Merge branch 'master' into gnome-team

13 files changed, 402 insertions, 393 deletions

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);
diff --git a/gnu/packages/patches/coq-fix-envvars.patch b/gnu/packages/patches/coq-fix-envvars.patch
deleted file mode 100644
index 6c48224c64..0000000000
--- a/gnu/packages/patches/coq-fix-envvars.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-From 0e76cda958a4d3e4bcbb96e171c26b6b3478c6c2 Mon Sep 17 00:00:00 2001
-From: Julien Lepiller <julien@lepiller.eu>
-Date: Thu, 10 Feb 2022 16:44:10 +0100
-Subject: [PATCH] Fix environment variable usage.
-
----
- boot/env.ml | 26 +++++++++++++++++++-------
- 1 file changed, 19 insertions(+), 7 deletions(-)
-
-diff --git a/boot/env.ml b/boot/env.ml
-index e8521e7..d834a3a 100644
---- a/boot/env.ml
-+++ b/boot/env.ml
-@@ -32,17 +32,29 @@ let fail_msg =
- 
- let fail s = Format.eprintf "%s@\n%!" fail_msg; exit 1
- 
-+let path_to_list p =
-+  let sep = if String.equal Sys.os_type "Win32" then ';' else ':' in
-+    String.split_on_char sep p
-+
- (* This code needs to be refactored, for now it is just what used to be in envvars  *)
- let guess_coqlib () =
-   Util.getenv_else "COQLIB" (fun () ->
-   let prelude = "theories/Init/Prelude.vo" in
--  Util.check_file_else
--    ~dir:Coq_config.coqlibsuffix
--    ~file:prelude
--    (fun () ->
--      if Sys.file_exists (Filename.concat Coq_config.coqlib prelude)
--      then Coq_config.coqlib
--      else fail ()))
-+  let coqlibpath = Util.getenv_else "COQLIBPATH" (fun () -> Coq_config.coqlibsuffix) in
-+  let paths = path_to_list coqlibpath in
-+  let valid_paths =
-+    List.filter
-+      (fun dir -> (Util.check_file_else ~dir:dir ~file:prelude (fun () -> "")) <> "")
-+      paths in
-+  match valid_paths with
-+  | [] ->
-+    if Sys.file_exists (Filename.concat Coq_config.coqlib prelude)
-+    then Coq_config.coqlib
-+    else
-+      fail "cannot guess a path for Coq libraries; please use -coqlib option \
-+            or ensure you have installed the package containing Coq's stdlib (coq-stdlib in OPAM) \
-+            If you intend to use Coq without a standard library, the -boot -noinit options must be used."
-+  | p::_ -> p)
- 
- (* Build layout uses coqlib = coqcorelib *)
- let guess_coqcorelib lib =
--- 
-2.34.0
-
diff --git a/gnu/packages/patches/go-github-com-skip2-go-qrcode-fix-tests.patch b/gnu/packages/patches/go-github-com-skip2-go-qrcode-fix-tests.patch
new file mode 100644
index 0000000000..631cb0cdab
--- /dev/null
+++ b/gnu/packages/patches/go-github-com-skip2-go-qrcode-fix-tests.patch
@@ -0,0 +1,37 @@
+From dd203f29a36bf518deacbc03e8562b0195c8345f Mon Sep 17 00:00:00 2001
+From: Dominic Martinez <dom@dominicm.dev>
+Date: Mon, 4 Apr 2022 12:06:03 -0400
+Subject: [PATCH] Fix failing qr decode test
+
+First convert integers into runes before performing a string conversion.
+---
+ qrcode_decode_test.go | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/qrcode_decode_test.go b/qrcode_decode_test.go
+index 1f4b1d3..2b0756b 100644
+--- a/qrcode_decode_test.go
++++ b/qrcode_decode_test.go
+@@ -122,7 +122,7 @@ func TestDecodeAllCharacters(t *testing.T) {
+ 
+ 	// zbarimg has trouble with null bytes, hence start from ASCII 1.
+ 	for i := 1; i < 256; i++ {
+-		content += string(i)
++		content += string(rune(i))
+ 	}
+ 
+ 	q, err := New(content, Low)
+@@ -154,7 +154,7 @@ func TestDecodeFuzz(t *testing.T) {
+ 		for j := 0; j < len; j++ {
+ 			// zbarimg seems to have trouble with special characters, test printable
+ 			// characters only for now.
+-			content += string(32 + r.Intn(94))
++			content += string(rune(32 + r.Intn(94)))
+ 		}
+ 
+ 		for _, level := range []RecoveryLevel{Low, Medium, High, Highest} {
+
+base-commit: da1b6568686e89143e94f980a98bc2dbd5537f13
+-- 
+2.34.0
+
diff --git a/gnu/packages/patches/libgeotiff-fix-tests-on-i386.patch b/gnu/packages/patches/libgeotiff-fix-tests-on-i386.patch
new file mode 100644
index 0000000000..e84f726a3d
--- /dev/null
+++ b/gnu/packages/patches/libgeotiff-fix-tests-on-i386.patch
@@ -0,0 +1,35 @@
+From 9990160268fafb71751d4f3a9ad724df70cb9451 Mon Sep 17 00:00:00 2001
+From: Bas Couwenberg <sebastic@xs4all.nl>
+Date: Fri, 1 Dec 2023 10:35:46 +0100
+Subject: [PATCH] Fix test failure on i386.
+
+---
+https://github.com/OSGeo/libgeotiff/pull/107
+
+ test/testlistgeo | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/test/testlistgeo b/test/testlistgeo
+index 48e92eb..ceec2e6 100755
+--- a/test/testlistgeo
++++ b/test/testlistgeo
+@@ -218,6 +218,9 @@ echo "" >>${OUT}
+ sed "s/ETRS89-extended/ETRS89/g" < ${OUT} > ${OUT}.tmp
+ mv ${OUT}.tmp ${OUT}
+ 
++sed "s/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.02\"E)/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.03\"E)/" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++
+ sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.normalized
+ 
+ sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
+@@ -230,6 +233,9 @@ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
+ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ 
++sed "s/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.02\"E)/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.03\"E)/" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++
+ # do 'diff' with distribution results
+ # after cleaning for avoid spurios result due 
+ # to different build dir
diff --git a/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch
new file mode 100644
index 0000000000..5d381d78e2
--- /dev/null
+++ b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch
@@ -0,0 +1,51 @@
+From 3806fdab4a17f44641a2113faec778e756e2be3d Mon Sep 17 00:00:00 2001
+From: Even Rouault <even.rouault@spatialys.com>
+Date: Tue, 29 Aug 2023 19:04:25 +0200
+Subject: [PATCH] Fix 'make check' to pass with PROJ 9.3 (fixes #89)
+
+---
+https://github.com/OSGeo/libgeotiff/pull/90
+
+ test/testlistgeo | 16 +++++++++++++---
+ 1 file changed, 13 insertions(+), 3 deletions(-)
+
+diff --git a/test/testlistgeo b/test/testlistgeo
+index 9a41e74..48e92eb 100755
+--- a/test/testlistgeo
++++ b/test/testlistgeo
+@@ -218,14 +218,24 @@ echo "" >>${OUT}
+ sed "s/ETRS89-extended/ETRS89/g" < ${OUT} > ${OUT}.tmp
+ mv ${OUT}.tmp ${OUT}
+ 
+-sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.tmp
++sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.normalized
++
++sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++
++sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ 
+ # do 'diff' with distribution results
+ # after cleaning for avoid spurios result due 
+ # to different build dir
+ sed -e "s/Testing listgeo .*test/Testing listgeo ..\/test/"  -i ${OUT}
+ echo "diff ${OUT} with testlistgeo_out.dist"
+-diff -u ${OUT} testlistgeo_out.dist.tmp
++diff -u ${OUT} testlistgeo_out.dist.normalized
+ if [ $? -ne 0 ] ; then
+     echo  ""
+     echo "PROBLEMS HAVE OCCURRED"
+@@ -236,7 +246,7 @@ else
+     echo "TEST OK"
+     echo "test file ${OUT} removed"
+     echo
+-    rm testlistgeo_out.dist.tmp
++    rm testlistgeo_out.dist.normalized
+     /bin/rm -f ${OUT}
+     exit 0
+ fi
diff --git a/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.1.patch b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.1.patch
new file mode 100644
index 0000000000..e9a28d1fcd
--- /dev/null
+++ b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.1.patch
@@ -0,0 +1,40 @@
+From 4f90e57fa1cac7afdd57e5f649775cb24aa15612 Mon Sep 17 00:00:00 2001
+From: Bas Couwenberg <sebastic@xs4all.nl>
+Date: Fri, 1 Dec 2023 08:23:20 +0100
+Subject: [PATCH] Fix test failure with PROJ 9.3.1.
+
+Closes: #104
+---
+https://github.com/OSGeo/libgeotiff/pull/105
+
+ test/testlistgeo | 10 ++++++++++
+ 1 file changed, 10 insertions(+)
+
+diff --git a/test/testlistgeo b/test/testlistgeo
+index 48e92eb..4331cc3 100755
+--- a/test/testlistgeo
++++ b/test/testlistgeo
+@@ -218,6 +218,11 @@ echo "" >>${OUT}
+ sed "s/ETRS89-extended/ETRS89/g" < ${OUT} > ${OUT}.tmp
+ mv ${OUT}.tmp ${OUT}
+ 
++sed "s/Projection = 15914 (BLM zone 14N (US survey .*))/Projection = 15914 (BLM zone 14N)/g" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++sed "s/Projection = 6753 (Oregon Columbia River West zone (.*))/Projection = 6753 (Oregon Columbia River West zone)/" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++
+ sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.normalized
+ 
+ sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
+@@ -230,6 +235,11 @@ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
+ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ 
++sed "s/Projection = 15914 (BLM zone 14N (US survey .*))/Projection = 15914 (BLM zone 14N)/" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++sed "s/Projection = 6753 (Oregon Columbia River West zone (.*))/Projection = 6753 (Oregon Columbia River West zone)/" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++
+ # do 'diff' with distribution results
+ # after cleaning for avoid spurios result due 
+ # to different build dir
diff --git a/gnu/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch b/gnu/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch
deleted file mode 100644
index 2c344af821..0000000000
--- a/gnu/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-From aeca7656f499d7f4595319858f242276920e31bb Mon Sep 17 00:00:00 2001
-From: Louis Gesbert <louis.gesbert@ocamlpro.com>
-Date: Sat, 2 Dec 2017 12:51:01 +0100
-Subject: [PATCH] Fix for ocaml 4.06
-
----
- common/criteria_lexer.mll | 8 ++++----
- common/util.ml            | 2 +-
- 2 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/common/criteria_lexer.mll b/common/criteria_lexer.mll
-index 71f9178..fc4eae3 100644
---- a/common/criteria_lexer.mll
-+++ b/common/criteria_lexer.mll
-@@ -18,7 +18,7 @@
-     let c = Lexing.lexeme_char lexbuf 2 in (* the delimiter can be any character *)
-     (* find the terminating delimiter *)
-     let endpos =
--      try String.index_from lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) c with
-+      try Bytes.index_from lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) c with
-       |Invalid_argument _ ->
-           raise (Format822.Syntax_error (
-             Format822.error lexbuf "String too short"))
-@@ -27,9 +27,9 @@
-             Format822.error lexbuf (Printf.sprintf "cannot find: %c" c)))
-     in
-     let len = endpos - (lexbuf.lex_start_pos + 3) in
--    let s = String.sub lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) len in
--    lexbuf.Lexing.lex_curr_pos <- lexbuf.Lexing.lex_start_pos + ((String.length s)+4);
--    s
-+    let s = Bytes.sub lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) len in
-+    lexbuf.Lexing.lex_curr_pos <- lexbuf.Lexing.lex_start_pos + ((Bytes.length s)+4);
-+    Bytes.to_string s
- 
- }
- 
-diff --git a/common/util.ml b/common/util.ml
-index 598f266..36ca3d1 100644
---- a/common/util.ml
-+++ b/common/util.ml
-@@ -87,7 +87,7 @@ module MakeMessages(X : sig val label : string end) = struct
-   let clean label =
-     try 
-       let s = Filename.chop_extension (Filename.basename label) in
--      String.capitalize s
-+      String.capitalize_ascii s
-     with Invalid_argument _ -> label
- 
-   let create ?(enabled=false) label =
--- 
-2.11.0
-
diff --git a/gnu/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch b/gnu/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch
deleted file mode 100644
index 41494e7b3c..0000000000
--- a/gnu/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch
+++ /dev/null
@@ -1,133 +0,0 @@
-From b5314c20d8e3caf62fe0dc96ad937a2950158b23 Mon Sep 17 00:00:00 2001
-From: Louis Gesbert <louis.gesbert@ocamlpro.com>
-Date: Thu, 2 Mar 2017 12:19:56 +0100
-Subject: [PATCH] Install mli, cmx, etc.
-
----
- Makefile | 26 +++++++++++++-------------
- 1 file changed, 13 insertions(+), 13 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 09464ff..5044d7f 100644
---- a/Makefile
-+++ b/Makefile
-@@ -56,7 +56,7 @@ $(DOSELIBS)/cudf.%:
- 	@for i in _build/cudf/cudf.*; do \
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -67,7 +67,7 @@ $(DOSELIBS)/common.%: common/*.ml common/*.mli
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -78,7 +78,7 @@ $(DOSELIBS)/versioning.%: versioning/*.ml versioning/*.mli
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -88,7 +88,7 @@ $(DOSELIBS)/algo.%: algo/*.ml algo/*.mli $(DOSELIBS)/common.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -98,7 +98,7 @@ $(DOSELIBS)/debian.%: deb/*.ml deb/*.mli $(DOSELIBS)/pef.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -108,7 +108,7 @@ $(DOSELIBS)/opam.%: opam/*.ml opam/*.mli $(DOSELIBS)/pef.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -118,7 +118,7 @@ $(DOSELIBS)/npm.%: npm/*.ml npm/*.mli $(DOSELIBS)/versioning.% $(DOSELIBS)/pef.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -128,7 +128,7 @@ $(DOSELIBS)/rpm.%: rpm/*.ml $(DOSELIBS)/algo.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -138,7 +138,7 @@ $(DOSELIBS)/pef.%: pef/*.ml pef/*.mli
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -148,7 +148,7 @@ $(DOSELIBS)/csw.%: opencsw/*.ml $(DOSELIBS)/versioning.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -158,7 +158,7 @@ $(DOSELIBS)/doseparse.%: $(DOSELIBS)/pef.% $(DOSELIBS)/debian.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx $(DOSELIBS)/*.ml ; \
-+	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.ml ; \
- 	  fi ; \
- 	done
- 
-@@ -168,7 +168,7 @@ $(DOSELIBS)/doseparseNoRpm.%: $(DOSELIBS)/pef.% $(DOSELIBS)/debian.%
- 	  if [ -e $$i ]; then \
- 			cp $$i $(DOSELIBS) ;\
- 			rm $$i ;\
--			rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ;\
-+			rm -f $(DOSELIBS)/*.mlpack ;\
- 	  fi ; \
- 	done
- 
-@@ -223,7 +223,7 @@ INSTALL_STUFF_ = META
- INSTALL_STUFF_ += $(wildcard _build/doselibs/*.cma _build/doselibs/*.cmi)
- INSTALL_STUFF_ += $(wildcard _build/doselibs/*.cmxa _build/doselibs/*.cmxs)
- INSTALL_STUFF_ += $(wildcard _build/doselibs/*.a)
--#INSTALL_STUFF_ += $(wildcard _build/*/*.mli)
-+INSTALL_STUFF_ += $(wildcard _build/doselibs/*.mli) $(wildcard _build/doselibs/*.cmti) $(wildcard _build/doselibs/*.cmx)
- INSTALL_STUFF_ += $(wildcard _build/rpm/*.so)
- 
- exclude_cudf = $(wildcard _build/doselibs/*cudf* _build/cudf/*)
--- 
-2.11.0
-
diff --git a/gnu/packages/patches/ocaml-dose3-add-unix-dependency.patch b/gnu/packages/patches/ocaml-dose3-add-unix-dependency.patch
deleted file mode 100644
index d2cc44c784..0000000000
--- a/gnu/packages/patches/ocaml-dose3-add-unix-dependency.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From b94cf24739818e5aff397e0a83b19ea32dc81f42 Mon Sep 17 00:00:00 2001
-From: Louis Gesbert <louis.gesbert@ocamlpro.com>
-Date: Tue, 6 Feb 2018 10:15:45 +0100
-Subject: [PATCH 3/3] Add "unix" as dependency to dose3.common in META.in
-
----
- META.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/META.in b/META.in
-index aa2cd8d..0f9d337 100644
---- a/META.in
-+++ b/META.in
-@@ -8,7 +8,7 @@ package "common" (
- version = "@PACKAGE_VERSION@"
- archive(byte) = "common.cma"
- archive(native) = "common.cmxa"
--requires = "extlib, re.pcre, cudf, @ZIP@, @BZ2@"
-+requires = "extlib, re.pcre, cudf, unix, @ZIP@, @BZ2@"
- )
- 
- package "algo" (
--- 
-2.11.0
-
diff --git a/gnu/packages/patches/ocaml-dose3-dont-make-printconf.patch b/gnu/packages/patches/ocaml-dose3-dont-make-printconf.patch
deleted file mode 100644
index 84b6a3b81b..0000000000
--- a/gnu/packages/patches/ocaml-dose3-dont-make-printconf.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -6552,6 +6552,3 @@ if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
-   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
- $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
- fi
--
--
--make printconf
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)
diff --git a/gnu/packages/patches/spdlog-fix-tests.patch b/gnu/packages/patches/spdlog-fix-tests.patch
deleted file mode 100644
index 13dffb309e..0000000000
--- a/gnu/packages/patches/spdlog-fix-tests.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Remove after next release and package update:
-https://github.com/gabime/spdlog/commit/2ee8bac78e6525a8ad9a9196e65d502ce390d83a
-
-From 2ee8bac78e6525a8ad9a9196e65d502ce390d83a Mon Sep 17 00:00:00 2001
-From: xvitaly <vitaly@easycoding.org>
-Date: Sun, 23 Jul 2023 10:15:25 +0200
-Subject: [PATCH] Added missing square bracket to fix the level_to_string_view
- test. (#2827)
-
----
- tests/test_misc.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/test_misc.cpp b/tests/test_misc.cpp
-index 9f3cb1744..6199641ff 100644
---- a/tests/test_misc.cpp
-+++ b/tests/test_misc.cpp
-@@ -43,7 +43,7 @@ TEST_CASE("log_levels", "[log_levels]")
-     REQUIRE(log_info("Hello", spdlog::level::trace) == "Hello");
- }
- 
--TEST_CASE("level_to_string_view", "[convert_to_string_view")
-+TEST_CASE("level_to_string_view", "[convert_to_string_view]")
- {
-     REQUIRE(spdlog::level::to_string_view(spdlog::level::trace) == "trace");
-     REQUIRE(spdlog::level::to_string_view(spdlog::level::debug) == "debug");
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