* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2019-02-15 21:09 Brian Evans
0 siblings, 0 replies; 7+ messages in thread
From: Brian Evans @ 2019-02-15 21:09 UTC (permalink / raw
To: gentoo-commits
commit: 3a0588753c86399d7c514bc34d22f48687cbcbfe
Author: Brian Evans <grknight <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 15 21:09:14 2019 +0000
Commit: Brian Evans <grknight <AT> gentoo <DOT> org>
CommitDate: Fri Feb 15 21:09:14 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3a058875
sci-biology/ucsc-genome-browser: Revbump to fix dependencies
Non-maintainer commit
Closes: https://bugs.gentoo.org/667578
Closes: https://bugs.gentoo.org/666050
Package-Manager: Portage-2.3.60, Repoman-2.3.12
Signed-off-by: Brian Evans <grknight <AT> gentoo.org>
...rowser-260.ebuild => ucsc-genome-browser-260-r1.ebuild} | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
similarity index 93%
rename from sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
rename to sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
index 7ce025b2ae9..9b53170b1e8 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
inherit toolchain-funcs flag-o-matic webapp
@@ -18,16 +18,18 @@ REQUIRED_USE="server? ( mysql )"
WEBAPP_MANUAL_SLOT="yes"
-DEPEND="
- app-arch/unzip
+RDEPEND="
+ dev-libs/openssl:0=
+ media-libs/libpng:0=
!<sci-biology/ucsc-genome-browser-223
- mysql? ( virtual/mysql )
+ mysql? ( dev-db/mysql-connector-c:0= )
server? ( virtual/httpd-cgi )" # TODO: test with other webservers
-RDEPEND="${DEPEND}"
+DEPEND="${RDEPEND} app-arch/unzip"
S="${WORKDIR}/kent"
src_prepare() {
+ default
use server && webapp_src_preinst
sed \
-e 's/-Werror//' \
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2021-03-03 21:19 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2021-03-03 21:19 UTC (permalink / raw
To: gentoo-commits
commit: 7352a350f876c61ef8fec8e50da226330dfdf6f3
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 3 21:17:26 2021 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Wed Mar 3 21:19:45 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7352a350
sci-biology/ucsc-genome-browser: add gcc 10 workaround
Closes: https://bugs.gentoo.org/708064
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
index 9b53170b1e8..0423f509cec 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -30,7 +30,12 @@ S="${WORKDIR}/kent"
src_prepare() {
default
+
use server && webapp_src_preinst
+
+ # bug #708064
+ append-flags -fcommon
+
sed \
-e 's/-Werror//' \
-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2021-06-11 0:29 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2021-06-11 0:29 UTC (permalink / raw
To: gentoo-commits
commit: bbaa144be1ae371f080bd71813b288fa3f1ff51b
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 11 00:26:53 2021 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Jun 11 00:29:14 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bbaa144b
sci-biology/ucsc-genome-browser: fix VariableScope ((E)ROOT)
Signed-off-by: Sam James <sam <AT> gentoo.org>
.../ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
index 0423f509cec..f0bb0676ae8 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -64,14 +64,16 @@ src_compile() {
export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
- use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
- MYSQLINC="${ROOT}usr/include/mysql"
+ # TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7
+ # (and ideally use pkg-config here)
+ use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
+ MYSQLINC="${EPREFIX%/}/usr/include/mysql"
use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
- mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die
- use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT"
+ mkdir -p "${BINDIR}" "${SCRIPTS}" "${ENCODE_PIPELINE_BIN}" || die
+ use server && mkdir -p "${CGI_BIN}" "${DOCUMENTROOT}"
emake -C src clean
emake -C src/lib
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2024-06-01 23:21 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2024-06-01 23:21 UTC (permalink / raw
To: gentoo-commits
commit: 443760b1a3018610b10bbf69a6b4b52331d4fc95
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 1 23:20:12 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jun 1 23:20:12 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=443760b1
sci-biology/ucsc-genome-browser: BDEPEND on cpio
Closes: https://bugs.gentoo.org/688748
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
index 769a4481eeee..ef96f491fb51 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
@@ -27,7 +27,10 @@ RDEPEND="
server? ( virtual/httpd-cgi )
"
DEPEND="${RDEPEND}"
-BDEPEND="app-arch/unzip"
+BDEPEND="
+ app-alternatives/cpio
+ app-arch/unzip
+"
pkg_setup() {
use server && webapp_pkg_setup
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2024-06-01 23:21 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2024-06-01 23:21 UTC (permalink / raw
To: gentoo-commits
commit: cdb7db92ed8e655db3e0af0077aca1bd90a2d352
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 1 23:15:44 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jun 1 23:15:44 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cdb7db92
sci-biology/ucsc-genome-browser: fix USE=-server
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
index 85fa73e1b509..2219008438c1 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -18,16 +18,22 @@ REQUIRED_USE="server? ( mysql )"
WEBAPP_MANUAL_SLOT="yes"
+# TODO: test with other webservers
RDEPEND="
dev-libs/openssl:0=
media-libs/libpng:0=
!<sci-biology/ucsc-genome-browser-223
mysql? ( dev-db/mysql-connector-c:0= )
- server? ( virtual/httpd-cgi )" # TODO: test with other webservers
+ server? ( virtual/httpd-cgi )
+"
DEPEND="${RDEPEND} app-arch/unzip"
S="${WORKDIR}/kent"
+pkg_setup() {
+ use server && webapp_pkg_setup
+}
+
src_prepare() {
default
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2024-06-01 23:21 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2024-06-01 23:21 UTC (permalink / raw
To: gentoo-commits
commit: b7cf0f3d7cbe8fa13b188d50b16f47fd726c4e2a
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 1 23:15:05 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jun 1 23:15:05 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b7cf0f3d
sci-biology/ucsc-genome-browser: workaround modern C issues
Build with -std=gnu89 as it has many issues.
Closes: https://bugs.gentoo.org/831491
Closes: https://bugs.gentoo.org/919200
Closes: https://bugs.gentoo.org/921261
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
index f0bb0676ae85..85fa73e1b509 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -35,6 +35,8 @@ src_prepare() {
# bug #708064
append-flags -fcommon
+ # bug #831491, bug #919200, bug #921261
+ append-flags -std=gnu89
sed \
-e 's/-Werror//' \
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/
@ 2024-06-01 23:21 Sam James
0 siblings, 0 replies; 7+ messages in thread
From: Sam James @ 2024-06-01 23:21 UTC (permalink / raw
To: gentoo-commits
commit: 7955b031affbce3bce05db8f44802c37a34c6c46
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 1 23:18:24 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jun 1 23:19:09 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7955b031
sci-biology/ucsc-genome-browser: EAPI 8
Signed-off-by: Sam James <sam <AT> gentoo.org>
...r1.ebuild => ucsc-genome-browser-260-r2.ebuild} | 26 ++++++++++------------
1 file changed, 12 insertions(+), 14 deletions(-)
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
similarity index 88%
rename from sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
rename to sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
index 2219008438c1..769a4481eeee 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
@@ -1,34 +1,33 @@
# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
+WEBAPP_MANUAL_SLOT="yes"
+# TODO: use WEBAPP_OPTIONAL?
inherit toolchain-funcs flag-o-matic webapp
DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
HOMEPAGE="http://genome.ucsc.edu/"
SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
+S="${WORKDIR}/kent"
LICENSE="blat"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="+mysql +server static-libs"
-
REQUIRED_USE="server? ( mysql )"
-WEBAPP_MANUAL_SLOT="yes"
-
# TODO: test with other webservers
RDEPEND="
- dev-libs/openssl:0=
- media-libs/libpng:0=
+ dev-libs/openssl:=
+ media-libs/libpng:=
!<sci-biology/ucsc-genome-browser-223
- mysql? ( dev-db/mysql-connector-c:0= )
+ mysql? ( dev-db/mysql-connector-c:= )
server? ( virtual/httpd-cgi )
"
-DEPEND="${RDEPEND} app-arch/unzip"
-
-S="${WORKDIR}/kent"
+DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
pkg_setup() {
use server && webapp_pkg_setup
@@ -72,10 +71,9 @@ src_compile() {
export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
- # TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7
- # (and ideally use pkg-config here)
- use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
- MYSQLINC="${EPREFIX%/}/usr/include/mysql"
+ # TODO: use pkg-config here
+ use mysql && export MYSQLLIBS="-L${ESYSROOT}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
+ MYSQLINC="${ESYSROOT}/usr/include/mysql"
use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
^ permalink raw reply related [flat|nested] 7+ messages in thread
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