Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

9 files changed, 65 insertions, 85 deletions

diff --git a/sci-mathematics/pest/ChangeLog b/sci-mathematics/pest/ChangeLog
index a8bbaa214..67e52b8fb 100644
--- a/sci-mathematics/pest/ChangeLog
+++ b/sci-mathematics/pest/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Nov 2010; Tim Cera <timcera@earthlink.net> pest-12.1.ebuild:
+  Fixed come code for some of the utility programs.
+
+*pest-12.1 (16 Nov 2010)
+
+  16 Nov 2010; Tim Cera <timcera@earthlink.net> -pest-12.0.ebuild,
+  +pest-12.1.ebuild:
+  sci-mathematics/pest: Version bump and minor changes.
+
 *pest-12.0 (26 Jan 2010)
 
   26 Jan 2010; Tim Cera <timcera@earthlink.net> -pest-11.3.ebuild,
diff --git a/sci-mathematics/pest/Manifest b/sci-mathematics/pest/Manifest
index b6ebdc3d2..44512bc18 100644
--- a/sci-mathematics/pest/Manifest
+++ b/sci-mathematics/pest/Manifest
@@ -1,6 +1,6 @@
 DIST addendum.pdf 1029933 RMD160 2d0f620559ead34aace3dc3cc4e8bf8b92882be4 SHA1 d806bd3603d39e2ab0cdecce58325f93898d64d0 SHA256 e4a8d050020bec968a6526e4aa6a7dc3cc01c51d118c773b5930d1d9a3260569
-DIST pest-12.0.tar.zip 1046731 RMD160 20b1040f204d134ef3a3479172e73445fa1d1d19 SHA1 98aee846bfab39cd4efc5373a5239a0d42aa38f9 SHA256 181615682aca7b76f32a43ecd20c9260fa7646bf52b67137b4885927da39c088
+DIST pest-12.1.tar.zip 1065554 RMD160 d0b8164cfeda65213bfd76bd46a1042a933bb6b1 SHA1 46b82fdf56ed6a47a76c05ebf3f2de941c4bf511 SHA256 b84b95551d839636433db7eb719a11ef37c0d89a736f2cfdf27b37e7a81833c6
 DIST pestman.pdf 1743872 RMD160 13fa38e0c5885db7bbacebc43afa718a11bd7ede SHA1 0a2243298332f4a19504e0983fb42e744a302911 SHA256 48a9f657c2a49b9e4a231a9573871a497f79634ac614587af82b0dbb41fbf893
-EBUILD pest-12.0.ebuild 1797 RMD160 48eef7cf0bafe2f3845ee191f4ff675e7169bbc6 SHA1 c629a6ae25846294b4a227697977b104f799deb6 SHA256 234ff9a4a4cabdf508c458c446a3bee6992ca3fa280ce0c5d25f99a54df686e5
-MISC ChangeLog 772 RMD160 57170befa2bdfce60359ae0957975fc87d5f8377 SHA1 65032e79747dfeeea4c15a59bb475e57d08ad53f SHA256 5ae13425e6f3e96e6204701e3014681bf5f3fcd7fd53f5ddfcbc1e87b8fe5c14
+EBUILD pest-12.1.ebuild 2096 RMD160 11f32dfb6f31268616635f165281f471f19094b4 SHA1 5015b1b29fc05bdb4d1db60f1d70b28b01ebc3bb SHA256 f97900f24b50ec72bd5186ce6bc07298867c1e3de1315a8421211f440d57256f
+MISC ChangeLog 943 RMD160 9d2a37663bfd0e2f3eda0606a6a208dd3104b33e SHA1 80308ce7b8aca61c1fe25218221a9259377218e9 SHA256 ed920c4397423c886b1f635777b87c58d9df4cb6b38142cd2673044f7e22d6c4
 MISC metadata.xml 382 RMD160 582743add3713788f6b66839dbb323f4f4c317cf SHA1 09bb79f2ccc27ed21f72496cb8f727eeb586ee2b SHA256 6f81bf54599563d6ae7525ac3212a0c6f52a0ec6a2611322cdabf0c167c61757
diff --git a/sci-mathematics/pest/pest-12.0.ebuild b/sci-mathematics/pest/pest-12.1.ebuild
index c12d9c12a..0a28ae19a 100644
--- a/sci-mathematics/pest/pest-12.0.ebuild
+++ b/sci-mathematics/pest/pest-12.1.ebuild
@@ -2,12 +2,16 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI="2"
+
 inherit fortran versionator
 
+MY_P="${P/-/}"
+
 DESCRIPTION="Model-independent Parameter ESTimation for model calibration and
 predictive uncertainty analysis."
 HOMEPAGE="http://www.pesthomepage.org"
-SRC_URI="http://www.pesthomepage.org/files/${P}.tar.zip
+SRC_URI="http://www.pesthomepage.org/getfiles.php?file=${MY_P}.tar.zip -> ${P}.tar.zip
 	doc? ( http://www.pesthomepage.org/files/pestman.pdf
 	       http://www.pesthomepage.org/files/addendum.pdf )"
 
@@ -30,8 +34,10 @@ S="${WORKDIR}/${PN}"
 src_unpack() {
 	mkdir "${S}" && cd "${S}"
 	unpack "${P}.tar.zip"
-	unpack ./"${PN}$(get_major_version).tar"
+	unpack ./"${MY_P}.tar"
+}
 
+src_prepare() {
 	# I decided it was cleaner to make all edits with sed, rather than a patch.
 	sed -i \
 		-e "s;^F90=.*;F90=${FORTRANC};" \
@@ -44,6 +50,12 @@ src_unpack() {
 		-e "s;^INSTALLDIR=.*;INSTALLDIR=${D}/usr/bin;" \
 		-e 's;^install :;install :\n\tinstall -d $(INSTALLDIR);' \
 		 makefile
+
+	# These changes are just for 12.1 - should go away
+	sed -i \
+	    -e 's/\(.*jco2jco .*jco2jco.*\)/\1 openun.o/' \
+	    -e 's/\(.*jcochek .*jcochek.o.*\)/\1 openun.o/' pestutl1.mak
+	sed -i -e '/.*integer.*ies2ipar.*$/ d' cmaes_p.F sceua_p.F
 }
 
 src_compile() {
diff --git a/sci-visualization/ferret-bin/ChangeLog b/sci-visualization/ferret-bin/ChangeLog
index 922c00190..1b3708ce0 100644
--- a/sci-visualization/ferret-bin/ChangeLog
+++ b/sci-visualization/ferret-bin/ChangeLog
@@ -2,6 +2,19 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ferret-bin-6.6.4 (16 Nov 2010)
+
+  16 Nov 2010; Tim Cera <timcera@earthlink.net> -ferret-bin-6.4.ebuild,
+  -ferret-bin-6.5.ebuild, +ferret-bin-6.6.4.ebuild:
+  Version bump.
+
+*ferret-bin-6.6.2 (10 Aug 2010)
+
+  10 Aug 2010; Tim Cera <timcera@earthlink.net> -ferret-bin-6.4.ebuild,
+  +ferret-bin-6.6.2.ebuild:
+  Version bump. Ferret now requires libcurl.so.3, where only libcurl.so.4 is
+  available so added symlink.
+
 *ferret-bin-6.5 (09 Apr 2010)
 
   09 Apr 2010; Tim Cera <timcera@earthlink.net> +ferret-bin-6.5.ebuild:
diff --git a/sci-visualization/ferret-bin/Manifest b/sci-visualization/ferret-bin/Manifest
index 320da39f8..8d47ba410 100644
--- a/sci-visualization/ferret-bin/Manifest
+++ b/sci-visualization/ferret-bin/Manifest
@@ -1,14 +1,9 @@
 AUX 99ferret 673 RMD160 4d3486b9c9612c0c2491c21744dae34d1a2d667c SHA1 0d93a2f271a7aed837fe79cd73504a266412e007 SHA256 23e1c54a4ee63f74ab44285d4362838a4cd49572aee9478c5b58a95458f81d6e
-DIST amd64fer_environment.v64.tar.gz 7517382 RMD160 348e9ef504c6deb6304b4b813bd472fc4a3a5147 SHA1 81b5d1567828a82dd998363d1d9f4459b677a2b5 SHA256 2ae6d448b37dfcb3b438e46b3b75ca9a152ea54b973dc413a09f85fc37938c27
-DIST amd64fer_environment.v65.tar.gz 7540244 RMD160 ceda414aa13b10ba27743630e714b9e2f5a58412 SHA1 91f20ffbb856a167ff039b67f33281555842acae SHA256 a9b4df0241216bd73cc9d71dc3aab3f907018b7350364f6d69c5b8642b4b517c
-DIST amd64fer_executables.v64.tar.gz 6353614 RMD160 7108a13669dd4484b2c5de6e218d31037e9ca062 SHA1 41ed6d671d355f0ef187e49e503552349cc78ec4 SHA256 b8f56070b01f7027bf05e60c9d9a48641f37909f6114d742f1cc6ffa6f5e2f98
-DIST amd64fer_executables.v65.tar.gz 6242809 RMD160 9f43dd4f83d6d68a41dcccb62fc2a636ad896b8d SHA1 1fcaf929b70de5eec1177b47365fed6f348eda82 SHA256 db23b23a435f550557046b9f181a18476f4aa5de9b5fb0909a711b6e2722f455
+DIST amd64fer_environment.v664.tar.gz 8079499 RMD160 dd0d4f84440fb78aebd42a8c2963935d261e82cc SHA1 864dace46d24ad8c9373b5a85066f6afbbd7e05a SHA256 de02d54e825e1f32d8fefc651027202941a8985425202f1872bab84119bed698
+DIST amd64fer_executables.v664.tar.gz 5408420 RMD160 bb8eb43e9b835a51d66b33990c173e2a11fe5194 SHA1 395c0dd4498d0a0a2baf182bd70408f0bc8b5c6a SHA256 4212f24f079a599cbb5a15cd21f41b723ebe710208de4efc14b58222feb95c58
 DIST fer_dsets.tar.gz 39991296 RMD160 dc3c8c67d86bcddad6bf1d984b524e1121ea5286 SHA1 4e0f514b7ae1441597e0f06fd06eda5797025ce6 SHA256 094645b275520321940002d286e792877a4867e2576832e246ab3d3f113425f3
-DIST x86fer_environment.v64.tar.gz 7519737 RMD160 01cf4ed3e71dbc758e1fd18bd17b36b9a89d5f27 SHA1 65f5e13797460f215c6f6f3c965d88b92b4cf9d7 SHA256 1dd264a8623e30e091fe133af8a9392b4a1015a4d5a4a77e2f821a5014902623
-DIST x86fer_environment.v65.tar.gz 7539235 RMD160 889ba4770aa4c0028ad22433ead028adbc100db8 SHA1 bbb174bbf68c9d54a292781f236cf4a34e814db3 SHA256 cfb876a925b418074b0cf3ff8225e349f414e7b1bd034e6f28c2a2540043623c
-DIST x86fer_executables.v64.tar.gz 5838185 RMD160 fb0172243690f8ad98d46b946784fd728dcc2502 SHA1 08c5fd8bbb2d9679af47b71339077cc4765b26ab SHA256 7d8c23243d0edf0bd61cb495bbb82a6b55636862b29b9a250aeda397a434e749
-DIST x86fer_executables.v65.tar.gz 5815631 RMD160 d46cb56dd21c8ba61a553bb5b7476e38e02c93d3 SHA1 4eba69f27247894d5eacc536f6bb5ae5f42124c0 SHA256 97fcf84a6bd2bb1de406f97606a748ff754ecdfc4514e3afd5fa2f581b984659
-EBUILD ferret-bin-6.4.ebuild 1500 RMD160 bcbcf50c5f4cfa52d60a3dee1cbcfd8c3756360f SHA1 f02acd29160f888b1791eaa65afe309b76d0e734 SHA256 8f9055540719eba8b112f234d469e262caa7ce00317c8837f2a5791d077c0eda
-EBUILD ferret-bin-6.5.ebuild 1500 RMD160 bcbcf50c5f4cfa52d60a3dee1cbcfd8c3756360f SHA1 f02acd29160f888b1791eaa65afe309b76d0e734 SHA256 8f9055540719eba8b112f234d469e262caa7ce00317c8837f2a5791d077c0eda
-MISC ChangeLog 1174 RMD160 d377035b3b92f6dead5ae569a3717d4493e2d3ef SHA1 8ecc80941af96e7f6522f087d1b2097997a32491 SHA256 851f8d85b82be2aeb73c38d680139a1361a9b45bd07528b50b4546b385c1b8d8
+DIST x86fer_environment.v664.tar.gz 7671499 RMD160 40912a10e921d1814a6a72a4c31f1230d4008804 SHA1 cc74b21df222236bae5e8038bedf4a6640ccc7fb SHA256 bf011446669aea636e3c3eff07c72792c6319ce12e3a589d8bd7b8ecd65503ec
+DIST x86fer_executables.v664.tar.gz 3813127 RMD160 1070576386af84e256da40f3bb21e76912f75a99 SHA1 5301cc8ae3e5611f34cc370fe1b0f9f49629ca42 SHA256 34416d6934dea3c938f51d18869b36fd78f2ca31d403e8303cd007f3c1a38e89
+EBUILD ferret-bin-6.6.4.ebuild 1576 RMD160 c533e5c40f9107acdb34561601c275d2316bb2a3 SHA1 352b82d8e7f63db2f95a13adb9d64f823ed082ad SHA256 a84387c478d1605407eae32b392dba9bd78019ffbf937fd809afd53df45a1084
+MISC ChangeLog 1709 RMD160 f83bc23549134197b4e1fe7213cca6233f1f1d4d SHA1 8068e562d08db44ab0b389beb41a112753145dc5 SHA256 59daaeb29bc423006aa8d881d27a82e60371c0761b0223d177651a3985bc93b4
 MISC metadata.xml 362 RMD160 81d21aa9fb0e54a53c2db8ea0965a59a633417fa SHA1 8e0c5a42c19d225c6b0087173dfd3498fb6098ad SHA256 114c2d067f3f6e4e809739707c042f4a2959895fe4f8dfdd86f52857d6e4532a
diff --git a/sci-visualization/ferret-bin/ferret-bin-6.5.ebuild b/sci-visualization/ferret-bin/ferret-bin-6.5.ebuild
deleted file mode 100644
index 45e531a57..000000000
--- a/sci-visualization/ferret-bin/ferret-bin-6.5.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-MY_PV=${PV/\./}
-
-MY_FER_ENV="fer_environment.v${MY_PV}.tar.gz"
-MY_FER_EXE="fer_executables.v${MY_PV}.tar.gz"
-
-DESCRIPTION="Ferret is an interactive computer visualization and analysis environment"
-HOMEPAGE="http://ferret.pmel.noaa.gov/Ferret/"
-SRC_URI="ftp://ftp.pmel.noaa.gov/ferret/pub/data/fer_dsets.tar.gz
-	x86? ( ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32/${MY_FER_ENV} -> x86${MY_FER_ENV}
-	       ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32/${MY_FER_EXE} -> x86${MY_FER_EXE} )
-	amd64? ( ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux/${MY_FER_ENV} -> amd64${MY_FER_ENV}
-	         ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux/${MY_FER_EXE} -> amd64${MY_FER_EXE} )"
-
-LICENSE="PMEL-FERRET"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	>=app-crypt/mit-krb5-1.6.3-r6
-	x11-base/xorg-server
-	~virtual/libstdc++-3.3"
-
-BASEDIR="/opt/ferret-bin"
-
-src_unpack() {
-	mkdir "${S}"
-	cd "${S}"
-	use x86 && unpack "x86${MY_FER_ENV}"
-	use amd64 && unpack "amd64${MY_FER_ENV}"
-	cd "${S}"/bin
-	use x86 && unpack "x86${MY_FER_EXE}"
-	use amd64 && unpack "amd64${MY_FER_EXE}"
-	cd "${S}"
-	mkdir data
-	cd data
-	unpack "fer_dsets.tar.gz"
-}
-
-src_install() {
-	mkdir -p ext_func/libs
-	mv bin/*.so ext_func/libs
-
-	mkdir -p "${D}/${BASEDIR}"
-	mv "${S}"/* "${D}/${BASEDIR}"
-
-	doenvd "${FILESDIR}"/99ferret
-}
-
-pkg_postinst() {
-	env-update
-}
-
-pkg_postrm() {
-	env-update
-}
diff --git a/sci-visualization/ferret-bin/ferret-bin-6.4.ebuild b/sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild
index 45e531a57..fa19c3407 100644
--- a/sci-visualization/ferret-bin/ferret-bin-6.4.ebuild
+++ b/sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild
@@ -4,7 +4,9 @@
 
 EAPI="2"
 
-MY_PV=${PV/\./}
+inherit versionator eutils
+
+MY_PV=$(delete_all_version_separators "${PV}" )
 
 MY_FER_ENV="fer_environment.v${MY_PV}.tar.gz"
 MY_FER_EXE="fer_executables.v${MY_PV}.tar.gz"
@@ -12,10 +14,10 @@ MY_FER_EXE="fer_executables.v${MY_PV}.tar.gz"
 DESCRIPTION="Ferret is an interactive computer visualization and analysis environment"
 HOMEPAGE="http://ferret.pmel.noaa.gov/Ferret/"
 SRC_URI="ftp://ftp.pmel.noaa.gov/ferret/pub/data/fer_dsets.tar.gz
-	x86? ( ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32/${MY_FER_ENV} -> x86${MY_FER_ENV}
-	       ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32/${MY_FER_EXE} -> x86${MY_FER_EXE} )
-	amd64? ( ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux/${MY_FER_ENV} -> amd64${MY_FER_ENV}
-	         ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux/${MY_FER_EXE} -> amd64${MY_FER_EXE} )"
+	x86? ( ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32_nc4/${MY_FER_ENV} -> x86${MY_FER_ENV}
+	       ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32_nc4/${MY_FER_EXE} -> x86${MY_FER_EXE} )
+	amd64? ( ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux_nc4/${MY_FER_ENV} -> amd64${MY_FER_ENV}
+	         ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux_nc4/${MY_FER_EXE} -> amd64${MY_FER_EXE} )"
 
 LICENSE="PMEL-FERRET"
 SLOT="0"
diff --git a/sys-cluster/glusterfs/Manifest b/sys-cluster/glusterfs/Manifest
index 673e0251e..77925e518 100644
--- a/sys-cluster/glusterfs/Manifest
+++ b/sys-cluster/glusterfs/Manifest
@@ -1,6 +1,6 @@
 AUX 50glusterfs-mode-gentoo.el 169 RMD160 406c0dd2d79d054f059fcae29961fb6b7950e367 SHA1 5cb956b94b2704d244a4031093305de3243a7a86 SHA256 2467d044665d16dd95f78f7a7a104099ce00849cd0a2a86b110fe4c91b316a9d
 AUX glusterd-workdir.patch 1520 RMD160 e29b4f685d5fed0a9e2c3cac9365fa403e03839f SHA1 ea31d2fa6310a39ca80d3ea3e9c49f59bbf7ce84 SHA256 9b8095e2d1251e5b5a17682eec6b9a8f9916f1607969a794915ec72743a25ae8
-AUX glusterd.initd 465 RMD160 7038d49871f0503d0f4fc14f97e9543ba8543fb3 SHA1 225136e1fffdf7e506f05985a954a91cc38d70bf SHA256 39b442f41c985fd51d8f3c91e438f6b607536260d5808041a1d9c67f4fa302e0
+AUX glusterd.initd 725 RMD160 253a60ca39670513953ab544f1d6e53e35ea4ac1 SHA1 469651fe0d82c1bbb132b396f77ca5d7dc8af1e5 SHA256 c6df1a770fc219f370927694a1d7d3bb2d7654e214d9b88eb1f1424064e488a3
 AUX glusterfs-2.0.8-docdir.patch 1644 RMD160 6961d29068c6b556f195615b789188f28e80b181 SHA1 4ff29870fae0039f390945ccaee3bcd25c87ae70 SHA256 d2922af3e15faae8ae06102a757b158b510b27cc11ad9ffe643ca67e2046ba07
 AUX glusterfs-3.1.0-parallel-build.patch 659 RMD160 a5127f529387a0f9a543c666d139beac6f8b306c SHA1 bf1d566d9b306b44f0a26db7d2c9ddaa10f8a872 SHA256 7aeb616d41bf898d1df2cf4773802e88e41e13271184eab03c46034a9c22027c
 AUX glusterfs.confd 129 RMD160 ba0a6f22452b70cb3a7eb6f3bdd2b06e7c441b04 SHA1 c83f9e5c0becaf798b30b1709ea7086b56dd2992 SHA256 a9023ba1112ceb4597c654228f0beb0053ed695aeb32c65e0749a7157fab563d
diff --git a/sys-cluster/glusterfs/files/glusterd.initd b/sys-cluster/glusterfs/files/glusterd.initd
index 995ae5327..027d22037 100644
--- a/sys-cluster/glusterfs/files/glusterd.initd
+++ b/sys-cluster/glusterfs/files/glusterd.initd
@@ -7,6 +7,7 @@ PIDFILE=/var/run/glusterd.pid
 
 depend() {
 	need net
+	before netmount
 }
 
 start() {
@@ -20,5 +21,16 @@ start() {
 stop() {
 	ebegin "Stopping glusterd"
 	start-stop-daemon --stop -q --pidfile "${PIDFILE}"
+	eindent
+
+	einfo "Unmounting GlusterFS filesystems"
+	umount -t fuse.glusterfs -a
+
+	einfo "Killing remaining GlusterFS processes"
+	for PID in $(find /var/lib/glusterd/ -type f -name "*.pid" -exec cat {} \;); do
+		kill "${PID}"
+	done
+
+	eoutdent
 	eend $?
 }