gentoo auto-resync : 06:10:2024 - 04:27:04

6 files changed, 51 insertions, 4 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index e701bedec319..ac63a95cef05 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/gfan/Manifest b/sci-mathematics/gfan/Manifest
index eb4c57d1c9bf..afffdccc6244 100644
--- a/sci-mathematics/gfan/Manifest
+++ b/sci-mathematics/gfan/Manifest
@@ -2,9 +2,10 @@ AUX gfan-0.6.2-Makefile.patch 6603 BLAKE2B 48f9b4280418aef41d502d770c070ec1dcef9
 AUX gfan-0.6.2-find-name.patch 433 BLAKE2B 452e286223f4607f42e0895bba443c1534e491dc5e182f6f14c1d5d0d63c5992684b36ad0d028b68c286644e7ccc84786b0e49c311fcbe0fa6151a60ee3001d9 SHA512 f561189e887af930fa09ffa8870e9fbc4e5d5ed1b1a1b81c2001ea3d2a404b025a640eb7a4d504e448a60be4c58af3a3d00421abb48762bb2b32357e862252fc
 AUX gfan-0.6.2-fix-0602ResultantFanProjection.patch 689 BLAKE2B 4531bd59dc7a356b2907b043dc71a5e34e647dd15822d3e3846785bb27162ba607eea8492b972574c1f64a227d428b1db0b385a7a54624f5d33b3f4522bd7fe6 SHA512 0de03e0f40f7cde6ae8709a8c6f26cd39458752d1480c49635e58ce57c0b0ff1c03382bd41097af7609ee6320f98d83f600e7dde842fe545b758982e704e52eb
 AUX gfan-0.6.2-fix-spelling-errors.patch 2826 BLAKE2B 1a5b662dafd42834c9254d79cad84717d5b407c0fd14bf3f58320203b847953284597aa2add8dcb7eaa40700fa2a5c6e1c0ba99c2715d7fb0c6deedc45c44c8e SHA512 a30947bda62723f0d5a916d1a05de52fd67a2a3d4303b5774e7517407f531df67eb2968be255aab91634d46fdb61243e8b38ac355eef02c01c4ee95576e10159
+AUX gfan-0.6.2-glibcxx-assertions.patch 1473 BLAKE2B 7b78600ca7bdc5cd23b5d0b0799756cc95d95bdc5f951cb8f2c8a589ce0ea452ecbf22d1435d39d217d3e5301565b5c11eec2d33f8e6a6934a6108792ca7b1a0 SHA512 802527986dc9c783d016648b4cce986cea3f76c38cb631a6e90569569b136880c14c5fbfe0f5d5de0c838cc149ac6313a85e2fefd5d2117b5999771688921e82
 AUX gfan-0.6.2-testsuite.patch 3223 BLAKE2B ddb94775a13bd503df5c9563750a6b4b68c9e72e1a19aaa0415c5484e07765dfd28ba02b3a0fab65a0b9cd5c61afafbc6a3d862a1de68ece57ef9d8bb2835c16 SHA512 d62e765a39ee1a8cb149fcae8afb538b19a91206dd0b8cf0ac2b681b28569e44f492b770b9e61d7573f2d52f265ad4cf25671197c204238a89075709753a83e6
 AUX gfan-0.6.2-xcode9.3_compat.patch 367 BLAKE2B fb7c685a4dd811fed83e2734a16507b1792e3a97c666d0e7de1d2ed53a7b9b43c5319517f9eef829f47147dc725f2c4ead38968fa3868baa1d16630a8b844636 SHA512 129d2c35777f82bf2a1581450ecb12dd6811fb72b583748b30665c0f9b20d39646233d9b40fb64a3c7790360514a51b30e49c53d83c34d259f664bf820ae1ce2
 DIST gfan0.6.2.tar.gz 1321059 BLAKE2B 1ed61e1e084a1ceb65dd21848440bc3a90486c0ce4012b3b64c8029e89636696d2b0e5446ea156d2cf050b5db179c7c2f25c97e683cecf6e9616e8553d8513bf SHA512 5961820750af2522fdc1a86c0254742c3b003607a8707df5d6cd5f0bc6461e4d3db3b1d3cb537979d57eb9dff387974a58aeb91d0b5246d7c701cadc5a2cf4cf
 EBUILD gfan-0.6.2-r4.ebuild 2007 BLAKE2B 21d014cbabb76f661135ffc1c1ce72b016448511e0ec7cb71cffc6f68fec9328c140f268ae3dce2a7ed58ee5559f56c274fb9ce1f7edcc000a9f0606f013bd3d SHA512 76b1e4b63458d5992b5036a7fff2f0e9be5ec0269fcd8a3d2854db21a89f8efd54b9d043049e9e9ac969852f975a8774735c6c426ac03068078c75c1517d0f2a
-EBUILD gfan-0.6.2-r5.ebuild 1971 BLAKE2B b50e2c1bbcbd4269850575bd4f36bb42dcad534d3a55e4257bf3281e907dfe0730deb81fbb66373356ec474e9273b4c9b40ae227842edce682e68530be0de2f6 SHA512 5eed708f34f910390a024e45b9a613ab424729122f58bae8573832f4f217c3f6424309c7f068f162d797a0c19f8d56926b97054c4ece1d9d62094a8848a913e3
+EBUILD gfan-0.6.2-r6.ebuild 2203 BLAKE2B 5656e7f447f44a8a2a080d7f369fdfb0b391f946386c6794744531bbdcab190177834c46c59e53e49dce27160879208a4d0158f3e15a210ffc094f45941c1c04 SHA512 f2832bb4d281566178925912bdbdf9c68b4f59235d231186c2caefb7422776b4501cf7722ad7539840a349e2cc16ccd00d2fba4bd0b0982e3f861e7367026967
 MISC metadata.xml 1344 BLAKE2B 1a1d24099e2338877b068dee2b9e17feb4063de3a681a3b8d6a707c863708d6f380bb4864eb2fd5fef8ed49d6b1a770a8d1b4c12ce722b4f7fe113876de0b792 SHA512 8d5c93337a82b132c66c8d7e64c97deedcfdc724e9874bf308e6d817f71e663bc2b281ea133ae15e30096f5c801f88116b11e4d36dd8dd8eec526b5bc16d5f54
diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-glibcxx-assertions.patch b/sci-mathematics/gfan/files/gfan-0.6.2-glibcxx-assertions.patch
new file mode 100644
index 000000000000..00c616d036fe
--- /dev/null
+++ b/sci-mathematics/gfan/files/gfan-0.6.2-glibcxx-assertions.patch
@@ -0,0 +1,39 @@
+From f0e9e24f1f20801bd49c78b30b951433f834a2c7 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Sat, 5 Oct 2024 08:48:57 -0400
+Subject: [PATCH] src/gfanlib_tropicalhomotopy.h: avoid out-of-bounds vector
+ indexes
+
+Add a check to ensure that we don't try to access the -1st element of
+a vector. The code would be trying to subtract zero from the entry, so
+it was "harmless," but it does crash glibcxx when assertions are
+enabled (as they are on hardened Gentoo). This should allow the
+SageMath "mixed volume" tests to pass.
+---
+ src/gfanlib_tropicalhomotopy.h | 10 ++++++----
+ 1 file changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/src/gfanlib_tropicalhomotopy.h b/src/gfanlib_tropicalhomotopy.h
+index f3127ba..f6db26e 100644
+--- a/src/gfanlib_tropicalhomotopy.h
++++ b/src/gfanlib_tropicalhomotopy.h
+@@ -454,10 +454,12 @@ template<class mvtyp, class mvtypDouble, class mvtypDivisor>
+ 			//chioices are "relative" so no update is needed.
+ 
+ 			choices=parent.choices;
+-			int numberToDrop=(subconfigurationIndex!=0) ? numberToDrop=k+1 : 0;
+-
+-			choices[subconfigurationIndex-1].first-=numberToDrop;
+-			choices[subconfigurationIndex-1].second-=numberToDrop;
++			int numberToDrop = 0;
++			if (subconfigurationIndex != 0) {
++				numberToDrop=k+1;
++				choices[subconfigurationIndex-1].first-=numberToDrop;
++				choices[subconfigurationIndex-1].second-=numberToDrop;
++			}
+ 
+ 			denominator=parent.denominator;
+ 			int offsetOld=0;
+-- 
+2.45.2
+
diff --git a/sci-mathematics/gfan/gfan-0.6.2-r5.ebuild b/sci-mathematics/gfan/gfan-0.6.2-r6.ebuild
index 47fbcc3b8e1d..538326ff4359 100644
--- a/sci-mathematics/gfan/gfan-0.6.2-r5.ebuild
+++ b/sci-mathematics/gfan/gfan-0.6.2-r6.ebuild
@@ -16,7 +16,13 @@ SLOT="0"
 KEYWORDS="~amd64 ~arm ~riscv ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc"
 
-BDEPEND="doc? ( virtual/latex-base )"
+# texlive-plaingeneric is needed for \usepackage{ulem} in
+# the manual. ghostscript-gpl provides the "dvipdf" command.
+BDEPEND="doc? (
+	app-text/ghostscript-gpl
+	dev-texlive/texlive-plaingeneric
+	virtual/latex-base
+)"
 DEPEND="dev-libs/gmp:0=[cxx(+)]
 	sci-libs/cddlib:0="
 RDEPEND="${DEPEND}"
@@ -27,6 +33,7 @@ PATCHES=(
 	"${FILESDIR}/${PN}-0.6.2-fix-0602ResultantFanProjection.patch"
 	"${FILESDIR}/${PN}-0.6.2-fix-spelling-errors.patch"
 	"${FILESDIR}/${PN}-0.6.2-find-name.patch"
+	"${FILESDIR}/${PN}-0.6.2-glibcxx-assertions.patch"
 )
 
 pkg_setup() {
diff --git a/sci-mathematics/singular/Manifest b/sci-mathematics/singular/Manifest
index 15cd94addd48..94af63c33d53 100644
--- a/sci-mathematics/singular/Manifest
+++ b/sci-mathematics/singular/Manifest
@@ -2,7 +2,7 @@ AUX 60singular-gentoo.el 298 BLAKE2B 5b42e2083037e2ff2ace5597ddebfb079920e09ed91
 AUX singular-4.3.2_p16-lto.patch 825 BLAKE2B e5adfbb5febd9722330362815be23c49431a8953d17fb63669749971b8a0aba59f242a1ea17c5b06c5054146853e2f480eb74b91af4db80dac4c0101415275e7 SHA512 efd33048a125b8e3026583802ac5060947c2313c98cd4ba6046f2de62703a2923212b28a0f633ff801f58592b7deaef1f0f84c643f4131a0e672e12ff506008f
 AUX singular-4.3.2_p16-test-underlinking.patch 8292 BLAKE2B 9b63377bf203be189be2f4840f098f9b0ce72857030eb2ac8abc6d7f768b5c0e1fbc268c732b08811e8fdab77fd49c26463adadc764114dca23d4ca6eeac6225 SHA512 8fcccfdbb40904972a70ba11a3cc9f9d15852f370d842883d21a19bc7aea45feb7516037e49ff1396a9520e277d7c497c7394f339112332c6594b0205a1965c0
 DIST singular-4.3.2p16.tar.gz 20880476 BLAKE2B ce226a6867b764e593ddbf2c71220d9ea14ccdfd956046d5a94dfb768a97927ca3cf961a9ea808cb77028f2c65d989032202d3a0bde555ace945df1e987077a8 SHA512 1dae0e229e124db03e5e240c3ab2f1049c9f77cf369f701c4a2d0767ba9c23baab2d5d14271e415a3ccbf7b9a9297fcf324b8ccc2841a5156d6ee846cb409de2
-DIST singular-4.4.0p2.tar.gz 20924020 BLAKE2B 0d663b830c37c96635303faeb14a55e0eff05bc378a3263cf83374893056b1c3175718f6b0870ac0c906a92eda59db0ca91a39a7b69a88d298a4a7993b9249d1 SHA512 df3faf025f30ab1c60460f661c4cec945a410311ca89d0756eafb57b430bb53ecec103b90ca91891fc7b1e720938a8259a9b256b6acd322c021c33e628b6654b
+DIST singular-4.4.0p6.tar.gz 21097819 BLAKE2B ce78f63b2f90113ba92811a1e02b568328a92dc686d86fa653209c127f8895811e87ca4684dd1df5c2a54e8952cb1b0654055653e4b4734d9729a7de6f6faaa9 SHA512 b88e60f5665cfab7ccb5a2620190d08c1538f876cce24a24c7baddec40554fd0093cc47db89758f0bbf24f7ca298849a9fe700ce2070c8c52861d3bd48d2cc0d
 EBUILD singular-4.3.2_p16-r1.ebuild 2630 BLAKE2B abd50d631f7407043c5fc6a8748fb798a3548c643c5b88bf1303fa63a3da36753668cd9d8293a6659c52664d3c0e33fee5f90221ec56404a49c0f5514bf7602e SHA512 56f62d3035e33937f641e4242063f6176ab6cc4391f0575240ce06591fbb40f51efdcbd60c19be68c84fe2d2dc9295233613158e7be8f81020cf0622506bd654
-EBUILD singular-4.4.0_p2.ebuild 2493 BLAKE2B 3622d734ba8416853ec924a4002f6678056ddaaab72ee78de01fcb44b51737e74c3a4db2d182ee579366b3c28e0861cc558693a3c19fa0e648a5e284763ddc8e SHA512 40ac5cc03a036799ddbd15914f847423da2f5b5a855425a55a3ba83bace669ca814c9f7440fe90797865b2fb96f4815135ed83d4551b80456ca41511cc89262f
+EBUILD singular-4.4.0_p6.ebuild 2493 BLAKE2B 3622d734ba8416853ec924a4002f6678056ddaaab72ee78de01fcb44b51737e74c3a4db2d182ee579366b3c28e0861cc558693a3c19fa0e648a5e284763ddc8e SHA512 40ac5cc03a036799ddbd15914f847423da2f5b5a855425a55a3ba83bace669ca814c9f7440fe90797865b2fb96f4815135ed83d4551b80456ca41511cc89262f
 MISC metadata.xml 862 BLAKE2B a6e991149cb925158806177b1b4a76da2b747b3273b395c14455993a99f4cf83de141980303a068b9068983b8adf4da884b81e80546a3d2dd162f188dc759385 SHA512 9e40cf7b3841bcf8289f24903e392df2a812b6d815f71da41d95a81bb89f493ab1afcef749ef47960ba683dc3433d2c4488015990806dde0b560ffe3bb6ca545
diff --git a/sci-mathematics/singular/singular-4.4.0_p2.ebuild b/sci-mathematics/singular/singular-4.4.0_p6.ebuild
index 7cadc4a9aeac..7cadc4a9aeac 100644
--- a/sci-mathematics/singular/singular-4.4.0_p2.ebuild
+++ b/sci-mathematics/singular/singular-4.4.0_p6.ebuild