[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Brian Evans]

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//' \

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Sam James]

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" \

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Sam James]

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

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Sam James]

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

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Sam James]

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
 

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Sam James]

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//' \

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ucsc-genome-browser/

[Sam James]

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"