[gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/, sci-biology/seqan/files/
commit: e7bef38a50bcb75a40e9738e75bdfc37a9ded969
Author: Andreas Sturmlechner gentoo org>
AuthorDate: Sun Mar 7 16:31:44 2021 +
Commit: Andreas Sturmlechner gentoo org>
CommitDate: Sun Mar 7 18:53:20 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e7bef38a
sci-biology/seqan: Port to EAPI-7, cmake.eclass, https
- Fix cmake config install path
- Fix pkgconfig install path
- Fix examples install path
- Fix build with BUILD_SHARED_LIBS=ON default
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andreas Sturmlechner gentoo.org>
.../seqan-2.4.0-cmake-add_library-static.patch | 38 ++
.../seqan/files/seqan-2.4.0-installpaths.patch | 24 ++
.../{seqan-2.4.0.ebuild => seqan-2.4.0-r1.ebuild} | 36 +---
sci-biology/seqan/seqan-2.4.0.ebuild | 27 ++-
4 files changed, 88 insertions(+), 37 deletions(-)
diff --git a/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
new file mode 100644
index 000..7617d9f9a66
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
@@ -0,0 +1,38 @@
+From 1877d143ad9f42d80692073538e3f32b37e15967 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner
+Date: Sun, 7 Mar 2021 19:35:44 +0100
+Subject: [PATCH] Fix linking with BUILD_SHARED_LIBS=ON default in EAPI-7
+
+Signed-off-by: Andreas Sturmlechner
+---
+ apps/mason2/CMakeLists.txt | 2 +-
+ apps/pair_align/lib/CMakeLists.txt | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/apps/mason2/CMakeLists.txt b/apps/mason2/CMakeLists.txt
+index 2218187..c042ea7 100644
+--- a/apps/mason2/CMakeLists.txt
b/apps/mason2/CMakeLists.txt
+@@ -52,7 +52,7 @@ add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
+ add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
+
+ # We define a library for the reusable parts of Mason.
+-add_library (mason_sim
++add_library (mason_sim STATIC
+ external_split_merge.h
+ external_split_merge.cpp
+ fragment_generation.h
+diff --git a/apps/pair_align/lib/CMakeLists.txt
b/apps/pair_align/lib/CMakeLists.txt
+index 75faef7..3b9576e 100644
+--- a/apps/pair_align/lib/CMakeLists.txt
b/apps/pair_align/lib/CMakeLists.txt
+@@ -53,5 +53,5 @@ endforeach(GAPS_T)
+
+ # This part can be used instead for cmake version greater or equal to 2.8.8.
+ # This requires to update the script above as well.
+-add_library(pair_align_lib pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
++add_library(pair_align_lib STATIC pair_align_lib.cpp pair_align_lib.h
${LIB_TARGETS})
+ target_link_libraries(pair_align_lib ${SEQAN_LIBRARIES})
+--
+2.30.1
+
diff --git a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
new file mode 100644
index 000..35f0718f9d8
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
@@ -0,0 +1,24 @@
+--- a/util/cmake/SeqAnBuildSystem.cmake2018-01-11 12:32:45.591134000
+0100
b/util/cmake/SeqAnBuildSystem.cmake2018-01-11 12:51:55.193282581
+0100
+@@ -399,10 +399,10 @@
+ # Install pkg-config file, except on Windows.
+ if (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+ configure_file("util/pkgconfig/seqan.pc.in"
"${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY)
+-install(FILES
"${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc"
DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig)
++install(FILES
"${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc"
DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+ # Install FindSeqAn TODO(h-2) rename seqan-config.cmake to
seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle
+-install(FILES
"${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION
${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/)
++install(FILES
"${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION
${CMAKE_INSTALL_LIBDIR}/cmake/seqan2/)
+
+ # Install headers
+ file (GLOB HEADERS
+@@ -473,7 +473,7 @@
+ set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc"
CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE)
+ endif ()
+ set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}")
+-set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}")
++set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/examples/")
+ endif ()
+ endmacro (seqan_setup_install_vars)
+
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild
b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
similarity index 67%
copy from sci-biology/seqan/seqan-2.4.0.ebuild
copy to sci-biology/seqan/seqan-2.4.0-r1.ebuild
[gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/, sci-biology/seqan/files/
commit: bc0e06623a12a5686bc1fd87f95ab8d3344eab78
Author: David Seifert gentoo org>
AuthorDate: Sat Apr 9 18:56:34 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Apr 9 18:57:11 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bc0e0662
sci-biology/seqan: Remove old and broken ebuilds
Package-Manager: portage-2.2.28
sci-biology/seqan/Manifest | 2 -
sci-biology/seqan/files/seqan-2.0.0-zlib.patch | 15 ---
sci-biology/seqan/seqan-1.3.1-r1.ebuild| 50 -
sci-biology/seqan/seqan-1.4.2.ebuild | 60 --
sci-biology/seqan/seqan-2.0.0.ebuild | 51 --
5 files changed, 178 deletions(-)
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index d7fdca8..ab534dc 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,4 +1,2 @@
-DIST seqan-1.3.1.zip 8787521 SHA256
87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512
dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4
WHIRLPOOL
5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b
DIST seqan-src-1.4.2.tar.gz 120601994 SHA256
2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512
dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
WHIRLPOOL
3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0
-DIST seqan-src-2.0.0.tar.gz 115731415 SHA256
69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512
9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a
WHIRLPOOL
afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4
DIST seqan-src-2.1.1.tar.gz 110874831 SHA256
df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c SHA512
b82eb93129921eb867785add46d63f667c07f40556cd431acc73489c1032c19ff65b49415697415bdc7b788ffb8a80ab8d9e987fa38fc39c2399ff265fdc333f
WHIRLPOOL
b684d14db0cf22c7d1428c589293ee69674225e5b91845532f3135950a5a6178d4434b783177b3622e8661247856a20b42a7fb9275df4324124d2b21d728790f
diff --git a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
deleted file mode 100644
index de14e9d..000
--- a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- include/seqan/stream/zipstream/zutil.h | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/include/seqan/stream/zipstream/zutil.h
b/include/seqan/stream/zipstream/zutil.h
-index 2806344..f8b41e6 100644
a/include/seqan/stream/zipstream/zutil.h
-+++ b/include/seqan/stream/zipstream/zutil.h
-@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by
2-zlib_error */
-
- /* functions */
-
-+#define OF(x) x
- #ifdef HAVE_STRERROR
-extern char *strerror OF((int));
- # define zstrerror(errnum) strerror(errnum)
diff --git a/sci-biology/seqan/seqan-1.3.1-r1.ebuild
b/sci-biology/seqan/seqan-1.3.1-r1.ebuild
deleted file mode 100644
index 2bcb7f6..000
--- a/sci-biology/seqan/seqan-1.3.1-r1.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils flag-o-matic python-single-r1
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/;
-SRC_URI="http://ftp.seqan.de/releases/${P}.zip;
-
-SLOT="0"
-LICENSE="BSD GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
- ~sci-biology/samtools-0.1.19"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${P}/cmake
-
-pkg_setup() {
- if [[ ${MERGE_TYPE} != binary ]]; then
- [[ $(gcc-major-version) -gt 4 ]] || \
- ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -gt 8
]] ) \
- && die "Sorry, but gcc 4.9 or higher is unsupported"
- fi
-}
-
-src_prepare() {
- append-cppflags -I"${EPREFIX}/usr/include/bam"
- rm -rf "${S}"/../lib/samtools || die
-
- sed \
- -e "s:docs:docs/.:g" \
- -e "/DESTINATION/s:seqan:doc/${PF}/html:g" \
- -i CMakeLists.txt || die
-
- sed \
- -e "/DESTINATION/s:bin):share/${PN}):g" \
- -i apps/CMakeLists.txt || die
-
- cmake-utils_src_prepare
-}
diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild
b/sci-biology/seqan/seqan-1.4.2.ebuild
deleted file mode 100644
index 4b9740c..000
--- a/sci-biology/seqan/seqan-1.4.2.ebuild
+++
[gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/, sci-biology/seqan/files/
commit: 6cd6d4f4e02a28fd020929485c88caaebc6b84c5
Author: David Seifert gentoo org>
AuthorDate: Sat Apr 9 18:23:54 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Apr 9 18:57:02 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6cd6d4f4
sci-biology/seqan: SLOT 1.4 and 2.1, allow for parallel installation
Gentoo-Bug: 566502
* EAPI=6
Package-Manager: portage-2.2.28
sci-biology/seqan/Manifest | 1 +
.../seqan/files/seqan-1.4.2-buildsystem.patch | 30 +
sci-biology/seqan/files/seqan.pc.in| 10 +++
sci-biology/seqan/seqan-1.4.2-r1.ebuild| 71 +
sci-biology/seqan/seqan-2.1.1.ebuild | 74 ++
5 files changed, 186 insertions(+)
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 1348715..d7fdca8 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,3 +1,4 @@
DIST seqan-1.3.1.zip 8787521 SHA256
87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512
dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4
WHIRLPOOL
5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b
DIST seqan-src-1.4.2.tar.gz 120601994 SHA256
2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512
dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
WHIRLPOOL
3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0
DIST seqan-src-2.0.0.tar.gz 115731415 SHA256
69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512
9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a
WHIRLPOOL
afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4
+DIST seqan-src-2.1.1.tar.gz 110874831 SHA256
df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c SHA512
b82eb93129921eb867785add46d63f667c07f40556cd431acc73489c1032c19ff65b49415697415bdc7b788ffb8a80ab8d9e987fa38fc39c2399ff265fdc333f
WHIRLPOOL
b684d14db0cf22c7d1428c589293ee69674225e5b91845532f3135950a5a6178d4434b783177b3622e8661247856a20b42a7fb9275df4324124d2b21d728790f
diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
new file mode 100644
index 000..4c7893e
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
@@ -0,0 +1,30 @@
+Add default disabled flag to enable generation of documentation.
+For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a
+support library for legacy tools.
+
+--- seqan-1.4.2/CMakeLists.txt
seqan-1.4.2/CMakeLists.txt
+@@ -123,10 +123,12 @@
+ add_subdirectory (core)
+ message (STATUS "Configuring extras")
+ add_subdirectory (extras)
++if (NOT SEQAN_NO_DOX)
+ message (STATUS "Configuring docs")
+ add_subdirectory (docs)
+ message (STATUS "Configuring manual")
+ add_subdirectory (manual)
++endif ()
+ message (STATUS "Configuring sandbox")
+ add_subdirectory (sandbox)
+ message (STATUS "Configuring util/py_lib")
+--- seqan-1.4.2/docs/main.py
seqan-1.4.2/docs/main.py
+@@ -123,7 +123,7 @@
+
+ # Done, print end message.
+ print 'Documentation created/updated.'
+-return dddoc_html.WARNING_COUNT > 0
++return 0
+
+
+ def main(argv):
diff --git a/sci-biology/seqan/files/seqan.pc.in
b/sci-biology/seqan/files/seqan.pc.in
new file mode 100644
index 000..f917fae
--- /dev/null
+++ b/sci-biology/seqan/files/seqan.pc.in
@@ -0,0 +1,10 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${prefix}
+includedir=${prefix}/include
+
+Name: @CMAKE_PROJECT_NAME@
+Description: C++ library for biological sequence analysis
+URL: http://www.seqan.de
+Version: @SEQAN_VERSION_STRING@
+Requires: zlib
+Cflags: -I${includedir}
diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild
b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
new file mode 100644
index 000..28e6cad
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/;
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz;
+
+SLOT="$(get_version_component_range 1-2)"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cpu_flags_x86_sse4_1 test"
+DEPEND="sys-libs/zlib
+ app-arch/bzip2
+ test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
