* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-01-10 19:09 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 19:09 UTC (permalink / raw
To: gentoo-commits
commit: c455313102692e7398687f10eb9e7aaafa7da9f2
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 19:09:19 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 19:09:19 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c4553131
sci-biology/ncbi-blast+: add RESTRICT="!test? ( test )"
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 12b249c8b..a8e257086 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -29,7 +29,7 @@ IUSE="
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
-#KEYWORDS=""
+RESTRICT="!test? ( test )"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 85b764cc4..b14255938 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -28,7 +28,7 @@ IUSE="
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
-#KEYWORDS=""
+RESTRICT="!test? ( test )"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 7709cab39..ad927b0b1 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -28,7 +28,7 @@ IUSE="
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
-#KEYWORDS=""
+RESTRICT="!test? ( test )"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 641b37467..b71c3d48d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -29,7 +29,7 @@ IUSE="
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
-#KEYWORDS=""
+RESTRICT="!test? ( test )"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 466101138..7f63bf77d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -29,7 +29,7 @@ IUSE="
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
-#KEYWORDS=""
+RESTRICT="!test? ( test )"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2022-01-25 19:15 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 19:15 UTC (permalink / raw
To: gentoo-commits
commit: 2b9013674acbf9152ff846053a545469c5bfef41
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 16:22:37 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 16:22:37 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b901367
sci-biology/ncbi-blast+: drop non-existing blocker
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 3 +--
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 3 +--
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 3 +--
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 3 +--
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 3 +--
5 files changed, 5 insertions(+), 10 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 623759901..eba2877e2 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -37,7 +37,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index d4ae93742..a2ff79859 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,7 +32,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index f0269f0b5..b7840175d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,7 +32,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index b232894b4..4498c9cf6 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -33,7 +33,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 623759901..eba2877e2 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -37,7 +37,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-12-16 11:07 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-12-16 11:07 UTC (permalink / raw
To: gentoo-commits
commit: 9abf1096ce447b6059e163b52f759d59fc9f0b84
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 16 11:05:01 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Dec 16 11:05:01 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9abf1096
sci-biology/ncbi-blast+: fix MissingInherits
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 7c8eec1a7..d4ae93742 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -76,6 +76,10 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}/c++"
# ncbi-blast-2.2.30+-src/c++
+PATCHES=(
+ "${FILESDIR}"/"${P}"__fix_lib_deps.patch
+)
+
src_prepare() {
# filter-ldflags -Wl,--as-needed
# append-ldflags -Wl,--no-undefined
@@ -117,7 +121,6 @@ src_prepare() {
## epatch ${PATCHES[@]}
# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- epatch "${FILESDIR}"/"${P}"__fix_lib_deps.patch
# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-08-31 9:45 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-08-31 9:45 UTC (permalink / raw
To: gentoo-commits
commit: fa19a4819a3604a5fa02aa0b3e9075b116c9b40f
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:37:58 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:37:58 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa19a481
sci-biology/ncbi-blast+: add MissingUseDepDefault
Package-Manager: Portage-3.0.22, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index a8015cf70..94c273172 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:=[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index b17d7b00e..783f3a266 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:=[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 58fbcd288..7874c2295 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:=[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 29ba54e42..c04fb4cae 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -34,7 +34,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:=[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index a8015cf70..94c273172 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:=[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
^ permalink raw reply related [flat|nested] 23+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-07-03 10:44 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-07-03 10:44 UTC (permalink / raw
To: gentoo-commits
commit: 73a518c3c059b290cb046541f76cde0a55d8156d
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 3 10:44:35 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jul 3 10:44:35 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=73a518c3
sci-biology/ncbi-blast+: allow newer versions of sys-libs/db
Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 40f338bc3..a8015cf70 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 08103e703..b17d7b00e 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index fbd1a9d4c..58fbcd288 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index ec3426cfb..29ba54e42 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -34,7 +34,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 40f338bc3..a8015cf70 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
^ permalink raw reply related [flat|nested] 23+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-03-16 18:57 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-03-16 18:57 UTC (permalink / raw
To: gentoo-commits
commit: 8d30c38957773846cdb1cef9b1be0f3229824a39
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:53:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:53:20 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8d30c389
Revert "sci-biology/ncbi-blast+: drop py2 only versions"
This reverts commit 185edf7edae700779fb362e1adba1042514420da.
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
...-blast+-2.8.1.ebuild => ncbi-blast+-2.2.30.ebuild} | 19 +++++--------------
...-blast+-2.8.1.ebuild => ncbi-blast+-2.2.31.ebuild} | 16 +++++-----------
...i-blast+-2.8.1.ebuild => ncbi-blast+-2.6.0.ebuild} | 7 +++----
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
4 files changed, 14 insertions(+), 30 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
similarity index 95%
copy from sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
copy to sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 40f338bc3..05c844b1c 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -3,14 +3,13 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
@@ -67,8 +66,7 @@ DEPEND="
xpm? ( x11-libs/libXpm )
dev-libs/lzo
app-arch/bzip2
- dev-libs/libpcre
- dev-db/lmdb"
+ dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
# Intentionally omitted USE flags:
# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
@@ -124,10 +122,7 @@ src_prepare() {
## epatch ${PATCHES[@]}
# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.patch
+ epatch "${FILESDIR}"/"${P}"__fix_lib_deps.patch
# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
@@ -241,9 +236,7 @@ src_configure() {
$(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
- #
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
- # $(use_with opengl glew-mx)
+ $(use_with opengl glew-mx)
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
@@ -268,8 +261,6 @@ src_configure() {
$(use_with curl curl "${EPREFIX}/usr")
# $(use_with X x "${EPREFIX}/usr")
# $(use_with X x) # there is no --with-x option
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
- --without-vdb
)
# http://www.ncbi.nlm.nih.gov/books/NBK7167/
@@ -289,7 +280,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
- ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
+ ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
#--without-debug \
# --with-bin-release \
# --with-bincopy \
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
similarity index 96%
copy from sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
copy to sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 40f338bc3..0118086c8 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -3,17 +3,16 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
@@ -67,8 +66,7 @@ DEPEND="
xpm? ( x11-libs/libXpm )
dev-libs/lzo
app-arch/bzip2
- dev-libs/libpcre
- dev-db/lmdb"
+ dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
# Intentionally omitted USE flags:
# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
@@ -241,9 +239,7 @@ src_configure() {
$(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
- #
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
- # $(use_with opengl glew-mx)
+ $(use_with opengl glew-mx)
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
@@ -268,8 +264,6 @@ src_configure() {
$(use_with curl curl "${EPREFIX}/usr")
# $(use_with X x "${EPREFIX}/usr")
# $(use_with X x) # there is no --with-x option
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
- --without-vdb
)
# http://www.ncbi.nlm.nih.gov/books/NBK7167/
@@ -289,7 +283,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
- ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
+ ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
#--without-debug \
# --with-bin-release \
# --with-bincopy \
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
similarity index 99%
copy from sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
copy to sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 40f338bc3..ccedf666d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
@@ -67,8 +67,7 @@ DEPEND="
xpm? ( x11-libs/libXpm )
dev-libs/lzo
app-arch/bzip2
- dev-libs/libpcre
- dev-db/lmdb"
+ dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
# Intentionally omitted USE flags:
# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
@@ -289,7 +288,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
- ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
+ ${myconf[@]} || die
#--without-debug \
# --with-bin-release \
# --with-bincopy \
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 40f338bc3..72f8fd0b1 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-03-16 18:57 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-03-16 18:57 UTC (permalink / raw
To: gentoo-commits
commit: 887ddf2183097cf431da81cdcc4f693d268128bb
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:57:50 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:57:50 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=887ddf21
sci-biology/ncbi-blast+: drop python support on old
is python2
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 12 ++++--------
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 12 ++++--------
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 12 ++++--------
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
4 files changed, 13 insertions(+), 25 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 05c844b1c..08103e703 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -3,9 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit eutils flag-o-matic multilib toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
@@ -25,13 +23,11 @@ IUSE="
debug static-libs static threads pch
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
RESTRICT="!test? ( test )"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
# sys-libs/db should be compiled with USE=cxx
DEPEND="
<sys-devel/gcc-10:=
@@ -48,7 +44,6 @@ DEPEND="
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
gnutls? ( net-libs/gnutls )
- python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
icu? ( dev-libs/icu )
expat? ( dev-libs/expat )
@@ -242,7 +237,8 @@ src_configure() {
$(use_with freetype freetype "${EPREFIX}/usr")
# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
$(usex odbc --with-odbc="${EPREFIX}/usr" "")
- $(use_with python python "${EPREFIX}/usr")
+ # is python2
+ --without-python
$(use_with boost boost "${EPREFIX}/usr")
$(use_with sqlite sqlite3 "${EPREFIX}/usr")
$(use_with icu icu "${EPREFIX}/usr")
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 0118086c8..fbd1a9d4c 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -3,9 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit eutils flag-o-matic multilib toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
@@ -25,13 +23,11 @@ IUSE="
debug static-libs static threads pch
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
RESTRICT="!test? ( test )"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
# sys-libs/db should be compiled with USE=cxx
DEPEND="
<sys-devel/gcc-10:=
@@ -48,7 +44,6 @@ DEPEND="
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
gnutls? ( net-libs/gnutls )
- python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
icu? ( dev-libs/icu )
expat? ( dev-libs/expat )
@@ -245,7 +240,8 @@ src_configure() {
$(use_with freetype freetype "${EPREFIX}/usr")
# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
$(usex odbc --with-odbc="${EPREFIX}/usr" "")
- $(use_with python python "${EPREFIX}/usr")
+ # is python2
+ --without-python
$(use_with boost boost "${EPREFIX}/usr")
$(use_with sqlite sqlite3 "${EPREFIX}/usr")
$(use_with icu icu "${EPREFIX}/usr")
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index ccedf666d..ec3426cfb 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -3,9 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit eutils flag-o-matic multilib toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
@@ -26,13 +24,11 @@ IUSE="
debug static-libs static threads pch
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86"
RESTRICT="!test? ( test )"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
# sys-libs/db should be compiled with USE=cxx
DEPEND="
<sys-devel/gcc-10:=
@@ -49,7 +45,6 @@ DEPEND="
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
gnutls? ( net-libs/gnutls )
- python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
icu? ( dev-libs/icu )
expat? ( dev-libs/expat )
@@ -248,7 +243,8 @@ src_configure() {
$(use_with freetype freetype "${EPREFIX}/usr")
# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
$(usex odbc --with-odbc="${EPREFIX}/usr" "")
- $(use_with python python "${EPREFIX}/usr")
+ # is python2
+ --without-python
$(use_with boost boost "${EPREFIX}/usr")
$(use_with sqlite sqlite3 "${EPREFIX}/usr")
$(use_with icu icu "${EPREFIX}/usr")
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 72f8fd0b1..40f338bc3 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-02-01 4:36 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 4:36 UTC (permalink / raw
To: gentoo-commits
commit: 185edf7edae700779fb362e1adba1042514420da
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 04:36:18 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 04:36:18 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=185edf7e
sci-biology/ncbi-blast+: drop py2 only versions
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 352 ---------------------
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 355 ---------------------
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 360 ----------------------
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
4 files changed, 1 insertion(+), 1068 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
deleted file mode 100644
index 05c844b1c..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ /dev/null
@@ -1,352 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
- debug static-libs static threads pch
- test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
- sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
- boost? ( dev-libs/boost )
- curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite:3 )
- mysql? ( virtual/mysql )
- fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl media-libs/glew:0= )
- mesa? ( media-libs/mesa[osmesa] )
- glut? ( media-libs/freeglut )
- freetype? ( media-libs/freetype )
- gnutls? ( net-libs/gnutls )
- python? ( ${PYTHON_DEPS} )
- cppunit? ( dev-util/cppunit )
- icu? ( dev-libs/icu )
- expat? ( dev-libs/expat )
- sablotron? ( app-text/sablotron )
- xml? ( dev-libs/libxml2 )
- xslt? ( dev-libs/libxslt )
- xerces? ( dev-libs/xerces-c )
- xalan? ( dev-libs/xalan-c )
- muparser? ( dev-cpp/muParser )
- hdf5? ( sci-libs/hdf5[cxx] )
- gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
- png? ( media-libs/libpng:0= )
- tiff? ( media-libs/tiff:0= )
- xpm? ( x11-libs/libXpm )
- dev-libs/lzo
- app-arch/bzip2
- dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-# The default (heavily patched) embedded copy should work, or you can
-# leave it off altogether -- the only public apps that make use of it are
-# samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# filter-ldflags -Wl,--as-needed
-# append-ldflags -Wl,--no-undefined
-# sed -i -e 's/-print-file-name=libstdc++.a//' \
-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-# src/build-system/configure || die
-# epatch \
-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-# "${FILESDIR}"/curl-types.patch \
-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-# "${FILESDIR}"/report_project_settings_configure.ac.patch \
-# "${FILESDIR}"/report_project_settings_configure.patch \
-# "${FILESDIR}"/make_install.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-## local PATCHES=(
-## "${FILESDIR}"/${P}-conf-opts.patch
-## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-## "${FILESDIR}"/${P}-linkage-tuneups.patch
-## "${FILESDIR}"/${P}-more-patches.patch
-## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-## "${FILESDIR}"/${P}-configure.patch
-## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-## "${FILESDIR}"/${P}-fix-install.patch
-## )
- # "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- epatch "${FILESDIR}"/"${P}"__fix_lib_deps.patch
- # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
- # https://bugs.gentoo.org/show_bug.cgi?id=514706
-
- tc-export CXX CC
-
-## cd src/build-system || die
-# eautoreconf
-
- # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
- # eautoconf # keep it disabled until we can ensure 2.59 is installed
- # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
- default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
- local myconf=()
- #--without-optimization turn off optimization flags in non-debug mode
- #--with-profiling build profiled versions of libs and apps
- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR)
- #--with-plugin-auto-load always enable the plugin manager by default
- #--with-bundles build bundles in addition to dylibs on Mac OS X
- #--with-bin-release build executables suitable for public release
- # no dll and such
- #--with-64 compile to 64-bit code
- #--with-universal build universal binaries on Mac OS X
- #--with-universal=CPUs build universal binaries targeting the given CPUs
- #--without-exe do not build executables
- #--with-relative-runpath=P specify an executable-relative DLL search path
- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
- #--with-limited-linker don't attempt to build especially large projects
- #--with-extra-action= script to call after the configuration is complete
- #--with-autodep automatic generation of dependencies (GNU make)
- #--with-fake-root=DIR appear to have been built under DIR
- #--with-build-root-sfx=X add a user-specified suffix to the build dir name
- #--without-execopy do not copy built executables to the BIN area
- #--with-lib-rebuilds ensure that apps use up-to-date libraries
- #--with-lib-rebuilds=ask ask whether to update each app's libraries
- #--without-deactivation keep old copies of libraries that no longer build
- #--without-makefile-auto-update do not auto-update generated makefiles
- #--with-projects=FILE build projects listed in FILE by default
- #--without-flat-makefile do not generate an all-encompassing flat makefile
- #--with-configure-dialog allow interactive flat makefile project selection
- #--with-saved-settings=F load configuration settings from the file F
- #--with-check-tools=... use the specified tools for testing
- #--with-ncbi-public ensure compatibility for all in-house platforms
- #--with-sybase-local=DIR use local SYBASE install (DIR is optional)
- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
- #--without-sp do not use SP libraries
- #--without-orbacus do not use ORBacus CORBA libraries
- #--with-orbacus=DIR use ORBacus installation in DIR
- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR)
- #--with-sablot=DIR use Sablotron installation in DIR
- #--without-sablot, do not use Sablotron
- #--with-oechem=DIR use OpenEye OEChem installation in DIR
- #--without-oechem do not use OEChem
- #--with-sge=DIR use Sun Grid Engine installation in DIR
- #--without-sge do not use Sun Grid Engine
- #--with-magic=DIR use libmagic installation in DIR
- #--without-magic do not use libmagic
- #--without-local-lbsm turn off support for IPC with locally running LBSMD
- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt
- #--without-connext do not build non-public CONNECT library extensions
- #--without-serial do not build the serialization library and tools
- #--without-objects do not generate/build serializeable objects from ASNs
- #--without-dbapi do not build database connectivity libraries
- #--without-app do not build standalone applications like ID1_FETCH
- #--without-gui do not build most graphical projects
- #--without-algo do not build CPU-intensive algorithms
- #--without-internal do not build internal projects
- #--with-gbench ensure that Genome Workbench can be built
- #--without-gbench do not build Genome Workbench
- myconf+=(
- --with-dll
- --with-lfs
- --with-build-root="${S}"_build
- --without-suffix
- --without-hostspec
- --without-version
- --with-bincopy
- --without-strip
- --without-ccache
- --without-distcc
-# --with-ncbi-c
- --without-ctools
-# --with-sss
-# --with-sssutils
-# --with-sssdb
-# --with-included-sss
- --with-z="${EPREFIX}/usr"
- --with-bz2="${EPREFIX}/usr"
- --without-sybase
- --with-autodep
-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
- $(use_with debug)
- $(use_with debug max-debug)
- $(use_with debug symbols)
- $(use_with static-libs static)
- $(use_with static static-exe)
- $(use_with threads mt)
- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
- $(use_with test check)
- $(use_with pch)
- $(use_with lzo lzo "${EPREFIX}/usr")
- $(use_with pcre pcre "${EPREFIX}/usr")
- $(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with mysql mysql "${EPREFIX}/usr")
- $(use_with muparser muparser "${EPREFIX}/usr")
- $(usex fltk --with-fltk="${EPREFIX}/usr" "")
- $(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
- $(use_with opengl glut "${EPREFIX}/usr")
- $(use_with opengl glew "${EPREFIX}/usr")
- $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${EPREFIX}/usr" "")
- $(use_with python python "${EPREFIX}/usr")
- $(use_with boost boost "${EPREFIX}/usr")
- $(use_with sqlite sqlite3 "${EPREFIX}/usr")
- $(use_with icu icu "${EPREFIX}/usr")
- $(use_with expat expat "${EPREFIX}/usr")
- $(use_with xml libxml "${EPREFIX}/usr")
- $(use_with xml libxslt "${EPREFIX}/usr")
- $(use_with xerces xerces "${EPREFIX}/usr")
- $(use_with hdf5 hdf5 "${EPREFIX}/usr")
- $(use_with xalan xalan "${EPREFIX}/usr")
-# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
- --without-gif
- $(use_with jpeg jpeg "${EPREFIX}/usr")
- $(use_with tiff tiff "${EPREFIX}/usr")
- $(use_with png png "${EPREFIX}/usr")
- $(use_with xpm xpm "${EPREFIX}/usr")
- $(use_with curl curl "${EPREFIX}/usr")
-# $(use_with X x "${EPREFIX}/usr")
-# $(use_with X x) # there is no --with-x option
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
- # TODO
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
- # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-# ECONF_SOURCE="src/build-system" \
-# econf \
- bash \
- ./src/build-system/configure \
- --srcdir="${S}" \
- --prefix="${EPREFIX}/usr" \
- --libdir=/usr/lib64 \
- --with-flat-makefile \
- ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${ED}"/usr \
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \
-# || die
-# econf ${myconf[@]}
-}
-
-src_compile() {
- ## all_r would ignore the --with-projects contents and build more
- ## emake all_r -C GCC*-Release*/build || die
- ## all_p with compile only selected/required components
- ##cd "${S}"_build &&\
- ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
- #emake all_p -C "${S}"_build/build
-
- #
- # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
- #
- # The next release should automatically address such underlinking, albeit
- # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to
- # add or extend more DLL_LIB settings, to which end you may find the
- # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
- # helpful. For instance,
- #
- # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
- #
- # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
- #
- # DLL_LIB = xncbi
- #
- # (You can find the path to that makefile by examining
- # .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
- #
- # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
- emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${S}"_build/lib/ncbi || die
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-# dobin "${S}"_build/bin/*
-# dolib.so "${S}"_build/lib/*so*
-# dolib.a "${S}"_build/lib/*.a
-# doheader "${S}"_build/inc/*
-
- # File collisions with sci-biology/ncbi-tools
- mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
- mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
- mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
- mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
- doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
- einfo 'Please run "source /etc/profile" before using this package in the current shell.'
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
deleted file mode 100644
index 0118086c8..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ /dev/null
@@ -1,355 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
- debug static-libs static threads pch
- test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
- sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
- boost? ( dev-libs/boost )
- curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite:3 )
- mysql? ( virtual/mysql )
- fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl media-libs/glew:0= )
- mesa? ( media-libs/mesa[osmesa] )
- glut? ( media-libs/freeglut )
- freetype? ( media-libs/freetype )
- gnutls? ( net-libs/gnutls )
- python? ( ${PYTHON_DEPS} )
- cppunit? ( dev-util/cppunit )
- icu? ( dev-libs/icu )
- expat? ( dev-libs/expat )
- sablotron? ( app-text/sablotron )
- xml? ( dev-libs/libxml2 )
- xslt? ( dev-libs/libxslt )
- xerces? ( dev-libs/xerces-c )
- xalan? ( dev-libs/xalan-c )
- muparser? ( dev-cpp/muParser )
- hdf5? ( sci-libs/hdf5[cxx] )
- gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
- png? ( media-libs/libpng:0= )
- tiff? ( media-libs/tiff:0= )
- xpm? ( x11-libs/libXpm )
- dev-libs/lzo
- app-arch/bzip2
- dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-# The default (heavily patched) embedded copy should work, or you can
-# leave it off altogether -- the only public apps that make use of it are
-# samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# filter-ldflags -Wl,--as-needed
-# append-ldflags -Wl,--no-undefined
-# sed -i -e 's/-print-file-name=libstdc++.a//' \
-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-# src/build-system/configure || die
-# epatch \
-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-# "${FILESDIR}"/curl-types.patch \
-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-# "${FILESDIR}"/report_project_settings_configure.ac.patch \
-# "${FILESDIR}"/report_project_settings_configure.patch \
-# "${FILESDIR}"/make_install.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-## local PATCHES=(
-## "${FILESDIR}"/${P}-conf-opts.patch
-## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-## "${FILESDIR}"/${P}-linkage-tuneups.patch
-## "${FILESDIR}"/${P}-more-patches.patch
-## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-## "${FILESDIR}"/${P}-configure.patch
-## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-## "${FILESDIR}"/${P}-fix-install.patch
-## )
- # "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.patch
- # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
- # https://bugs.gentoo.org/show_bug.cgi?id=514706
-
- tc-export CXX CC
-
-## cd src/build-system || die
-# eautoreconf
-
- # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
- # eautoconf # keep it disabled until we can ensure 2.59 is installed
- # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
- default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
- local myconf=()
- #--without-optimization turn off optimization flags in non-debug mode
- #--with-profiling build profiled versions of libs and apps
- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR)
- #--with-plugin-auto-load always enable the plugin manager by default
- #--with-bundles build bundles in addition to dylibs on Mac OS X
- #--with-bin-release build executables suitable for public release
- # no dll and such
- #--with-64 compile to 64-bit code
- #--with-universal build universal binaries on Mac OS X
- #--with-universal=CPUs build universal binaries targeting the given CPUs
- #--without-exe do not build executables
- #--with-relative-runpath=P specify an executable-relative DLL search path
- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
- #--with-limited-linker don't attempt to build especially large projects
- #--with-extra-action= script to call after the configuration is complete
- #--with-autodep automatic generation of dependencies (GNU make)
- #--with-fake-root=DIR appear to have been built under DIR
- #--with-build-root-sfx=X add a user-specified suffix to the build dir name
- #--without-execopy do not copy built executables to the BIN area
- #--with-lib-rebuilds ensure that apps use up-to-date libraries
- #--with-lib-rebuilds=ask ask whether to update each app's libraries
- #--without-deactivation keep old copies of libraries that no longer build
- #--without-makefile-auto-update do not auto-update generated makefiles
- #--with-projects=FILE build projects listed in FILE by default
- #--without-flat-makefile do not generate an all-encompassing flat makefile
- #--with-configure-dialog allow interactive flat makefile project selection
- #--with-saved-settings=F load configuration settings from the file F
- #--with-check-tools=... use the specified tools for testing
- #--with-ncbi-public ensure compatibility for all in-house platforms
- #--with-sybase-local=DIR use local SYBASE install (DIR is optional)
- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
- #--without-sp do not use SP libraries
- #--without-orbacus do not use ORBacus CORBA libraries
- #--with-orbacus=DIR use ORBacus installation in DIR
- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR)
- #--with-sablot=DIR use Sablotron installation in DIR
- #--without-sablot, do not use Sablotron
- #--with-oechem=DIR use OpenEye OEChem installation in DIR
- #--without-oechem do not use OEChem
- #--with-sge=DIR use Sun Grid Engine installation in DIR
- #--without-sge do not use Sun Grid Engine
- #--with-magic=DIR use libmagic installation in DIR
- #--without-magic do not use libmagic
- #--without-local-lbsm turn off support for IPC with locally running LBSMD
- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt
- #--without-connext do not build non-public CONNECT library extensions
- #--without-serial do not build the serialization library and tools
- #--without-objects do not generate/build serializeable objects from ASNs
- #--without-dbapi do not build database connectivity libraries
- #--without-app do not build standalone applications like ID1_FETCH
- #--without-gui do not build most graphical projects
- #--without-algo do not build CPU-intensive algorithms
- #--without-internal do not build internal projects
- #--with-gbench ensure that Genome Workbench can be built
- #--without-gbench do not build Genome Workbench
- myconf+=(
- --with-dll
- --with-lfs
- --with-build-root="${S}"_build
- --without-suffix
- --without-hostspec
- --without-version
- --with-bincopy
- --without-strip
- --without-ccache
- --without-distcc
-# --with-ncbi-c
- --without-ctools
-# --with-sss
-# --with-sssutils
-# --with-sssdb
-# --with-included-sss
- --with-z="${EPREFIX}/usr"
- --with-bz2="${EPREFIX}/usr"
- --without-sybase
- --with-autodep
-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
- $(use_with debug)
- $(use_with debug max-debug)
- $(use_with debug symbols)
- $(use_with static-libs static)
- $(use_with static static-exe)
- $(use_with threads mt)
- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
- $(use_with test check)
- $(use_with pch)
- $(use_with lzo lzo "${EPREFIX}/usr")
- $(use_with pcre pcre "${EPREFIX}/usr")
- $(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with mysql mysql "${EPREFIX}/usr")
- $(use_with muparser muparser "${EPREFIX}/usr")
- $(usex fltk --with-fltk="${EPREFIX}/usr" "")
- $(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
- $(use_with opengl glut "${EPREFIX}/usr")
- $(use_with opengl glew "${EPREFIX}/usr")
- $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${EPREFIX}/usr" "")
- $(use_with python python "${EPREFIX}/usr")
- $(use_with boost boost "${EPREFIX}/usr")
- $(use_with sqlite sqlite3 "${EPREFIX}/usr")
- $(use_with icu icu "${EPREFIX}/usr")
- $(use_with expat expat "${EPREFIX}/usr")
- $(use_with xml libxml "${EPREFIX}/usr")
- $(use_with xml libxslt "${EPREFIX}/usr")
- $(use_with xerces xerces "${EPREFIX}/usr")
- $(use_with hdf5 hdf5 "${EPREFIX}/usr")
- $(use_with xalan xalan "${EPREFIX}/usr")
-# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
- --without-gif
- $(use_with jpeg jpeg "${EPREFIX}/usr")
- $(use_with tiff tiff "${EPREFIX}/usr")
- $(use_with png png "${EPREFIX}/usr")
- $(use_with xpm xpm "${EPREFIX}/usr")
- $(use_with curl curl "${EPREFIX}/usr")
-# $(use_with X x "${EPREFIX}/usr")
-# $(use_with X x) # there is no --with-x option
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
- # TODO
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
- # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-# ECONF_SOURCE="src/build-system" \
-# econf \
- bash \
- ./src/build-system/configure \
- --srcdir="${S}" \
- --prefix="${EPREFIX}/usr" \
- --libdir=/usr/lib64 \
- --with-flat-makefile \
- ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${ED}"/usr \
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \
-# || die
-# econf ${myconf[@]}
-}
-
-src_compile() {
- ## all_r would ignore the --with-projects contents and build more
- ## emake all_r -C GCC*-Release*/build || die
- ## all_p with compile only selected/required components
- ##cd "${S}"_build &&\
- ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
- #emake all_p -C "${S}"_build/build
-
- #
- # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
- #
- # The next release should automatically address such underlinking, albeit
- # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to
- # add or extend more DLL_LIB settings, to which end you may find the
- # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
- # helpful. For instance,
- #
- # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
- #
- # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
- #
- # DLL_LIB = xncbi
- #
- # (You can find the path to that makefile by examining
- # .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
- #
- # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
- emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${S}"_build/lib/ncbi || die
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-# dobin "${S}"_build/bin/*
-# dolib.so "${S}"_build/lib/*so*
-# dolib.a "${S}"_build/lib/*.a
-# doheader "${S}"_build/inc/*
-
- # File collisions with sci-biology/ncbi-tools
- mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
- mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
- mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
- mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
- doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
- einfo 'Please run "source /etc/profile" before using this package in the current shell.'
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
deleted file mode 100644
index ccedf666d..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ /dev/null
@@ -1,360 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
- debug static-libs static threads pch
- test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
- sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
- boost? ( dev-libs/boost )
- curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite:3 )
- mysql? ( virtual/mysql )
- fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl media-libs/glew:0= )
- mesa? ( media-libs/mesa[osmesa] )
- glut? ( media-libs/freeglut )
- freetype? ( media-libs/freetype )
- gnutls? ( net-libs/gnutls )
- python? ( ${PYTHON_DEPS} )
- cppunit? ( dev-util/cppunit )
- icu? ( dev-libs/icu )
- expat? ( dev-libs/expat )
- sablotron? ( app-text/sablotron )
- xml? ( dev-libs/libxml2 )
- xslt? ( dev-libs/libxslt )
- xerces? ( dev-libs/xerces-c )
- xalan? ( dev-libs/xalan-c )
- muparser? ( dev-cpp/muParser )
- hdf5? ( sci-libs/hdf5[cxx] )
- gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
- png? ( media-libs/libpng:0= )
- tiff? ( media-libs/tiff:0= )
- xpm? ( x11-libs/libXpm )
- dev-libs/lzo
- app-arch/bzip2
- dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-# The default (heavily patched) embedded copy should work, or you can
-# leave it off altogether -- the only public apps that make use of it are
-# samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# filter-ldflags -Wl,--as-needed
-# append-ldflags -Wl,--no-undefined
-# sed -i -e 's/-print-file-name=libstdc++.a//' \
-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-# src/build-system/configure || die
-# epatch \
-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-# "${FILESDIR}"/curl-types.patch \
-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-# "${FILESDIR}"/report_project_settings_configure.ac.patch \
-# "${FILESDIR}"/report_project_settings_configure.patch \
-# "${FILESDIR}"/make_install.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-## local PATCHES=(
-## "${FILESDIR}"/${P}-conf-opts.patch
-## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-## "${FILESDIR}"/${P}-linkage-tuneups.patch
-## "${FILESDIR}"/${P}-more-patches.patch
-## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-## "${FILESDIR}"/${P}-configure.patch
-## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-## "${FILESDIR}"/${P}-fix-install.patch
-## )
- # "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.patch
- # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
- # https://bugs.gentoo.org/show_bug.cgi?id=514706
-
- tc-export CXX CC
-
-## cd src/build-system || die
-# eautoreconf
-
- # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
- # eautoconf # keep it disabled until we can ensure 2.59 is installed
- # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
- default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
- local myconf=()
- #--without-optimization turn off optimization flags in non-debug mode
- #--with-profiling build profiled versions of libs and apps
- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR)
- #--with-plugin-auto-load always enable the plugin manager by default
- #--with-bundles build bundles in addition to dylibs on Mac OS X
- #--with-bin-release build executables suitable for public release
- # no dll and such
- #--with-64 compile to 64-bit code
- #--with-universal build universal binaries on Mac OS X
- #--with-universal=CPUs build universal binaries targeting the given CPUs
- #--without-exe do not build executables
- #--with-relative-runpath=P specify an executable-relative DLL search path
- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
- #--with-limited-linker don't attempt to build especially large projects
- #--with-extra-action= script to call after the configuration is complete
- #--with-autodep automatic generation of dependencies (GNU make)
- #--with-fake-root=DIR appear to have been built under DIR
- #--with-build-root-sfx=X add a user-specified suffix to the build dir name
- #--without-execopy do not copy built executables to the BIN area
- #--with-lib-rebuilds ensure that apps use up-to-date libraries
- #--with-lib-rebuilds=ask ask whether to update each app's libraries
- #--without-deactivation keep old copies of libraries that no longer build
- #--without-makefile-auto-update do not auto-update generated makefiles
- #--with-projects=FILE build projects listed in FILE by default
- #--without-flat-makefile do not generate an all-encompassing flat makefile
- #--with-configure-dialog allow interactive flat makefile project selection
- #--with-saved-settings=F load configuration settings from the file F
- #--with-check-tools=... use the specified tools for testing
- #--with-ncbi-public ensure compatibility for all in-house platforms
- #--with-sybase-local=DIR use local SYBASE install (DIR is optional)
- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
- #--without-sp do not use SP libraries
- #--without-orbacus do not use ORBacus CORBA libraries
- #--with-orbacus=DIR use ORBacus installation in DIR
- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR)
- #--with-sablot=DIR use Sablotron installation in DIR
- #--without-sablot, do not use Sablotron
- #--with-oechem=DIR use OpenEye OEChem installation in DIR
- #--without-oechem do not use OEChem
- #--with-sge=DIR use Sun Grid Engine installation in DIR
- #--without-sge do not use Sun Grid Engine
- #--with-magic=DIR use libmagic installation in DIR
- #--without-magic do not use libmagic
- #--without-local-lbsm turn off support for IPC with locally running LBSMD
- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt
- #--without-connext do not build non-public CONNECT library extensions
- #--without-serial do not build the serialization library and tools
- #--without-objects do not generate/build serializeable objects from ASNs
- #--without-dbapi do not build database connectivity libraries
- #--without-app do not build standalone applications like ID1_FETCH
- #--without-gui do not build most graphical projects
- #--without-algo do not build CPU-intensive algorithms
- #--without-internal do not build internal projects
- #--with-gbench ensure that Genome Workbench can be built
- #--without-gbench do not build Genome Workbench
- myconf+=(
- --with-dll
- --with-lfs
- --with-build-root="${S}"_build
- --without-suffix
- --without-hostspec
- --without-version
- --with-bincopy
- --without-strip
- --without-ccache
- --without-distcc
-# --with-ncbi-c
- --without-ctools
-# --with-sss
-# --with-sssutils
-# --with-sssdb
-# --with-included-sss
- --with-z="${EPREFIX}/usr"
- --with-bz2="${EPREFIX}/usr"
- --without-sybase
- --with-autodep
-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
- $(use_with debug)
- $(use_with debug max-debug)
- $(use_with debug symbols)
- $(use_with static-libs static)
- $(use_with static static-exe)
- $(use_with threads mt)
- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
- $(use_with test check)
- $(use_with pch)
- $(use_with lzo lzo "${EPREFIX}/usr")
- $(use_with pcre pcre "${EPREFIX}/usr")
- $(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with mysql mysql "${EPREFIX}/usr")
- $(use_with muparser muparser "${EPREFIX}/usr")
- $(usex fltk --with-fltk="${EPREFIX}/usr" "")
- $(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
- $(use_with opengl glut "${EPREFIX}/usr")
- $(use_with opengl glew "${EPREFIX}/usr")
- #
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
- # $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${EPREFIX}/usr" "")
- $(use_with python python "${EPREFIX}/usr")
- $(use_with boost boost "${EPREFIX}/usr")
- $(use_with sqlite sqlite3 "${EPREFIX}/usr")
- $(use_with icu icu "${EPREFIX}/usr")
- $(use_with expat expat "${EPREFIX}/usr")
- $(use_with xml libxml "${EPREFIX}/usr")
- $(use_with xml libxslt "${EPREFIX}/usr")
- $(use_with xerces xerces "${EPREFIX}/usr")
- $(use_with hdf5 hdf5 "${EPREFIX}/usr")
- $(use_with xalan xalan "${EPREFIX}/usr")
-# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
- --without-gif
- $(use_with jpeg jpeg "${EPREFIX}/usr")
- $(use_with tiff tiff "${EPREFIX}/usr")
- $(use_with png png "${EPREFIX}/usr")
- $(use_with xpm xpm "${EPREFIX}/usr")
- $(use_with curl curl "${EPREFIX}/usr")
-# $(use_with X x "${EPREFIX}/usr")
-# $(use_with X x) # there is no --with-x option
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
- --without-vdb
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
- # TODO
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
- # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-# ECONF_SOURCE="src/build-system" \
-# econf \
- bash \
- ./src/build-system/configure \
- --srcdir="${S}" \
- --prefix="${EPREFIX}/usr" \
- --libdir=/usr/lib64 \
- --with-flat-makefile \
- ${myconf[@]} || die
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${ED}"/usr \
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \
-# || die
-# econf ${myconf[@]}
-}
-
-src_compile() {
- ## all_r would ignore the --with-projects contents and build more
- ## emake all_r -C GCC*-Release*/build || die
- ## all_p with compile only selected/required components
- ##cd "${S}"_build &&\
- ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
- #emake all_p -C "${S}"_build/build
-
- #
- # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
- #
- # The next release should automatically address such underlinking, albeit
- # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to
- # add or extend more DLL_LIB settings, to which end you may find the
- # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
- # helpful. For instance,
- #
- # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
- #
- # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
- #
- # DLL_LIB = xncbi
- #
- # (You can find the path to that makefile by examining
- # .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
- #
- # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
- emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${S}"_build/lib/ncbi || die
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-# dobin "${S}"_build/bin/*
-# dolib.so "${S}"_build/lib/*so*
-# dolib.a "${S}"_build/lib/*.a
-# doheader "${S}"_build/inc/*
-
- # File collisions with sci-biology/ncbi-tools
- mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
- mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
- mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
- mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
- doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
- einfo 'Please run "source /etc/profile" before using this package in the current shell.'
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 72f8fd0b1..40f338bc3 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-01-19 17:16 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 17:16 UTC (permalink / raw
To: gentoo-commits
commit: 91f8cfa957d7c5b0e9049050e4249e8847fb2164
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 17:13:54 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 17:13:54 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=91f8cfa9
sci-biology/ncbi-blast+: update HOMEPAGE
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 7641c42f9..40f338bc3 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -13,7 +13,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 5a72b2c8b..05c844b1c 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -12,7 +12,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index d71ed4d9a..0118086c8 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -12,7 +12,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 999e439e6..ccedf666d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -13,7 +13,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 79d44ae52..72f8fd0b1 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -13,7 +13,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 58091d85aff0441d3a03ac81322449049c263d12
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:25:09 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:25:09 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=58091d85
sci-biology/ncbi-blast+: fix rdepend
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index f313b4e01..7641c42f9 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -78,7 +78,7 @@ DEPEND="
# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-RDEPEND="${BDEPEND}"
+RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}/c++"
# ncbi-blast-2.2.30+-src/c++
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-01-13 21:06 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-01-13 21:06 UTC (permalink / raw
To: gentoo-commits
commit: e57d4a3b016f7a69cd279a4b003a1ec84b04a6c8
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 13 21:00:22 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 13 21:00:22 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e57d4a3b
sci-biology/ncbi-blast+: use https for homepage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index a8e257086..f313b4e01 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -13,7 +13,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index b14255938..5a72b2c8b 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -12,7 +12,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index ad927b0b1..d71ed4d9a 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -12,7 +12,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index b71c3d48d..999e439e6 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -13,7 +13,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 7f63bf77d..79d44ae52 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -13,7 +13,7 @@ MY_P="ncbi-blast-${PV}+-src"
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2021-01-05 18:22 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:22 UTC (permalink / raw
To: gentoo-commits
commit: 9ae44cc31398e49952ae8c2d92885c916e5538c6
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 10:03:56 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:20:18 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ae44cc3
sci-biology/ncbi-blast+: depend on gcc<10, add 2.11.0 version
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../{ncbi-blast+-2.8.1.ebuild => ncbi-blast+-2.11.0.ebuild} | 9 +++++----
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 5 +++--
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 5 +++--
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 5 +++--
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 5 +++--
5 files changed, 17 insertions(+), 12 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
similarity index 99%
copy from sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
copy to sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index ca3e682ac..12b249c8b 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
@@ -28,13 +28,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
#KEYWORDS=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
@@ -77,7 +78,7 @@ DEPEND="
# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-RDEPEND="${DEPEND}"
+RDEPEND="${BDEPEND}"
S="${WORKDIR}/${MY_P}/c++"
# ncbi-blast-2.2.30+-src/c++
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index d6c529b57..85b764cc4 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -27,13 +27,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
#KEYWORDS=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 40d060bf5..7709cab39 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.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=7
@@ -27,13 +27,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
#KEYWORDS=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 0a826b779..641b37467 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -28,13 +28,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
#KEYWORDS=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index ca3e682ac..466101138 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.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=7
@@ -28,13 +28,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
#KEYWORDS=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2019-03-28 21:54 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2019-03-28 21:54 UTC (permalink / raw
To: gentoo-commits
commit: 83b76a8c9aab16e157cd482e5ac3508d30bc52a5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 28 21:54:30 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 28 21:54:30 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=83b76a8c
sci-biology/ncbi-blast+: emphasize alternative building from sources
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index c91a5d490..ca3e682ac 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -288,7 +288,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
- ${myconf[@]} || die
+ ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
#--without-debug \
# --with-bin-release \
# --with-bincopy \
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2019-03-25 12:16 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2019-03-25 12:16 UTC (permalink / raw
To: gentoo-commits
commit: 868fbe5eeaa38a05f1ae2775a286b8d2ae651572
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 12:15:59 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 12:15:59 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=868fbe5e
sci-biology/ncbi-blast+: EAPI7 bump, remove unused variable
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 8 ++++----
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 8 ++++----
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 6 +++---
.../{ncbi-blast+-2.6.0.ebuild => ncbi-blast+-2.8.1.ebuild} | 9 +++++----
4 files changed, 16 insertions(+), 15 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index dd6f3444f..d6c529b57 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-MY_PV="2.2.30"
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -134,6 +133,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
# eautoconf # keep it disabled until we can ensure 2.59 is installed
# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+ default
}
# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
@@ -279,7 +279,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
- ${myconf[@]} || die
+ ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
#--without-debug \
# --with-bin-release \
# --with-bincopy \
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 4622ac976..40d060bf5 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-MY_PV="2.2.30"
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -137,6 +136,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
# eautoconf # keep it disabled until we can ensure 2.59 is installed
# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+ default
}
# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
@@ -282,7 +282,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
- ${myconf[@]} || die
+ ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
#--without-debug \
# --with-bin-release \
# --with-bincopy \
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 6adbefad3..0a826b779 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-MY_PV="2.3.0"
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -138,6 +137,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
# eautoconf # keep it disabled until we can ensure 2.59 is installed
# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+ default
}
# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
similarity index 99%
copy from sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
copy to sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 6adbefad3..c91a5d490 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-MY_PV="2.3.0"
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -67,7 +66,8 @@ DEPEND="
xpm? ( x11-libs/libXpm )
dev-libs/lzo
app-arch/bzip2
- dev-libs/libpcre"
+ dev-libs/libpcre
+ dev-db/lmdb"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
# Intentionally omitted USE flags:
# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
@@ -138,6 +138,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
# eautoconf # keep it disabled until we can ensure 2.59 is installed
# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+ default
}
# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2017-04-28 17:58 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-04-28 17:58 UTC (permalink / raw
To: gentoo-commits
commit: 94213c11a5931dfd22ce57afdd7a12b9a40fa402
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 28 17:58:08 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 28 17:58:08 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94213c11
sci-biology/ncbi-blast+: version bump
Package-Manager: Portage-2.3.5, Repoman-2.3.2
.../{ncbi-blast+-2.3.0.ebuild => ncbi-blast+-2.6.0.ebuild} | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
similarity index 98%
rename from sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
rename to sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 7791cf3e5..6adbefad3 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -239,7 +239,9 @@ src_configure() {
$(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
- $(use_with opengl glew-mx)
+ #
+ # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
+ # $(use_with opengl glew-mx)
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
@@ -264,6 +266,8 @@ src_configure() {
$(use_with curl curl "${EPREFIX}/usr")
# $(use_with X x "${EPREFIX}/usr")
# $(use_with X x) # there is no --with-x option
+ # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
+ --without-vdb
)
# http://www.ncbi.nlm.nih.gov/books/NBK7167/
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2016-09-10 17:25 Justin Lecher
0 siblings, 0 replies; 23+ messages in thread
From: Justin Lecher @ 2016-09-10 17:25 UTC (permalink / raw
To: gentoo-commits
commit: 04203dc25ebeb3022c4f6e858652ac653fcf327e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 10 17:23:12 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Sep 10 17:24:43 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=04203dc2
sci-biology/ncbi-blast+: Drop obsolete dep
Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 3 +--
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 3 +--
sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild | 3 +--
3 files changed, 3 insertions(+), 6 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 608420b..023e89a 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -26,7 +26,7 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -240,7 +240,6 @@ src_configure() {
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
- $(use_with fastcgi fastcgi "${EPREFIX}/usr")
# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
$(usex odbc --with-odbc="${EPREFIX}/usr" "")
$(use_with python python "${EPREFIX}/usr")
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 47f90a0..3ac27be 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -26,7 +26,7 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -243,7 +243,6 @@ src_configure() {
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
- $(use_with fastcgi fastcgi "${EPREFIX}/usr")
# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
$(usex odbc --with-odbc="${EPREFIX}/usr" "")
$(use_with python python "${EPREFIX}/usr")
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
index 535c25c..9f04f92 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
@@ -27,7 +27,7 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ berkdb boost bzip2 cppunit curl expat fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -244,7 +244,6 @@ src_configure() {
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
- $(use_with fastcgi fastcgi "${EPREFIX}/usr")
# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
$(usex odbc --with-odbc="${EPREFIX}/usr" "")
$(use_with python python "${EPREFIX}/usr")
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2016-08-24 11:40 Justin Lecher
0 siblings, 0 replies; 23+ messages in thread
From: Justin Lecher @ 2016-08-24 11:40 UTC (permalink / raw
To: gentoo-commits
commit: 2cd393c02b72fc6566a77277f3da33879e7e9bbe
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 24 11:40:10 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Aug 24 11:40:20 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2cd393c0
sci-biology/ncbi-blast+: Fix SLOT operators
Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 2 +-
sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 7cbeb06..608420b 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -44,7 +44,7 @@ DEPEND="
sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl media-libs/glew )
+ opengl? ( virtual/opengl media-libs/glew:0= )
mesa? ( media-libs/mesa[osmesa] )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index c3326d4..47f90a0 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -44,7 +44,7 @@ DEPEND="
sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl media-libs/glew )
+ opengl? ( virtual/opengl media-libs/glew:0= )
mesa? ( media-libs/mesa[osmesa] )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
index a488d14..535c25c 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
@@ -45,7 +45,7 @@ DEPEND="
sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl media-libs/glew )
+ opengl? ( virtual/opengl media-libs/glew:0= )
mesa? ( media-libs/mesa[osmesa] )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
^ permalink raw reply related [flat|nested] 23+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2016-08-24 11:40 Justin Lecher
0 siblings, 0 replies; 23+ messages in thread
From: Justin Lecher @ 2016-08-24 11:40 UTC (permalink / raw
To: gentoo-commits
commit: ab6832012c18ea00bd0937471a6d46ccefad8bc4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 24 11:37:22 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Aug 24 11:40:20 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab683201
sci-biology/ncbi-blast+: Drop obsolete dep
Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 1 -
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 1 -
sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild | 1 -
3 files changed, 3 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 9191a03..7cbeb06 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -48,7 +48,6 @@ DEPEND="
mesa? ( media-libs/mesa[osmesa] )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
- fastcgi? ( www-apache/mod_fastcgi )
gnutls? ( net-libs/gnutls )
python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index bff6d0a..c3326d4 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -48,7 +48,6 @@ DEPEND="
mesa? ( media-libs/mesa[osmesa] )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
- fastcgi? ( www-apache/mod_fastcgi )
gnutls? ( net-libs/gnutls )
python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
index b10c764..a488d14 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
@@ -49,7 +49,6 @@ DEPEND="
mesa? ( media-libs/mesa[osmesa] )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
- fastcgi? ( www-apache/mod_fastcgi )
gnutls? ( net-libs/gnutls )
python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2016-02-11 18:53 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2016-02-11 18:53 UTC (permalink / raw
To: gentoo-commits
commit: e943fdf948e96f969a768f05433cc1430733e1ef
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 11 18:50:27 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 11 18:50:27 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e943fdf9
sci-biology/ncbi-blast+: version bump
Package-Manager: portage-2.2.26
sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild | 358 +++++++++++++++++++++++
1 file changed, 358 insertions(+)
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
new file mode 100644
index 0000000..b10c764
--- /dev/null
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
@@ -0,0 +1,358 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+MY_PV="2.3.0"
+MY_P="ncbi-blast-${PV}+-src"
+# workdir/ncbi-blast-2.2.30+-src
+# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
+# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
+
+DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+SRC_URI="
+ ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
+# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
+
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+ debug static-libs static threads pch
+ test wxwidgets odbc
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ sablotron sqlite tiff xerces xalan xml xpm xslt X"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+#KEYWORDS=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+ !sci-biology/ncbi-tools++
+ !sci-biology/sra_sdk
+ berkdb? ( sys-libs/db:4.3[cxx] )
+ boost? ( dev-libs/boost )
+ curl? ( net-misc/curl )
+ sqlite? ( dev-db/sqlite:3 )
+ mysql? ( virtual/mysql )
+ fltk? ( x11-libs/fltk )
+ opengl? ( virtual/opengl media-libs/glew )
+ mesa? ( media-libs/mesa[osmesa] )
+ glut? ( media-libs/freeglut )
+ freetype? ( media-libs/freetype )
+ fastcgi? ( www-apache/mod_fastcgi )
+ gnutls? ( net-libs/gnutls )
+ python? ( ${PYTHON_DEPS} )
+ cppunit? ( dev-util/cppunit )
+ icu? ( dev-libs/icu )
+ expat? ( dev-libs/expat )
+ sablotron? ( app-text/sablotron )
+ xml? ( dev-libs/libxml2 )
+ xslt? ( dev-libs/libxslt )
+ xerces? ( dev-libs/xerces-c )
+ xalan? ( dev-libs/xalan-c )
+ muparser? ( dev-cpp/muParser )
+ hdf5? ( sci-libs/hdf5[cxx] )
+ gif? ( media-libs/giflib )
+ jpeg? ( virtual/jpeg:0= )
+ png? ( media-libs/libpng:0= )
+ tiff? ( media-libs/tiff:0= )
+ xpm? ( x11-libs/libXpm )
+ dev-libs/lzo
+ app-arch/bzip2
+ dev-libs/libpcre"
+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
+# The default (heavily patched) embedded copy should work, or you can
+# leave it off altogether -- the only public apps that make use of it are
+# samples and tests, since NCBI's database servers are of course firewalled.
+
+# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}/c++"
+# ncbi-blast-2.2.30+-src/c++
+
+src_prepare() {
+# filter-ldflags -Wl,--as-needed
+# append-ldflags -Wl,--no-undefined
+# sed -i -e 's/-print-file-name=libstdc++.a//' \
+# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+# src/build-system/configure || die
+# epatch \
+# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
+# "${FILESDIR}"/curl-types.patch \
+# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \
+# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
+# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \
+# "${FILESDIR}"/report_project_settings_configure.ac.patch \
+# "${FILESDIR}"/report_project_settings_configure.patch \
+# "${FILESDIR}"/make_install.patch
+
+# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
+
+# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
+# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
+# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
+# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
+# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
+
+# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
+
+# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
+## local PATCHES=(
+## "${FILESDIR}"/${P}-conf-opts.patch
+## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+## "${FILESDIR}"/${P}-linkage-tuneups.patch
+## "${FILESDIR}"/${P}-more-patches.patch
+## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch
+## "${FILESDIR}"/${P}-configure.patch
+## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
+## "${FILESDIR}"/${P}-fix-install.patch
+## )
+ # "${FILESDIR}"/${P}-support-autoconf-2.60.patch
+## epatch ${PATCHES[@]}
+
+ # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
+ # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
+ # it is still present, plus in a few places was something else patched
+ # staying without any patches for now and lets see is it works on Gentoo
+ # epatch "${FILESDIR}"/fix_lib_deps.patch
+ # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
+ # https://bugs.gentoo.org/show_bug.cgi?id=514706
+
+ tc-export CXX CC
+
+## cd src/build-system || die
+# eautoreconf
+
+ # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
+ # eautoconf # keep it disabled until we can ensure 2.59 is installed
+ # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+}
+
+# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
+src_configure() {
+ local myconf=()
+ #--without-optimization turn off optimization flags in non-debug mode
+ #--with-profiling build profiled versions of libs and apps
+ #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR)
+ #--with-plugin-auto-load always enable the plugin manager by default
+ #--with-bundles build bundles in addition to dylibs on Mac OS X
+ #--with-bin-release build executables suitable for public release
+ # no dll and such
+ #--with-64 compile to 64-bit code
+ #--with-universal build universal binaries on Mac OS X
+ #--with-universal=CPUs build universal binaries targeting the given CPUs
+ #--without-exe do not build executables
+ #--with-relative-runpath=P specify an executable-relative DLL search path
+ #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
+ #--with-limited-linker don't attempt to build especially large projects
+ #--with-extra-action= script to call after the configuration is complete
+ #--with-autodep automatic generation of dependencies (GNU make)
+ #--with-fake-root=DIR appear to have been built under DIR
+ #--with-build-root-sfx=X add a user-specified suffix to the build dir name
+ #--without-execopy do not copy built executables to the BIN area
+ #--with-lib-rebuilds ensure that apps use up-to-date libraries
+ #--with-lib-rebuilds=ask ask whether to update each app's libraries
+ #--without-deactivation keep old copies of libraries that no longer build
+ #--without-makefile-auto-update do not auto-update generated makefiles
+ #--with-projects=FILE build projects listed in FILE by default
+ #--without-flat-makefile do not generate an all-encompassing flat makefile
+ #--with-configure-dialog allow interactive flat makefile project selection
+ #--with-saved-settings=F load configuration settings from the file F
+ #--with-check-tools=... use the specified tools for testing
+ #--with-ncbi-public ensure compatibility for all in-house platforms
+ #--with-sybase-local=DIR use local SYBASE install (DIR is optional)
+ #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
+ #--without-sp do not use SP libraries
+ #--without-orbacus do not use ORBacus CORBA libraries
+ #--with-orbacus=DIR use ORBacus installation in DIR
+ #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR)
+ #--with-sablot=DIR use Sablotron installation in DIR
+ #--without-sablot, do not use Sablotron
+ #--with-oechem=DIR use OpenEye OEChem installation in DIR
+ #--without-oechem do not use OEChem
+ #--with-sge=DIR use Sun Grid Engine installation in DIR
+ #--without-sge do not use Sun Grid Engine
+ #--with-magic=DIR use libmagic installation in DIR
+ #--without-magic do not use libmagic
+ #--without-local-lbsm turn off support for IPC with locally running LBSMD
+ #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt
+ #--without-connext do not build non-public CONNECT library extensions
+ #--without-serial do not build the serialization library and tools
+ #--without-objects do not generate/build serializeable objects from ASNs
+ #--without-dbapi do not build database connectivity libraries
+ #--without-app do not build standalone applications like ID1_FETCH
+ #--without-gui do not build most graphical projects
+ #--without-algo do not build CPU-intensive algorithms
+ #--without-internal do not build internal projects
+ #--with-gbench ensure that Genome Workbench can be built
+ #--without-gbench do not build Genome Workbench
+ myconf+=(
+ --with-dll
+ --with-lfs
+ --with-build-root="${S}"_build
+ --without-suffix
+ --without-hostspec
+ --without-version
+ --with-bincopy
+ --without-strip
+ --without-ccache
+ --without-distcc
+# --with-ncbi-c
+ --without-ctools
+# --with-sss
+# --with-sssutils
+# --with-sssdb
+# --with-included-sss
+ --with-z="${EPREFIX}/usr"
+ --with-bz2="${EPREFIX}/usr"
+ --without-sybase
+ --with-autodep
+# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
+ $(use_with debug)
+ $(use_with debug max-debug)
+ $(use_with debug symbols)
+ $(use_with static-libs static)
+ $(use_with static static-exe)
+ $(use_with threads mt)
+ $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
+ $(use_with test check)
+ $(use_with pch)
+ $(use_with lzo lzo "${EPREFIX}/usr")
+ $(use_with pcre pcre "${EPREFIX}/usr")
+ $(use_with gnutls gnutls "${EPREFIX}/usr")
+ $(use_with mysql mysql "${EPREFIX}/usr")
+ $(use_with muparser muparser "${EPREFIX}/usr")
+ $(usex fltk --with-fltk="${EPREFIX}/usr" "")
+ $(use_with opengl opengl "${EPREFIX}/usr")
+ $(use_with mesa mesa "${EPREFIX}/usr")
+ $(use_with opengl glut "${EPREFIX}/usr")
+ $(use_with opengl glew "${EPREFIX}/usr")
+ $(use_with opengl glew-mx)
+ $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
+ $(use_with wxwidgets wxwidgets-ucs)
+ $(use_with freetype freetype "${EPREFIX}/usr")
+ $(use_with fastcgi fastcgi "${EPREFIX}/usr")
+# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
+ $(usex odbc --with-odbc="${EPREFIX}/usr" "")
+ $(use_with python python "${EPREFIX}/usr")
+ $(use_with boost boost "${EPREFIX}/usr")
+ $(use_with sqlite sqlite3 "${EPREFIX}/usr")
+ $(use_with icu icu "${EPREFIX}/usr")
+ $(use_with expat expat "${EPREFIX}/usr")
+ $(use_with xml libxml "${EPREFIX}/usr")
+ $(use_with xml libxslt "${EPREFIX}/usr")
+ $(use_with xerces xerces "${EPREFIX}/usr")
+ $(use_with hdf5 hdf5 "${EPREFIX}/usr")
+ $(use_with xalan xalan "${EPREFIX}/usr")
+# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
+ --without-gif
+ $(use_with jpeg jpeg "${EPREFIX}/usr")
+ $(use_with tiff tiff "${EPREFIX}/usr")
+ $(use_with png png "${EPREFIX}/usr")
+ $(use_with xpm xpm "${EPREFIX}/usr")
+ $(use_with curl curl "${EPREFIX}/usr")
+# $(use_with X x "${EPREFIX}/usr")
+# $(use_with X x) # there is no --with-x option
+ )
+
+ # http://www.ncbi.nlm.nih.gov/books/NBK7167/
+ use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
+
+ # TODO
+ # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+ # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
+
+ einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
+
+# ECONF_SOURCE="src/build-system" \
+# econf \
+ bash \
+ ./src/build-system/configure \
+ --srcdir="${S}" \
+ --prefix="${EPREFIX}/usr" \
+ --libdir=/usr/lib64 \
+ --with-flat-makefile \
+ ${myconf[@]} || die
+#--without-debug \
+# --with-bin-release \
+# --with-bincopy \
+# --without-static \
+# --with-dll \
+# --with-mt \
+# --with-openmp \
+# --with-lfs \
+# --prefix="${ED}"/usr \
+# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
+# ${myconf} LDFLAGS="-Wl,--no-as-needed" \
+# || die
+# econf ${myconf[@]}
+}
+
+src_compile() {
+ ## all_r would ignore the --with-projects contents and build more
+ ## emake all_r -C GCC*-Release*/build || die
+ ## all_p with compile only selected/required components
+ ##cd "${S}"_build &&\
+ ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+ #emake all_p -C "${S}"_build/build
+
+ #
+ # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
+ #
+ # The next release should automatically address such underlinking, albeit
+ # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to
+ # add or extend more DLL_LIB settings, to which end you may find the
+ # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
+ # helpful. For instance,
+ #
+ # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
+ #
+ # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
+ #
+ # DLL_LIB = xncbi
+ #
+ # (You can find the path to that makefile by examining
+ # .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
+ #
+ # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
+ emake -C "${S}"_build/build -f Makefile.flat
+}
+
+src_install() {
+ rm -rvf "${S}"_build/lib/ncbi || die
+ emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+# dobin "${S}"_build/bin/*
+# dolib.so "${S}"_build/lib/*so*
+# dolib.a "${S}"_build/lib/*.a
+# doheader "${S}"_build/inc/*
+
+ # File collisions with sci-biology/ncbi-tools
+ mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
+ mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
+ mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
+ mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
+ mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
+
+ echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
+ doenvd "${S}/99${PN}"
+}
+
+pkg_postinst() {
+ einfo 'Please run "source /etc/profile" before using this package in the current shell.'
+ einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
+}
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2016-01-06 8:49 Justin Lecher
0 siblings, 0 replies; 23+ messages in thread
From: Justin Lecher @ 2016-01-06 8:49 UTC (permalink / raw
To: gentoo-commits
commit: 6dc5c0b8a6653268b5999449b161dd4cfb803da5
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 6 08:46:17 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 6 08:46:29 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6dc5c0b8
sci-biology/ncbi-blast+: Drop sqlite-2 support
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/ncbi-blast+/metadata.xml | 3 ---
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 7 +++----
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 7 +++----
3 files changed, 6 insertions(+), 11 deletions(-)
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
index 5a7151b..feff0f1 100644
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ b/sci-biology/ncbi-blast+/metadata.xml
@@ -25,9 +25,6 @@
<flag name="sablotron">Undocumented USE</flag>
</use>
<use>
- <flag name="sqlite3">Add support for <pkg>dev-db/sqlite:3</pkg></flag>
- </use>
- <use>
<flag name="xerces">Undocumented USE</flag>
</use>
<use>
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 3008025..9191a03 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -28,7 +28,7 @@ IUSE="
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
- sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+ sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
#KEYWORDS=""
@@ -41,8 +41,7 @@ DEPEND="
berkdb? ( sys-libs/db:4.3[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite:0 )
- sqlite3? ( dev-db/sqlite:3 )
+ sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl media-libs/glew )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 9b3c9b2..bff6d0a 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -28,7 +28,7 @@ IUSE="
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
- sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+ sablotron sqlite tiff xerces xalan xml xpm xslt X"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
#KEYWORDS=""
@@ -41,8 +41,7 @@ DEPEND="
berkdb? ( sys-libs/db:4.3[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite:0 )
- sqlite3? ( dev-db/sqlite:3 )
+ sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl media-libs/glew )
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2015-07-17 0:40 Andrew Savchenko
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Savchenko @ 2015-07-17 0:40 UTC (permalink / raw
To: gentoo-commits
commit: 251d0d61a873aabcd335c0487824308435add159
Author: Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Fri Jul 17 00:39:35 2015 +0000
Commit: Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Fri Jul 17 00:39:35 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=251d0d61
Fix repoman fatal error (invalid USE description)
sci-biology/ncbi-blast+/ChangeLog | 3 +++
sci-biology/ncbi-blast+/metadata.xml | 3 +++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog
index 0da59fd..19ac9ea 100644
--- a/sci-biology/ncbi-blast+/ChangeLog
+++ b/sci-biology/ncbi-blast+/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Jul 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml:
+ Add sqlite3 flag description.
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-blast+-2.2.30.ebuild:
sci-biology/ncbi-blast+: fix SLOT operators; correct python deps
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
index feff0f1..5a7151b 100644
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ b/sci-biology/ncbi-blast+/metadata.xml
@@ -25,6 +25,9 @@
<flag name="sablotron">Undocumented USE</flag>
</use>
<use>
+ <flag name="sqlite3">Add support for <pkg>dev-db/sqlite:3</pkg></flag>
+ </use>
+ <use>
<flag name="xerces">Undocumented USE</flag>
</use>
<use>
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 23+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: b4ed4b3dc7977bc337a22d72776d2540dc001676
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:27:46 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:27:46 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b4ed4b3d
sci-biology/ncbi-blast+: fix SLOT operators; correct python deps
Package-Manager: portage-2.2.17
---
sci-biology/ncbi-blast+/ChangeLog | 3 +++
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 16 ++++++++++------
2 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog
index 0e7a67d..0da59fd 100644
--- a/sci-biology/ncbi-blast+/ChangeLog
+++ b/sci-biology/ncbi-blast+/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-blast+-2.2.30.ebuild:
+ sci-biology/ncbi-blast+: fix SLOT operators; correct python deps
+
15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> metadata.xml:
added use flags to metadata.xml
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 6b95dc4..498a6af 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -4,7 +4,9 @@
EAPI=5
-inherit eutils flag-o-matic multilib toolchain-funcs
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
MY_PV="2.2.30"
MY_P="ncbi-blast-${PV}+-src"
@@ -30,6 +32,8 @@ IUSE="
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
#KEYWORDS=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
# sys-libs/db should be compiled with USE=cxx
DEPEND="
!sci-biology/ncbi-tools++
@@ -37,7 +41,7 @@ DEPEND="
berkdb? ( sys-libs/db:4.3[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite )
+ sqlite? ( dev-db/sqlite:0 )
sqlite3? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
@@ -47,7 +51,7 @@ DEPEND="
freetype? ( media-libs/freetype )
fastcgi? ( www-apache/mod_fastcgi )
gnutls? ( net-libs/gnutls )
- python? ( dev-lang/python )
+ python? ( ${PYTHON_DEPS} )
cppunit? ( dev-util/cppunit )
icu? ( dev-libs/icu )
expat? ( dev-libs/expat )
@@ -59,9 +63,9 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg )
- png? ( media-libs/libpng )
- tiff? ( media-libs/tiff )
+ jpeg? ( virtual/jpeg:0= )
+ png? ( media-libs/libpng:0= )
+ tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
dev-libs/lzo
app-arch/bzip2
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/
@ 2015-01-15 17:00 Christoph Junghans
0 siblings, 0 replies; 23+ messages in thread
From: Christoph Junghans @ 2015-01-15 17:00 UTC (permalink / raw
To: gentoo-commits
commit: 689d297c9357c98307106bcda90b375e180aa652
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 17:00:35 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 17:00:35 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=689d297c
added use flags to metadata.xml
Package-Manager: portage-2.2.14
---
sci-biology/ncbi-blast+/ChangeLog | 4 +++-
sci-biology/ncbi-blast+/metadata.xml | 27 +++++++++++++++++++++++++++
2 files changed, 30 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog
index 819f1f4..0e7a67d 100644
--- a/sci-biology/ncbi-blast+/ChangeLog
+++ b/sci-biology/ncbi-blast+/ChangeLog
@@ -2,10 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> metadata.xml:
+ added use flags to metadata.xml
+
*ncbi-blast+-2.2.30 (14 Jan 2015)
14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ncbi-blast+-2.2.30.ebuild, +files/disable-testsuite-compilation.txt,
+files/fix_lib_deps.patch, +metadata.xml:
ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch
-
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
index 2bc8930..feff0f1 100644
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ b/sci-biology/ncbi-blast+/metadata.xml
@@ -6,4 +6,31 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
+ <use>
+ <flag name="boost">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="cppunit">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="freetype">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="mesa">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="muparser">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="sablotron">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="xerces">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="xalan">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="xslt">Undocumented USE</flag>
+ </use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 23+ messages in thread
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