* [gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/files/, sci-biology/augustus/
@ 2025-02-11 1:38 Sam James
0 siblings, 0 replies; 3+ messages in thread
From: Sam James @ 2025-02-11 1:38 UTC (permalink / raw
To: gentoo-commits
commit: 46398746b50dc4be683f7777230477bef9780ee7
Author: Alfred Wingate <parona <AT> protonmail <DOT> com>
AuthorDate: Mon Feb 10 19:15:07 2025 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Tue Feb 11 01:36:17 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=46398746
sci-biology/augustus: include cstdint for gcc-13
Closes: https://bugs.gentoo.org/895204
Signed-off-by: Alfred Wingate <parona <AT> protonmail.com>
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/augustus/augustus-3.4.0-r3.ebuild | 6 +++-
.../files/augustus-3.4.0-missing-cstdint.patch | 39 ++++++++++++++++++++++
2 files changed, 44 insertions(+), 1 deletion(-)
diff --git a/sci-biology/augustus/augustus-3.4.0-r3.ebuild b/sci-biology/augustus/augustus-3.4.0-r3.ebuild
index 7c662aead62f..7f1bd71bdf41 100644
--- a/sci-biology/augustus/augustus-3.4.0-r3.ebuild
+++ b/sci-biology/augustus/augustus-3.4.0-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -31,6 +31,10 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
+PATCHES=(
+ "${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch
+)
+
src_compile() {
tc-export CC CXX
diff --git a/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch b/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch
new file mode 100644
index 000000000000..3c0095241636
--- /dev/null
+++ b/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch
@@ -0,0 +1,39 @@
+https://bugs.gentoo.org/895204
+
+https://github.com/Gaius-Augustus/Augustus/commit/1ed97dc4ce2909c5f89737005b8ea4a664fbe728
+https://github.com/Gaius-Augustus/Augustus/pull/395
+
+From 1ed97dc4ce2909c5f89737005b8ea4a664fbe728 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Sun, 11 Jun 2023 23:47:49 +0800
+Subject: [PATCH] fix: gcc13 failed with this
+
+--- a/include/sqliteDB.hh
++++ b/include/sqliteDB.hh
+@@ -11,6 +11,7 @@
+ #include <string>
+ #include <vector>
+ #include <sqlite3.h>
++#include <cstdint>
+
+ using namespace std;
+
+
+https://github.com/Gaius-Augustus/Augustus/commit/3dbe752e4cf3f6778168166a2c662d02d8623f15
+https://github.com/Gaius-Augustus/Augustus/pull/395
+
+From 3dbe752e4cf3f6778168166a2c662d02d8623f15 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Mon, 12 Jun 2023 01:32:02 +0800
+Subject: [PATCH] fix: without it compile fail
+
+--- a/auxprogs/homGeneMapping/include/sqliteDB.hh
++++ b/auxprogs/homGeneMapping/include/sqliteDB.hh
+@@ -13,6 +13,7 @@
+ #include <string>
+ #include <vector>
+ #include <sqlite3.h>
++#include <cstdint>
+
+ using namespace std;
+
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/files/, sci-biology/augustus/
@ 2025-02-13 8:45 Sam James
0 siblings, 0 replies; 3+ messages in thread
From: Sam James @ 2025-02-13 8:45 UTC (permalink / raw
To: gentoo-commits
commit: eb668702f3bd1a2f3b9ff0e7ad4f19edca41fb76
Author: Alfred Wingate <parona <AT> protonmail <DOT> com>
AuthorDate: Tue Feb 11 13:05:38 2025 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu Feb 13 08:45:32 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eb668702
sci-biology/augustus: fix gcc15 build
Closes: https://bugs.gentoo.org/949617
Signed-off-by: Alfred Wingate <parona <AT> protonmail.com>
Closes: https://github.com/gentoo/gentoo/pull/40531
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/augustus/augustus-3.5.0.ebuild | 1 +
.../augustus/files/augustus-3.5.0-fix-gcc15.patch | 20 ++++++++++++++++++++
2 files changed, 21 insertions(+)
diff --git a/sci-biology/augustus/augustus-3.5.0.ebuild b/sci-biology/augustus/augustus-3.5.0.ebuild
index 01f8dbc42621..86b618fa12ca 100644
--- a/sci-biology/augustus/augustus-3.5.0.ebuild
+++ b/sci-biology/augustus/augustus-3.5.0.ebuild
@@ -44,6 +44,7 @@ BDEPEND="
PATCHES=(
"${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch
+ "${FILESDIR}"/augustus-3.5.0-fix-gcc15.patch
)
pkg_setup() {
diff --git a/sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patch b/sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patch
new file mode 100644
index 000000000000..4c5916ad402f
--- /dev/null
+++ b/sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patch
@@ -0,0 +1,20 @@
+https://bugs.gentoo.org/949617
+https://github.com/Gaius-Augustus/Augustus/pull/431
+
+From b7cbe782e840c82da1eeb2aae7a1a757ecef9fb0 Mon Sep 17 00:00:00 2001
+From: Alfred Wingate <parona@protonmail.com>
+Date: Tue, 11 Feb 2025 14:57:23 +0200
+Subject: [PATCH] filterBam: include missing header for gcc15
+
+Bug: https://bugs.gentoo.org/949617
+Signed-off-by: Alfred Wingate <parona@protonmail.com>
+--- a/auxprogs/filterBam/src/headers/bamaccess.hh
++++ b/auxprogs/filterBam/src/headers/bamaccess.hh
+@@ -7,6 +7,7 @@
+ #include <iostream>
+ #include <vector>
+ #include <memory>
++#include <cstdint>
+
+ class BamAlignmentRecord;
+ typedef std::shared_ptr<BamAlignmentRecord> BamAlignmentRecord_;
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/files/, sci-biology/augustus/
@ 2025-05-20 19:12 Andreas Sturmlechner
0 siblings, 0 replies; 3+ messages in thread
From: Andreas Sturmlechner @ 2025-05-20 19:12 UTC (permalink / raw
To: gentoo-commits
commit: 2c862807546f666b21c5ab2c01ba3a1402f5c38a
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Mon May 19 20:38:27 2025 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Tue May 20 19:12:22 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2c862807
sci-biology/augustus: drop 2.5.5
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-biology/augustus/Manifest | 1 -
sci-biology/augustus/augustus-2.5.5.ebuild | 50 -------
.../augustus/files/augustus-2.5.5-sane-build.patch | 156 ---------------------
3 files changed, 207 deletions(-)
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
index 7bba72327fb5..178d054cf6f7 100644
--- a/sci-biology/augustus/Manifest
+++ b/sci-biology/augustus/Manifest
@@ -1,3 +1,2 @@
DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6
DIST augustus-3.5.0.tar.gz 225918930 BLAKE2B 26e934f3d3f50d183fb0ee7874352c5ac9af9877eaa40a9a6195ae79cfd9a78a321bd9261e8bd3435b1d4984589d0bdd4e0821ba6600c717d6afd95f511702de SHA512 0869e54b3126b3ab2f6fb2c28ff07b779265a139968e5277352f5230d3c317415324ca61dce4a0cd6c3f1fb5399447ae815bec7732a285ce652cf44e6cd23e5d
-DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f
diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild
deleted file mode 100644
index ed345330c4a7..000000000000
--- a/sci-biology/augustus/augustus-2.5.5.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://augustus.gobics.de/"
-SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="examples"
-
-S="${WORKDIR}/${PN}.${PV}"
-PATCHES=( "${FILESDIR}"/${P}-sane-build.patch )
-
-src_configure() {
- tc-export CC CXX
-}
-
-src_compile() {
- emake clean
- default
-}
-
-src_install() {
- dobin bin/*
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*.p*
-
- insinto /usr/libexec/${PN}
- doins scripts/*.conf
-
- insinto /usr/share/${PN}
- doins -r config
-
- echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > 99${PN} || die
- doenvd 99${PN}
-
- dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
-
- if use examples; then
- insinto /usr/share/${PN}/
- doins -r docs/tutorial examples
- fi
-}
diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch
deleted file mode 100644
index 39cd0762b1c1..000000000000
--- a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch
+++ /dev/null
@@ -1,156 +0,0 @@
- Makefile | 8 +++---
- scripts/Makefile | 6 +++-
- scripts/aln2wig/Makefile | 8 +++---
- scripts/compileSpliceCands/Makefile | 6 ++--
- src/Makefile | 43 ++++++++++++++++++----------------
- 5 files changed, 38 insertions(+), 33 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index e23a667..64610c8 100644
---- a/Makefile
-+++ b/Makefile
-@@ -3,9 +3,9 @@
- #
-
- all:
-- cd src && ${MAKE}
-- cd scripts && ${MAKE}
-+ $(MAKE) -C src
-+ $(MAKE) -C scripts
-
- clean:
-- cd src && ${MAKE} clean
-- cd scripts && ${MAKE} clean
-+ $(MAKE) -C src clean
-+ $(MAKE) -C scripts clean
-diff --git a/scripts/Makefile b/scripts/Makefile
-index 6d4dd67..ab6a885 100644
---- a/scripts/Makefile
-+++ b/scripts/Makefile
-@@ -1,5 +1,7 @@
- all :
-- cd aln2wig && ${MAKE}
-+ $(MAKE) -C aln2wig
-+ $(MAKE) -C compileSpliceCands
-
- clean :
-- cd aln2wig && ${MAKE} clean
-+ $(MAKE) -C aln2wig clean
-+ $(MAKE) -C compileSpliceCands
-diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile
-index 64d09f5..9752980 100644
---- a/scripts/aln2wig/Makefile
-+++ b/scripts/aln2wig/Makefile
-@@ -1,10 +1,10 @@
--CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb
-+CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic
-
- psl2wig : aln2wig.o
-- gcc $(CFLAGS) -o aln2wig aln2wig.o;
-- cp aln2wig ../../bin
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
-+ cp aln2wig ../../bin/
- psl2wig.o : aln2wig.c
-- gcc $(CFLAGS) -c aln2wig.c
-+ $(CC) $(CFLAGS) -c aln2wig.c
-
- all : psl2wig
-
-diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile
-index cddada5..8079791 100644
---- a/scripts/compileSpliceCands/Makefile
-+++ b/scripts/compileSpliceCands/Makefile
-@@ -1,8 +1,8 @@
- compileSpliceCands : compileSpliceCands.o list.h list.o
-- gcc -o compileSpliceCands compileSpliceCands.o list.o;
--# cp compileSpliceCands ../../bin
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
-+ cp compileSpliceCands ../../bin/
- compileSpliceCands.o : compileSpliceCands.c
-- gcc -Wall -pedantic -ansi -c compileSpliceCands.c
-+ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c
-
- all : compileSpliceCands
-
-diff --git a/src/Makefile b/src/Makefile
-index 71795b6..732b953 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -6,8 +6,8 @@
- # a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
- # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
- #
--CC = g++
--CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static
-+CXX ?= g++
-+CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static
- INCLS = -I../include -I.
- LIBS = # -lcwd
- OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \
-@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte
- PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign
- INFO = cflags
-
--all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info
-+all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin
-
- .SUFFIXES:
- .SUFFIXES: .cc .o .so
-
- .cc.o:
-- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS)
-+ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS)
-
--augustus: augustus.cc $(OBJS) $(DUMOBJS)
-- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+bin: $(PROGR)
-+ cp $(PROGR) ../bin/
-+
-+augustus: augustus.o $(OBJS) $(DUMOBJS)
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
- cp augustus ../bin/
-
--etraining: etraining.cc $(TOBJS) $(OBJS)
-- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+etraining: etraining.o $(TOBJS) $(OBJS)
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
- cp etraining ../bin/
-
--evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
-- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+evaluate: evaluate.o $(OBJS) $(DUMOBJS)
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-
--consensusFinder: consensusFinder.cc consensus.o
-- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+consensusFinder: consensusFinder.o consensus.o
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-
--curve2hints: curve2hints.cc exon_seg.o
-- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+curve2hints: curve2hints.o exon_seg.o
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-
--fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
-+fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \
- types.o properties.o geneticcode.o pp_profile.o lldouble.o
-- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
- cp fastBlockSearch ../bin/
-
--prepareAlign: pp_prepare_align.cc
-- $(CC) $(CFLAGS) -o $@ $^
-+prepareAlign: pp_prepare_align.o
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
- cp prepareAlign ../bin/
-
- info:
-- echo "$(CFLAGS)" > $(INFO)
-+ echo "$(CXXFLAGS)" > $(INFO)
-
- clean:
-- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO)
-+ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/*
-
- tidy: clean
- rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
^ permalink raw reply related [flat|nested] 3+ messages in thread
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2025-02-13 8:45 Sam James
2025-02-11 1:38 Sam James
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