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Repository mirror & CI
2025-04-24 19:20:11 +00:00
parent 9ea5ae9a19 1dd7e1d8e9
commit d2dc4be7b5
17 changed files with 765 additions and 14 deletions
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6
app-benchmarks/nbench/nbench-2.2.3-r2.ebuild
View File

@@ -1,11 +1,11 @@
# Copyright 1999-2022 Gentoo Authors
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
MY_P="${PN}-byte-${PV}"
inherit toolchain-funcs
inherit flag-o-matic toolchain-funcs
DESCRIPTION="Linux/Unix of release 2 of BYTE Magazine's BYTEmark benchmark"
HOMEPAGE="http://www.tux.org/~mayer/linux/bmark.html"
@@ -30,6 +30,8 @@ src_prepare() {
src_configure() {
tc-export CC
# bug #943907
append-cflags -std=gnu17
}
src_install() {

85
app-pda/pilot-link/files/pilot-link-0.12.5-C23.patch Normal file
View File

@@ -0,0 +1,85 @@
Correct build for C23
Wrong type for size variable, missing parameters in decls
Missing include and wrong types in bundled libusb library
https://bugs.gentoo.org/944433
https://bugs.gentoo.org/883101
--- a/src/parsedate.c
+++ b/src/parsedate.c
@@ -175,8 +175,8 @@
static time_t yyRelSeconds;
-extern struct tm *localtime();
-static void date_error();
+extern struct tm *localtime(const time_t *timep);
+static void date_error(char *s);
/* Enabling traces. */
--- a/src/parsedate.y
+++ b/src/parsedate.y
@@ -94,8 +94,8 @@
static time_t yyRelSeconds;
-extern struct tm *localtime();
-static void date_error();
+extern struct tm *localtime(const time_t *timep);
+static void date_error(char *s);
%}
%union {
--- a/src/pilot-read-todos.c
+++ b/src/pilot-read-todos.c
@@ -202,8 +202,8 @@
for (i = 0;; i++) {
int attr,
- category,
- len;
+ category;
+ ssize_t len;
struct ToDo todo;
--- a/libpisock/linuxusb.c
+++ b/libpisock/linuxusb.c
@@ -27,6 +27,7 @@
#include <stdio.h>
#include <sys/types.h>
#include <sys/stat.h>
+#include <sys/socket.h>
#include "pi-debug.h"
#include "pi-source.h"
@@ -48,8 +49,8 @@
static int u_open(pi_socket_t *ps, struct pi_sockaddr *addr, size_t addrlen);
static int u_close(pi_socket_t *ps);
-static int u_write(pi_socket_t *ps, unsigned char *buf, size_t len, int flags);
-static int u_read(pi_socket_t *ps, pi_buffer_t *buf, size_t len, int flags);
+static ssize_t u_write(pi_socket_t *ps, const unsigned char *buf, size_t len, int flags);
+static ssize_t u_read(pi_socket_t *ps, pi_buffer_t *buf, size_t len, int flags);
static int u_poll(pi_socket_t *ps, int timeout);
static int u_flush(pi_socket_t *ps, int flags);
@@ -188,8 +189,8 @@
* Returns: Nothing
*
***********************************************************************/
-static int
-u_write(pi_socket_t *ps, unsigned char *buf, size_t len, int flags)
+static ssize_t
+u_write(pi_socket_t *ps, const unsigned char *buf, size_t len, int flags)
{
int total,
nwrote;
@@ -281,7 +282,7 @@
* Returns: number of bytes read or negative otherwise
*
***********************************************************************/
-static int
+static ssize_t
u_read(pi_socket_t *ps, pi_buffer_t *buf, size_t len, int flags)
{
ssize_t rbuf = 0,

103
app-pda/pilot-link/pilot-link-0.12.5-r5.ebuild Normal file
View File

@@ -0,0 +1,103 @@
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit autotools flag-o-matic perl-module
DESCRIPTION="Suite of tools for moving data between a Palm device and a desktop"
# this is a new mirror; the distfile has the same content inside the tarball,
# but the tarball itself doesn't match due to recompression and Git
# indirection.
HOMEPAGE="https://github.com/jichu4n/pilot-link"
SRC_URI="
mirror://gentoo/${P}.tar.bz2
https://dev.gentoo.org/~soap/distfiles/${P}-gentoo-patchset-r2.tar.xz"
LICENSE="|| ( GPL-2 LGPL-2 )"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
IUSE="bluetooth perl png threads usb"
RESTRICT="test" #672872
RDEPEND="
dev-libs/popt
sys-libs/ncurses:=
sys-libs/readline:=
virtual/libiconv
bluetooth? ( net-wireless/bluez )
perl? ( dev-lang/perl:= )
png? ( media-libs/libpng:= )
usb? ( virtual/libusb:0 )"
DEPEND="${RDEPEND}"
BDEPEND="
virtual/pkgconfig
perl? ( dev-lang/perl )
sys-devel/bison"
PATCHES=(
"${WORKDIR}/${P}-gentoo-patchset"/
"${FILESDIR}/${P}-C23.patch"
)
src_prepare() {
default
eautoreconf
}
src_configure() {
# -Werror=lto-type-mismatch
# https://bugs.gentoo.org/924480
#
# Upstream is abandoned since 2016, existing issue offering gentoo-patchset
# has been ignored. No bug filed.
#
# The issue is in the internal compat code for *not* using libusb.
use usb || filter-lto
# tcl/tk support is disabled as per upstream request.
# readline is not really optional, bug #626504
# Does not build with Java 8
# Does not build with Python 3, bug #735238
econf \
--includedir="${EPREFIX}"/usr/include/libpisock \
--enable-conduits \
--with-readline \
$(use_enable threads) \
$(use_enable usb libusb) \
$(use_with png libpng) \
$(use_with bluetooth bluez) \
$(use_with perl) \
--without-java \
--without-tcl \
--without-python
if use perl; then
perl_set_version
cd bindings/Perl || die
perl-module_src_configure
fi
}
src_compile() {
emake
if use perl; then
cd bindings/Perl || die
local mymake=( OTHERLDFLAGS="${LDFLAGS} -L../../libpisock/.libs -lpisock" ) #308629
perl-module_src_compile
fi
}
src_install() {
default
dodoc doc/{README*,TODO}
if use perl; then
cd bindings/Perl || die
perl-module_src_install
fi
find "${ED}" -name '*.la' -delete || die
}

51
app-text/xml2doc/files/xml2doc-20030510-c99.patch Normal file
View File

@@ -0,0 +1,51 @@
https://bugs.gentoo.org/923170
--- a/src/defs.c
+++ b/src/defs.c
@@ -1,5 +1,7 @@
#include "defs.h"
+#include <stdlib.h>
+
int defs_init()
{
DocS.page=0;
--- a/src/defs.h
+++ b/src/defs.h
@@ -1,6 +1,7 @@
#ifndef _INCLUDE_DEFS_H_
#define _INCLUDE_DEFS_H_
+#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
--- a/src/main.c
+++ b/src/main.c
@@ -1,5 +1,7 @@
#include "main.h"
+#include <stdlib.h>
+
/*
*
* PDF_set_value(p,"nameofvalue",(float)value); // get/set
--- a/src/parse.c
+++ b/src/parse.c
@@ -1,5 +1,7 @@
#include "defs.h"
+#include <stdlib.h>
+
int parse(const char *file)
{
Doc[n].doc=xmlParseFile(file);
--- a/src/defs.c
+++ b/src/defs.c
@@ -12,6 +12,7 @@ int defs_init()
DocS.add.colors=(struct_colors *)malloc(1);
DocS.add.pages =(struct_pages *)malloc(1);
DocS.add.sizes =(struct_sizes *)malloc(1);
+ return 0;
}
int defs_default() // Set default values

8
app-text/xml2doc/xml2doc-20030510-r2.ebuild → app-text/xml2doc/xml2doc-20030510-r3.ebuild
View File

@@ -1,9 +1,9 @@
# Copyright 1999-2024 Gentoo Authors
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit autotools toolchain-funcs
inherit autotools flag-o-matic toolchain-funcs
DESCRIPTION="Tool to convert simple XML to a variety of formats (pdf, html, txt, manpage)"
HOMEPAGE="http://xml2doc.sourceforge.net"
@@ -24,6 +24,8 @@ PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
# Fix GCC 10 -fno-common change
"${FILESDIR}"/${P}-gcc10-no-common.patch
# bug #923170
"${FILESDIR}"/${P}-c99.patch
)
src_prepare() {
@@ -35,6 +37,8 @@ src_prepare() {
src_configure() {
tc-export CC
# bug #944764
append-cflags -std=gnu17
econf --disable-pdf
}

2
dev-cpp/prometheus-cpp/prometheus-cpp-1.2.4.ebuild
View File

@@ -11,7 +11,7 @@ SRC_URI="https://github.com/jupp0r/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~riscv x86"
KEYWORDS="amd64 ~riscv x86"
IUSE="test zlib"
RESTRICT="!test? ( test )"

2
dev-ruby/json/json-2.10.2.ebuild
View File

@@ -20,7 +20,7 @@ SRC_URI="https://github.com/ruby/json/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="|| ( BSD-2 Ruby )"
SLOT="$(ver_cut 1)"
KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~loong ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
KEYWORDS="~alpha amd64 arm ~arm64 ~hppa ~loong ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
IUSE="doc test"
DEPEND="dev-util/ragel"

359
dev-tex/rail/files/rail-1.2_p1-C23.patch Normal file
View File

@@ -0,0 +1,359 @@
Fix includes and function definitions and signatures
until whole thing compiles with C23.
https://bugs.gentoo.org/738854
https://bugs.gentoo.org/883267
https://bugs.gentoo.org/947155
--- a/gram.y
+++ b/gram.y
@@ -5,6 +5,7 @@
#include <stdio.h>
#include "rail.h"
+extern int yylex (void);
char optchar;
--- a/rail.c
+++ b/rail.c
@@ -21,6 +21,7 @@
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
+#include <unistd.h>
#include "patchlevel.h"
#include "rail.h"
@@ -54,9 +55,7 @@
int anonymous; /* anonymous rules */
-main(argc,argv)
-unsigned argc;
-char *argv[];
+int main(int argc, char *argv[])
{
char *arg, **argp;
unsigned len;
@@ -122,8 +121,7 @@
/*NOTREACHED*/
}
-int setopt(c,s)
-char c, *s;
+int setopt(char c, char *s)
{
int set;
@@ -167,7 +165,7 @@
return 1;
}
-usage()
+void usage(void)
{
fprintf(stderr,USAGE,myname);
exit(1);
@@ -175,23 +173,21 @@
/* error routine for yyparse() */
-yyerror(s)
-char *s;
+void yyerror(char *s)
{
fatal("%s",s);
}
/* wrap-up routine for yylex() */
-yywrap()
+int yywrap(void)
{
return(1);
}
/* check for non-NULL pointer */
-char *mcheck(s)
-char *s;
+char *mcheck(char *s)
{
if(s==NULL)
fatal("out of memory",(char *)NULL);
@@ -201,9 +197,7 @@
/* make a new body */
-BODYTYPE *newbody(kind,body1,body2)
-int kind;
-BODYTYPE *body1, *body2;
+BODYTYPE *newbody(int kind, BODYTYPE *body1, BODYTYPE *body2)
{
BODYTYPE *body;
@@ -226,8 +220,7 @@
/* free a body recursively */
-freebody(body)
-BODYTYPE *body;
+void freebody(BODYTYPE *body)
{
int i;
@@ -246,16 +239,14 @@
/* test if a body is empty */
-int isemptybody(body)
-BODYTYPE *body;
+int isemptybody(BODYTYPE *body)
{
return(body==NULL || body->kind==EMPTY);
}
/* add to a body list */
-static addlist(body1,body2)
-BODYTYPE *body1, *body2;
+void static addlist(BODYTYPE *body1, BODYTYPE *body2)
{
if(body1->nlist>=MAXLIST) {
yyerror("list too long");
@@ -265,9 +256,7 @@
/* add two body lists (for CAT, BAR, PLUS) */
-BODYTYPE *addbody(kind,body1,body2)
-int kind;
-BODYTYPE *body1, *body2;
+BODYTYPE *addbody(int kind, BODYTYPE *body1, BODYTYPE *body2)
{
BODYTYPE *body;
int i;
@@ -292,8 +281,7 @@
/* reverse all concatenations (for PLUS) */
-BODYTYPE *revbody(body)
-BODYTYPE *body;
+BODYTYPE *revbody(BODYTYPE *body)
{
int i,j;
BODYTYPE *tmp;
@@ -314,9 +302,7 @@
/* print a body for debugging */
-prtbody(indent,body)
-int indent;
-BODYTYPE *body;
+void prtbody(int indent, BODYTYPE *body)
{
int i;
@@ -376,9 +362,7 @@
/* output a body */
-outbody(id,body)
-IDTYPE *id;
-BODYTYPE *body;
+void outbody(IDTYPE *id, BODYTYPE *body)
{
posbody(body,0);
@@ -403,10 +387,7 @@
/* format a body */
-fmtbody(body,cent,arrow)
-BODYTYPE *body;
-char *cent;
-char arrow;
+void fmtbody(BODYTYPE *body, char *cent, char arrow)
{
BODYTYPE *body1;
int i;
@@ -494,8 +475,7 @@
/* position body (fill in height and ystart) */
-posbody(body,ystart)
-BODYTYPE *body;
+void posbody(BODYTYPE *body, int ystart)
{
BODYTYPE *body1;
int i;
@@ -551,8 +531,7 @@
/* output an index entry */
-outindex(id)
-IDTYPE *id;
+int outindex(IDTYPE *id)
{
if(id!=NULL)
fprintf(outf,"\\rail@index{%s}\n",id->name);
@@ -560,9 +539,7 @@
/* make a new rule list */
-RULETYPE *newrule(id,body)
-IDTYPE *id;
-BODYTYPE *body;
+RULETYPE *newrule(IDTYPE *id, BODYTYPE *body)
{
RULETYPE *rule;
@@ -576,8 +553,7 @@
/* free a rule list */
-freerule(rule)
-RULETYPE *rule;
+void freerule(RULETYPE *rule)
{
RULETYPE *rulep;
@@ -591,8 +567,7 @@
/* add two rule lists */
-RULETYPE *addrule(rule1,rule2)
-RULETYPE *rule1, *rule2;
+RULETYPE *addrule(RULETYPE *rule1, RULETYPE *rule2)
{
RULETYPE *rulep;
@@ -609,8 +584,7 @@
/* output a rule list */
-outrule(rule)
-RULETYPE *rule;
+void outrule(RULETYPE *rule)
{
while(rule!=NULL) {
@@ -625,8 +599,7 @@
/* look up an identifier */
-IDTYPE *lookup(name)
-char *name;
+IDTYPE *lookup(char *name)
{
IDTYPE *idp, **idq;
@@ -648,8 +621,7 @@
/* delete an identifier */
-delete(id)
-IDTYPE *id;
+void delete(IDTYPE *id)
{
IDTYPE *idp, **idq;
@@ -665,7 +637,7 @@
/* check that there are no undefined identifiers */
-checkdefs()
+void checkdefs(void)
{
IDTYPE *id;
@@ -676,8 +648,7 @@
/* complain about an undefined identifier */
-undef(id)
-IDTYPE *id;
+void undef(IDTYPE *id)
{
if(chkgram)
error("undefined identifier '%s'",id->name);
@@ -685,8 +656,7 @@
/* complain about a redefined identifier */
-redef(id)
-IDTYPE *id;
+void redef(IDTYPE *id)
{
if(chkgram)
error("redefined identifier '%s'",id->name);
@@ -694,8 +664,7 @@
/* display an error */
-error(f,s)
-char *f, *s;
+void error(char *f, char *s)
{
if(newline) {
printf("\n");
@@ -713,8 +682,7 @@
fprintf(stderr,"\n");
}
-fatal(f,s)
-char *f,*s;
+void fatal(char *f, char *s)
{
error(f,s);
--- a/rail.h
+++ b/rail.h
@@ -68,22 +68,31 @@
extern IDTYPE *errorid;
-extern char *mcheck();
+extern char *mcheck(char *s);
-extern BODYTYPE *newbody();
-extern freebody();
-extern int isemptybody();
-extern BODYTYPE *addbody();
-extern BODYTYPE *revbody();
-
-extern RULETYPE *newrule();
-extern freerule();
-extern RULETYPE *addrule();
-extern outrule();
-
-extern IDTYPE *lookup();
-extern delete();
-
-extern undef();
-extern redef();
-extern error();
+extern BODYTYPE *newbody(int kind, BODYTYPE *body1, BODYTYPE *body2);
+extern void freebody(BODYTYPE *body);
+extern int isemptybody(BODYTYPE *body);
+extern BODYTYPE *addbody(int kind, BODYTYPE *body1, BODYTYPE *body2);
+extern BODYTYPE *revbody(BODYTYPE *body);
+extern void posbody(BODYTYPE *body, int ystart);
+extern void fmtbody(BODYTYPE *body, char *cent, char arrow);
+
+extern RULETYPE *newrule(IDTYPE *id, BODYTYPE *body);
+extern void freerule(RULETYPE *rule);
+extern RULETYPE *addrule(RULETYPE *rule1, RULETYPE *rule2);
+extern void outrule(RULETYPE *rule);
+
+extern IDTYPE *lookup(char *name);
+extern void delete(IDTYPE *id);
+
+extern void undef(IDTYPE *id);
+extern void redef(IDTYPE *id);
+extern void error(char *f, char *s);
+extern void yyerror(char *s);
+extern int yywrap(void);
+
+int setopt(char c, char *s);
+void usage(void);
+void checkdefs(void);
+void fatal(char *f, char *s);

21
dev-tex/rail/files/rail-1.2_p1-makefile.patch Normal file
View File

@@ -0,0 +1,21 @@
Correct Makefile, enabling parallel build.
--- a/Makefile
+++ b/Makefile
@@ -51,11 +53,15 @@
rail.o: patchlevel.h
+.PHONY: gram.c gram.h clean
+
-gram.c gram.h: y.tab.c y.tab.h
+gram.c: y.tab.c
cmp -s gram.c y.tab.c || cp y.tab.c gram.c
+
+gram.h: y.tab.h
cmp -s gram.h y.tab.h || cp y.tab.h gram.h
-y.tab.c y.tab.h y.output: gram.y
+y.tab.c y.tab.h y.output &: gram.y
$(YACC) $(YFLAGS) -dv gram.y
rail: $(OBJS)

11
dev-tex/rail/rail-1.2_p1-r1.ebuild → dev-tex/rail/rail-1.2_p1-r2.ebuild
View File

@@ -1,7 +1,7 @@
# Copyright 1999-2024 Gentoo Authors
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
EAPI=8
inherit latex-package toolchain-funcs
@@ -18,8 +18,13 @@ BDEPEND="app-arch/unzip
app-alternatives/yacc
app-alternatives/lex"
PATCHES=(
"${FILESDIR}/${P}-C23.patch"
"${FILESDIR}/${P}-makefile.patch"
)
src_compile() {
emake -j1 \
emake \
CC="$(tc-getCC)" \
CFLAGS="-DYYDEBUG ${CFLAGS} ${LDFLAGS}" \
rail rail.dvi

32
net-wireless/bss/bss-0.8-r3.ebuild Normal file
View File

@@ -0,0 +1,32 @@
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit toolchain-funcs
DESCRIPTION="Bluetooth stack smasher / fuzzer"
HOMEPAGE="http://securitech.homeunix.org/blue/"
SRC_URI="http://securitech.homeunix.org/blue/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86"
DEPEND="net-wireless/bluez"
RDEPEND="${DEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-Makefile.patch
"${FILESDIR}"/${P}-includes.patch
)
src_configure() {
tc-export CC
}
src_install() {
dosbin bss
dodoc AUTHOR BUGS CHANGELOG CONTRIB NOTES README TODO \
replay_packet/replay_l2cap_packet.c
}

3
net-wireless/bss/files/bss-0.8-Makefile.patch
View File

@@ -1,3 +1,4 @@
Make build system respect CFLAGS and PREFIX
https://bugs.gentoo.org/725228
--- a/Makefile
+++ b/Makefile
@@ -25,7 +26,7 @@ https://bugs.gentoo.org/725228
- $(CC) -c $(L2P_SRC)
- $(CC) -c $(REP_SRC)
- $(CC) $(BSS_TMP) $(L2P_TMP) $(REP_TMP) -o $(BSS_OBJ) $(CFLAGS) $(BSS_FLAGS) $(BSS_LIBS)
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c $(BSS_SRC)
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c $(BSS_SRC)
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c $(L2P_SRC)
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c $(REP_SRC)
+ $(CC) $(LDFLAGS) $(BSS_TMP) $(L2P_TMP) $(REP_TMP) -o $(BSS_OBJ) $(CFLAGS) $(BSS_LIBS)

24
net-wireless/bss/files/bss-0.8-includes.patch Normal file
View File

@@ -0,0 +1,24 @@
Add missing includes for compilation with C23
https://bugs.gentoo.org/880799
diff '--color=auto' -ru bss-0.8.old/bss.c bss-0.8/bss.c
--- a/bss.c 2025-03-28 23:12:14.780857512 +0300
+++ b/bss.c 2025-03-28 23:13:44.003579006 +0300
@@ -34,6 +34,7 @@
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
+#include <time.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/socket.h>
diff '--color=auto' -ru bss-0.8.old/replace.c bss-0.8/replace.c
--- a/replace.c 2025-03-28 23:12:14.780857512 +0300
+++ b/replace.c 2025-03-28 23:14:07.107852000 +0300
@@ -10,6 +10,7 @@
// Modifications by Ollie Whitehouse <ol at uncon dot org>
//
#include <stdio.h>
+#include <string.h>
char *replace(char *string, char *oldpiece, char *newpiece) {

35
sci-biology/bamtools/bamtools-2.5.2-r1.ebuild Normal file
View File

@@ -0,0 +1,35 @@
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit cmake
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
HOMEPAGE="https://github.com/pezmaster31/bamtools"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
else
SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
KEYWORDS="~amd64 ~x86"
fi
LICENSE="MIT"
SLOT="0/${PV}" # no stable ABI yet
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
sys-libs/zlib:="
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
PATCHES=( "${FILESDIR}"/"${P}-cmake.patch" )
src_prepare() {
# delete bundled libs, just to be safe
rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
cmake_src_prepare
}

4
sci-biology/bamtools/bamtools-9999.ebuild
View File

@@ -1,7 +1,7 @@
# Copyright 1999-2020 Gentoo Authors
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
EAPI=8
inherit cmake

26
sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch Normal file
View File

@@ -0,0 +1,26 @@
Fix for CMake 4
https://bugs.gentoo.org/951630
https://github.com/pezmaster31/bamtools/commit/a610d2c0150d4b821aa4096e57eb77e4b0c14aa7
From a610d2c0150d4b821aa4096e57eb77e4b0c14aa7 Mon Sep 17 00:00:00 2001
From: David Seifert <SoapZA@users.noreply.github.com>
Date: Sat, 31 Jul 2021 15:46:18 +0200
Subject: [PATCH] CMakeLists.txt: CMake >= 3.11
* `INCLUDE_GUARD_NAME` in `GENERATE_EXPORT_HEADER()` was added in 3.11
Fixes: #216
---
CMakeLists.txt | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fc3a80c..2382802 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,5 @@
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.11)
+# need 3.11 for INCLUDE_GUARD_NAME in GENERATE_EXPORT_HEADER
project(
BamTools

7
sci-chemistry/moldy/moldy-2.16e-r2.ebuild
View File

@@ -1,9 +1,9 @@
# Copyright 1999-2023 Gentoo Authors
# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit toolchain-funcs
inherit flag-o-matic toolchain-funcs
DESCRIPTION="Molecular dynamics simulations platform"
HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html"
@@ -29,6 +29,9 @@ src_prepare() {
}
src_configure() {
# bug #944874
append-cflags -std=gnu17
#Individuals may want to edit the OPT* variables below.
#From the READ.ME:
#You may need to "hand-tune" compiler or optimization options,