68790] [PATCH 6/9] gnu: yaehmop: Update to 2023.03.1 David Elsing
@ 2024-01-28 23:02 ` David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests David Elsing
` (2 subsequent siblings)
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:02 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
The bug freeing static memory and the makefile have been improved upstream, so
we don't have to work around them anymore. Now, two static libraries are built
instead.
* gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a.
[source]: Switch to git reference from GitHub. Adjust snippet. Add patch from
the RDKit fork.
[arguments]: Remove 'dont-free-static-memory phase. Use provided
makefile. Adjust 'install phase.
* gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
gnu/local.mk | 2 +
gnu/packages/chemistry.scm | 131 ++++++++----------
.../patches/avalon-toolkit-rdkit-fixes.patch | 110 +++++++++++++++
3 files changed, 166 insertions(+), 77 deletions(-)
create mode 100644 gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index ab63bd5881..b5d61eb4dd 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -63,6 +63,7 @@
# Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
# Copyright © 2023 Herman Rimm <herman@rimm.ee>
# Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
+# Copyright © 2024 David Elsing <david.elsing@posteo.net>
#
# This file is part of GNU Guix.
#
@@ -952,6 +953,7 @@ dist_patch_DATA = \
%D%/packages/patches/audiofile-function-signature.patch \
%D%/packages/patches/automake-skip-amhello-tests.patch \
%D%/packages/patches/avahi-localstatedir.patch \
+ %D%/packages/patches/avalon-toolkit-rdkit-fixes.patch \
%D%/packages/patches/avidemux-install-to-lib.patch \
%D%/packages/patches/awesome-reproducible-png.patch \
%D%/packages/patches/awesome-4.3-fno-common.patch \
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 4a9dd97c5b..5e19bdf182 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -917,90 +917,67 @@ (define-public yaehmop
(define-public avalon-toolkit
(package
(name "avalon-toolkit")
- (version "1.2.0")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "mirror://sourceforge/avalontoolkit/"
- "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
- version ".source.tar"))
- (sha256
- (base32
- "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
- (modules '((guix build utils) (ice-9 ftw)))
- (snippet
- #~(begin
- (delete-file-recursively "../SourceDistribution/java")))))
+ (version "2.0.5a")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rohdebe1/ava-formake")
+ (commit (string-append "AvalonToolkit_" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1mfg40y5xc17sm59zdfc5sk22n9zm5zk0z1aw47chvl6hp465szk"))
+ (patches
+ (search-patches "avalon-toolkit-rdkit-fixes.patch"))
+ (modules '((guix build utils) (ice-9 ftw)))
+ (snippet
+ #~(begin
+ (delete-file-recursively "src/main/java")
+ (delete-file-recursively "src/test/target")))))
(build-system gnu-build-system)
(arguments
(list
- ;; There are no intended tests
+ ;; There is only one test, which is missing a file
#:tests? #f
#:phases
- #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk")))
- (modify-phases %standard-phases
- (add-after 'unpack 'chdir
- (lambda _ (chdir "common")))
- (delete 'configure)
- (add-before 'build 'dont-free-static-memory
- (lambda _
- (substitute* "reaccsio.c"
- (("MyFree\\(.*tempdir\\)" m)
- (string-append "/* freeing memory from getenv is bad */"
- "// " m)))))
- ;; The makefile has incorrect compiler flags and is missing some
- ;; object files, so we build it ourselves.
- (replace 'build
- (lambda _
- (for-each
- (lambda (part)
- (format #t "Compiling ~a.c ~~> ~a.o~%" part part)
- (invoke #$(cc-for-target) "-c" "-fPIC" "-O2"
- (string-append part ".c")
- "-o" (string-append part ".o")))
- (list "aacheck" "casutils" "denormal" "depictutil"
- "didepict" "fixcharges" "forio" "geometry"
- "graph" "hashcode" "layout" "local" "pattern"
- "perceive" "reaccsio" "rtutils" "set" "shortcut"
- "sketch" "ssmatch" "stereo" "symbol_lists"
- "symboltable" "utilities"))
- (display "Building libavalontoolkit.so\n")
- (apply invoke "gcc" "-fPIC" "-shared" "-lm"
- "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c"
- "struchk.c" "patclean.c" (find-files "." "\\.o$"))
- ;; patclean is not built here as there is an undeclared
- ;; variable in main().
- (for-each
- (lambda (program)
- (display (string-append "Building " program "\n"))
- (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
- (string-append "-Wl,-rpath=" #$output "/lib")
- "-DMAIN" (string-append program ".c") "-o" program))
- programs)))
- (replace 'install
- (lambda _
- ;; Executables
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key parallel-build? #:allow-other-keys)
+ (mkdir "build")
+ (mkdir-p "target/executables")
+ (mkdir-p "target/libraries")
+ (invoke "make" "programs" "-j"
+ (if parallel-build?
+ (number->string (parallel-job-count))
+ "1"))))
+ (replace 'install
+ (lambda _
+ ;; Executables
+ (let ((programs '("canonizer" "matchtest" "smi2mol" "struchk")))
(for-each
(lambda (program)
- (install-file program (string-append #$output "/bin")))
- programs)
- (for-each
- (lambda (name)
- (symlink (string-append #$output "/bin/smi2mol")
- (string-append #$output "/bin/" name)))
- '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
- ;; Library
- (install-file "libavalontoolkit.so"
- (string-append #$output "/lib"))
- (for-each
- (lambda (file)
- (install-file file (string-append #$output
- "/include/avalontoolkit")))
- (find-files "." "\\.h$"))
- (install-file "../license.txt"
- (string-append #$output "/share/doc/"
- #$name "-" #$version "/"))))))))
+ (install-file (string-append "target/executables/" program)
+ (string-append #$output "/bin")))
+ programs))
+ (for-each
+ (lambda (name)
+ (symlink (string-append #$output "/bin/smi2mol")
+ (string-append #$output "/bin/" name)))
+ '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
+ ;; Library
+ (install-file "target/libraries/libavalon_tools.a"
+ (string-append #$output "/lib"))
+ (install-file "target/libraries/libavalon4rdkit.a"
+ (string-append #$output "/lib"))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append #$output
+ "/include/avalontoolkit")))
+ (find-files "src/main/C/include" "\\.h$"))
+ (install-file "license.txt"
+ (string-append #$output "/share/doc/"
+ #$name "-" #$version "/")))))))
(home-page "https://sourceforge.net/projects/avalontoolkit/")
(synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
(description "This package contains a library and programs for
diff --git a/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch
new file mode 100644
index 0000000000..c93a9869ed
--- /dev/null
+++ b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch
@@ -0,0 +1,110 @@
+Patches taken from the rdkit fork at this commit (there version
+AvalonToolkit_2.0.6-pre.2):
+https://github.com/rdkit/ava-formake/commit/d05bee0382b8f4696b2b4b05b0038fb7d559520a
+
+diff -ur a/src/main/C/common/reaccsio.c b/src/main/C/common/reaccsio.c
+--- a/src/main/C/common/reaccsio.c
++++ b/src/main/C/common/reaccsio.c
+@@ -322,34 +322,49 @@
+ fprintf(fp,"\n");
+ }
+
++#define MAX_BONDLINE_FIELDS 7
++#define BONDLINE_FIELD_LEN 3
++
+ int ReadREACCSBond(Fortran_FILE *fp, struct reaccs_bond_t *bp)
+ {
+- int nitems, i;
+- char buffer[MAX_BUFFER+1];
++ int nitems, i, j, k;
++ int bond_line_len, n_chars, pos;
++ int *ptrarray[MAX_BONDLINE_FIELDS];
++ char c;
++ char buffer[BONDLINE_FIELD_LEN+1];
+
+ if (fp->status != FORTRAN_NORMAL) return(fp->status);
+
+- strncpy(buffer,fp->buffer,MAX_BUFFER);
+- /* zero pad only atom numbers! */
+- for (i=0; i<6; i++) if (buffer[i] == ' ') buffer[i] = '0';
+-
+ bp->stereo_symbol = 0;
+ bp->dummy = 0;
+ bp->topography = 0;
+ bp->reaction_mark = NONE;
+- // make sure spaces are interpreted the Fortran-way
+- for (i=9; i<strlen(buffer) && i<21; i+=3)
+- {
+- if ((i+1)<strlen(buffer) && buffer[i+1]==' ') buffer[i+1] = '0';
+- if ((i+2)<strlen(buffer) && buffer[i+2]==' ') buffer[i+2] = '0';
++ ptrarray[0] = &bp->atoms[0];
++ ptrarray[1] = &bp->atoms[1];
++ ptrarray[2] = &bp->bond_type;
++ ptrarray[3] = &bp->stereo_symbol;
++ ptrarray[4] = &bp->dummy;
++ ptrarray[5] = &bp->topography;
++ ptrarray[6] = &bp->reaction_mark;
++ bond_line_len = strlen(fp->buffer);
++ nitems = bond_line_len ? (bond_line_len - 1) / BONDLINE_FIELD_LEN + 1 : 0;
++ if (nitems > MAX_BONDLINE_FIELDS)
++ nitems = MAX_BONDLINE_FIELDS;
++ for (i = 0; i < nitems; ++i)
++ {
++ pos = i * BONDLINE_FIELD_LEN;
++ memset(buffer, 0, BONDLINE_FIELD_LEN + 1);
++ n_chars = bond_line_len - pos;
++ if (n_chars > BONDLINE_FIELD_LEN)
++ n_chars = BONDLINE_FIELD_LEN;
++ for (j = 0, k = 0; j < n_chars; ++j)
++ {
++ c = fp->buffer[pos + j];
++ if (c != ' ')
++ buffer[k++] = c;
++ }
++ sscanf(buffer, "%3d", ptrarray[i]);
+ }
+- nitems = sscanf(buffer,
+- "%3d%3d%3d%3d%3d%3d%3d",
+- &bp->atoms[0], &bp->atoms[1],
+- &bp->bond_type, &bp->stereo_symbol,
+- &bp->dummy,
+- &bp->topography, &bp->reaction_mark);
+-
+ if (nitems >= 3)
+ {
+ GetBuffer(fp);
+@@ -1582,6 +1597,8 @@
+
+ PrintREACCSMolecule(fp, mp,"");
+
++ fputc('\0', fp);
++ fflush(fp);
+ rewind(fp);
+
+ MolStr = _ReadFile(fp);
+diff -ur a/src/main/C/programs/struchk.c b/src/main/C/programs/struchk.c
+--- a/src/main/C/programs/struchk.c
++++ b/src/main/C/programs/struchk.c
+@@ -1581,6 +1581,22 @@
+
+ if ((result & SIZE_CHECK_FAILED) == 0)
+ {
++ for (i = 0; i < mp->n_bonds; ++i) {
++ for (j = 0; j < 2; ++j) {
++ if (mp->bond_array[i].atoms[j] < 1 || mp->bond_array[i].atoms[j] > mp->n_atoms)
++ {
++ snprintf(msg_buffer, MAXMSG,
++ "%10s : illegal atom # (%d, max allowed is %d) in bond %d",
++ mp->name, mp->bond_array[i].atoms[j], mp->n_atoms, i + 1);
++ AddMsgToList(msg_buffer);
++ result |= SIZE_CHECK_FAILED;
++ }
++ }
++ }
++ }
++
++ if ((result & SIZE_CHECK_FAILED) == 0)
++ {
+ if (convert_atom_texts)
+ {
+ tmp = ConvertAtomAliases(mp);
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (6 preceding siblings ...)
2024-01-28 23:02 ` [bug#68790] [PATCH 7/9] gnu: avalon-toolkit: Update to 2.0.5a David Elsing
@ 2024-01-28 23:02 ` David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4 David Elsing
2024-02-13 12:18 ` [bug#68790] [PATCH 0/9] Update rdkit and its dependencies Christopher Baines
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:02 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add
"CFLAGS=-fno-builtin-malloc" to #:configure-flags.
---
gnu/packages/chemistry.scm | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 5e19bdf182..98141737ac 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -708,7 +708,12 @@ (define-public freesasa
#~(list "--enable-check"
"--enable-parser-generator"
"CXXFLAGS=-std=c++17"
- "--enable-doxygen")
+ "--enable-doxygen"
+ ;; Some tests rely on replacing malloc with a wrapper which
+ ;; fails in a controlled way, but this does not work if the call
+ ;; is replaced. This was fixed upstream, remove once there is a
+ ;; new release.
+ "CFLAGS=-fno-builtin-malloc")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'remove-libc++-linking
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4.
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (7 preceding siblings ...)
2024-01-28 23:02 ` [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests David Elsing
@ 2024-01-28 23:02 ` David Elsing
2024-02-13 12:18 ` [bug#68790] [PATCH 0/9] Update rdkit and its dependencies Christopher Baines
9 siblings, 0 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 23:02 UTC (permalink / raw)
To: 68790; +Cc: David Elsing
* gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4.
[arguments]: Skip testConrec test in check phase.
[native-inputs]: Replace catch2 with catch2-3.
* gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust
patch.
[supported-systems]: New field.
---
gnu/packages/chemistry.scm | 15 +-
...rdkit-unbundle-external-dependencies.patch | 208 ++++++++++--------
2 files changed, 126 insertions(+), 97 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 98141737ac..bd27bfad7a 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1073,7 +1073,7 @@ (define-public ringdecomposerlib
(define-public rdkit
(package
(name "rdkit")
- (version "2022.03.5")
+ (version "2023.09.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1084,7 +1084,7 @@ (define-public rdkit
(file-name (git-file-name name version))
(sha256
(base32
- "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
+ "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8"))
(patches
(search-patches "rdkit-unbundle-external-dependencies.patch"))
(modules '((guix build utils)))
@@ -1183,7 +1183,10 @@ (define-public rdkit
"substructLibraryTest" "pyFeatures"
"pythonTestDirML" "pythonTestDirChem"
;; Catching Python exception fails
- "pyRanker") "|")
+ "pyRanker"
+ ;; Flaky test depending on floating point rounding
+ "testConrec"
+ ) "|")
")")))))))))
(inputs
(list avalon-toolkit
@@ -1200,7 +1203,7 @@ (define-public rdkit
(native-inputs
(list bison
boost
- catch2
+ catch2-3
eigen
flex
freesasa
@@ -1214,4 +1217,8 @@ (define-public rdkit
(description "RDKit is a C++ and Python library for cheminformatics, which
includes (among other things) the analysis and modification of molecules in 2D
and 3D and descriptor generation for machine learning.")
+ ;; For 32 bit systems, there is a bug in Boost.Python:
+ ;; https://github.com/boostorg/python/issues/312. Additionally, several
+ ;; other test fail.
+ (supported-systems %64bit-supported-systems)
(license license:bsd-3)))
diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
index 8ee0611d3b..e22ff57ee0 100644
--- a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
+++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
@@ -58,99 +58,82 @@ diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLis
index 3e31195fc..314ba35b5 100644
--- a/External/AvalonTools/CMakeLists.txt
+++ b/External/AvalonTools/CMakeLists.txt
-@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
+@@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
return()
endif(NOT RDK_BUILD_AVALON_SUPPORT)
+-set(AVALON_VERSION "2.0.5-pre.3")
-if(NOT DEFINED AVALONTOOLS_DIR)
-- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution")
-- set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c")
+- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}")
+- set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c")
- set(needDownload "TRUE")
-- if(EXISTS "${fileToPatch}")
-- file(READ "${fileToPatch}" buffer)
-- if("${buffer}" MATCHES "//MyFree\\(\\(char \\*\\)tempdir\\);")
-- set(needDownload "FALSE")
-- endif()
+- if(EXISTS "${fileToCheck}")
+- set(needDownload "FALSE")
- endif()
-else()
- string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
- set(needDownload "FALSE")
-endif()
-
--set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common)
+-set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C")
+-set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common")
+-set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include")
+-set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs")
-
-if(needDownload)
- if(NOT DEFINED AVALONTOOLS_URL)
-- set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar")
+- set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz")
- endif()
- if(NOT DEFINED AVALONTOOLS_MD5SUM)
-- set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54")
+- set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351")
- endif()
- if(NOT DEFINED AVALONTOOLS_BASE)
- string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}")
- endif()
- downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM})
-- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf
-- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_1.2.0.source.tar
+- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf
+- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-- # apply patch to AvalonTools
-- configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
-- file(READ "${fileToPatch}" buffer)
-- string(REGEX REPLACE "MyFree\\(\\(char \\*\\)tempdir\\);"
-- "//MyFree((char *)tempdir);" buffer "${buffer}")
-- file(WRITE "${fileToPatch}" "${buffer}")
--endif()
-
- if (MSVC)
- add_definitions("/D_CRT_SECURE_NO_WARNINGS")
- add_compile_options(/wd4224 /wd4101 /wd4018 /wd4996 /wd4244 /wd4305 /wd4013 /wd4146 /wd4334 /wd4715 /wd4715 /nologo)
- endif(MSVC)
-
--set(avalon_clib_srcs ${AVALON_SRC_PATH}/layout.c
-- ${AVALON_SRC_PATH}/symboltable.c
-- ${AVALON_SRC_PATH}/patclean.c
-- ${AVALON_SRC_PATH}/utilities.c
-- ${AVALON_SRC_PATH}/symbol_lists.c
-- ${AVALON_SRC_PATH}/stereo.c
-- ${AVALON_SRC_PATH}/set.c
-- ${AVALON_SRC_PATH}/perceive.c
-- ${AVALON_SRC_PATH}/local.c
-- ${AVALON_SRC_PATH}/graph.c
-- ${AVALON_SRC_PATH}/geometry.c
-- ${AVALON_SRC_PATH}/forio.c
-- ${AVALON_SRC_PATH}/depictutil.c
-- ${AVALON_SRC_PATH}/denormal.c
-- ${AVALON_SRC_PATH}/casutils.c
-- ${AVALON_SRC_PATH}/ssmatch.c
-- ${AVALON_SRC_PATH}/rtutils.c
-- ${AVALON_SRC_PATH}/smi2mol.c
-- ${AVALON_SRC_PATH}/didepict.c
-- ${AVALON_SRC_PATH}/pattern.c
-- ${AVALON_SRC_PATH}/canonizer.c
-- ${AVALON_SRC_PATH}/aacheck.c
-- ${AVALON_SRC_PATH}/fixcharges.c
-- ${AVALON_SRC_PATH}/struchk.c
-- ${AVALON_SRC_PATH}/reaccsio.c
-- ${AVALON_SRC_PATH}/hashcode.c
-- )
--
--# we need this to ensure that builds continue
--# to work on linux systems with older versions
--# of glibc when we're building with gcc-4.1.
--# Without this flag, we'll endup requiring
--# glibc 2.7.
--if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
-- add_definitions(-D_GNU_SOURCE=1)
-endif()
-
--if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
-- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format")
+-if(CMAKE_C_COMPILER_ID STREQUAL "GNU")
+- add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result )
-endif()
--if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-result -Wformat-overflow=0 -Wformat=0 -Wno-format-security -Wno-implicit-function-declaration")
+-if(CMAKE_C_COMPILER_ID STREQUAL "Clang")
+- add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare)
-endif()
+-if (MSVC)
+- add_definitions("/D_CRT_SECURE_NO_WARNINGS")
+- add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo)
+-endif(MSVC)
-
--
+-set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c
+- ${AVALON_COMMON_PATH}/symboltable.c
+- ${AVALON_COMMON_PATH}/patclean.c
+- ${AVALON_COMMON_PATH}/utilities.c
+- ${AVALON_COMMON_PATH}/symbol_lists.c
+- ${AVALON_COMMON_PATH}/stereo.c
+- ${AVALON_COMMON_PATH}/set.c
+- ${AVALON_COMMON_PATH}/perceive.c
+- ${AVALON_COMMON_PATH}/local.c
+- ${AVALON_COMMON_PATH}/graph.c
+- ${AVALON_COMMON_PATH}/geometry.c
+- ${AVALON_COMMON_PATH}/forio.c
+- ${AVALON_COMMON_PATH}/depictutil.c
+- ${AVALON_COMMON_PATH}/denormal.c
+- ${AVALON_COMMON_PATH}/casutils.c
+- ${AVALON_COMMON_PATH}/ssmatch.c
+- ${AVALON_COMMON_PATH}/rtutils.c
+- ${AVALON_COMMON_PATH}/smi2mol.c
+- ${AVALON_COMMON_PATH}/didepict.c
+- ${AVALON_COMMON_PATH}/pattern.c
+- ${AVALON_COMMON_PATH}/canonizer.c
+- ${AVALON_COMMON_PATH}/aacheck.c
+- ${AVALON_COMMON_PATH}/fixcharges.c
+- ${AVALON_PROGRAMS_PATH}/struchk.c
+- ${AVALON_COMMON_PATH}/reaccsio.c
+- ${AVALON_COMMON_PATH}/hashcode.c
+- )
-
-rdkit_library(avalon_clib ${avalon_clib_srcs})
-target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
@@ -159,11 +142,11 @@ index 3e31195fc..314ba35b5 100644
-endif()
-
-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
--include_directories(${AVALON_SRC_PATH})
+-include_directories(${AVALON_INCLUDE_PATH})
-
rdkit_library(AvalonLib AvalonTools.cpp SHARED
- LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
-+ LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
++ LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD)
rdkit_headers(AvalonTools.h DEST GraphMol)
rdkit_test(testAvalonLib1 test1.cpp
@@ -278,7 +261,7 @@ diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeL
index 08dd1fe04..66ecd5834 100644
--- a/External/RingFamilies/CMakeLists.txt
+++ b/External/RingFamilies/CMakeLists.txt
-@@ -1,47 +1,6 @@
+@@ -1,47 +1,7 @@
-add_custom_target(ringdecomposerlib_support ALL)
-
if(NOT RDK_USE_URF)
@@ -324,10 +307,9 @@ index 08dd1fe04..66ecd5834 100644
-rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "")
-
-
--set(RDK_URF_LIBS RingDecomposerLib
-- CACHE STRING "the libraries for the URF calculation" FORCE)
+rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib)
-+set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "" FORCE)
+ set(RDK_URF_LIBS RingDecomposerLib
+ CACHE STRING "the libraries for the URF calculation" FORCE)
diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
new file mode 100644
index 000000000..e69de29bb
@@ -335,40 +317,60 @@ diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
index f1027b3bd..8bee2f910 100644
--- a/External/YAeHMOP/CMakeLists.txt
+++ b/External/YAeHMOP/CMakeLists.txt
-@@ -18,32 +18,8 @@ endif()
+@@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
- include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+ add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
--ExternalProject_Add(yaehmop_project
-- GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
-- GIT_TAG master
-- UPDATE_COMMAND ""
-- PATCH_COMMAND ""
-- PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
-- SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
-- SOURCE_SUBDIR "tightbind"
-- CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-- TEST_COMMAND "")
--
--include_directories(${PROJECT_BINARY_DIR}/include)
--link_directories(${PROJECT_BINARY_DIR}/lib)
--link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
+-if(NOT DEFINED YAEHMOP_DIR)
+- set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop")
+-endif()
+-
+-if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
+- set(RELEASE_NO "2023.03.1")
+- set(MD5 "e6450f13e02c54d024233b993c3c7ff6")
+- downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
+- "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
+- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+- ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz
+- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-
+- file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}")
+-else()
+- message("-- Found YAeHMOP source in ${YAEHMOP_DIR}")
+-endif()
+-
+-set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/..
+- CACHE STRING "yaehmop Include File" FORCE)
+-include_directories(${yaehmop_INCLUDE_DIRS})
+-
+-if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN)
+- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+-endif()
+-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+-endif()
+-
+-# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency)
+-add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True)
+-
+-# set install dir for the yaehmop library:
+-INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets
+- DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
+- COMPONENT runtime )
+-
+-
+-
-
-set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
-install(FILES ${EHT_PARAM_FILE}
- DESTINATION ${RDKit_ShareDir}/Data
- COMPONENT data)
-
--message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
--message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
--
-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
+rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol )
target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
--add_dependencies(EHTLib yaehmop_project)
rdkit_headers(EHTTools.h DEST GraphMol)
rdkit_catch_test(testEHTLib1 test1.cpp
- LINK_LIBRARIES EHTLib FileParsers SmilesParse )
diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp
index 7a229f51f..71033dc5c 100644
--- a/External/YAeHMOP/EHTTools.cpp
@@ -382,3 +384,23 @@ index 7a229f51f..71033dc5c 100644
}
namespace RDKit {
+@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId,
+ }
+
+ } // end of namespace EHTTools
+-} // end of namespace RDKit
+\ No newline at end of file
++} // end of namespace RDKit
+diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt
+index 759a9f360..114d24532 100644
+--- a/External/YAeHMOP/Wrap/CMakeLists.txt
++++ b/External/YAeHMOP/Wrap/CMakeLists.txt
+@@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools
+ DEST Chem
+ LINK_LIBRARIES
+ EHTLib )
++
++target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP)
+
+ add_pytest(pyEHTTools
+ ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)
--
2.41.0
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#68790] [PATCH 0/9] Update rdkit and its dependencies
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
` (8 preceding siblings ...)
2024-01-28 23:02 ` [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4 David Elsing
@ 2024-02-13 12:18 ` Christopher Baines
9 siblings, 0 replies; 11+ messages in thread
From: Christopher Baines @ 2024-02-13 12:18 UTC (permalink / raw)
To: David Elsing; +Cc: 68790-done, 68790
[-- Attachment #1: Type: text/plain, Size: 1307 bytes --]
David Elsing <david.elsing@posteo.net> writes:
> This patch series updates rdkit and some of its dependencies.
>
> I incorporated the patch from [1], which was addressed upstream, but is
> not in a new release yet.
>
> It seems like RDKit is only tested on 64 bit systems upstream and
> several tests fail on i686 (including one due to a known bug in
> Boost.Python [2]), therefore I set supported-systems to
> %64bit-supported-systems.
>
> Avalon Toolkit moved to a new repository [3], which was forked for RDKit
> [4]. As the changes in the fork are small and only fixes, I put them in
> a patch and use [3] as upstream.
>
> [1] https://issues.guix.gnu.org/64559
> [2] https://github.com/boostorg/python/issues/312
> [3] https://github.com/rohdebe1/ava-formake
> [4] https://github.com/rdkit/ava-formake
>
> David Elsing (9):
> gnu: tinydir: Update to 1.2.6.
> gnu: fast-float: Update to 6.0.0.
> gnu: gemmi: Update to 0.6.4.
> gnu: maeparser: Update to 1.3.1.
> gnu: coordgenlibs: Update to 3.0.2.
> gnu: yaehmop: Update to 2023.03.1.
> gnu: avalon-toolkit: Update to 2.0.5a.
> gnu: freesasa: Fix memerr tests.
> gnu: rdkit: Update to 2023.09.4.
Thanks for the patches David, they look good to me so I've pushed them
all to master as e5bfc462dd695a570fe88c4c6d6efee808fd1a56.
Chris
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^ permalink raw reply [flat|nested] 11+ messages in thread
end of thread, other threads:[~2024-02-13 12:20 UTC | newest]
Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 2/9] gnu: fast-float: Update to 6.0.0 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 4/9] gnu: maeparser: Update to 1.3.1 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 5/9] gnu: coordgenlibs: Update to 3.0.2 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 6/9] gnu: yaehmop: Update to 2023.03.1 David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 7/9] gnu: avalon-toolkit: Update to 2.0.5a David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4 David Elsing
2024-02-13 12:18 ` [bug#68790] [PATCH 0/9] Update rdkit and its dependencies Christopher Baines
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