From ee68772f2b54b5c47b169a1a2a2febd57ba44e49 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Fri, 7 Aug 2015 11:03:58 +0000 Subject: Drop old, fixes bug #478592 Signed-off-by: Justin Lecher Package-Manager: portage-2.2.20/cvs/Linux x86_64 Manifest-Sign-Key: 0xE9402A79B03529A2! --- sci-chemistry/pdb2pqr/ChangeLog | 8 +- sci-chemistry/pdb2pqr/Manifest | 42 +++--- sci-chemistry/pdb2pqr/files/1.7.0-install.patch | 131 ----------------- .../pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch | 105 -------------- .../pdb2pqr/files/pdb2pqr-1.4.0-install.patch | 134 ----------------- .../pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch | 33 ----- .../pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch | 75 ---------- .../pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch | 30 ---- sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild | 159 --------------------- 9 files changed, 25 insertions(+), 692 deletions(-) delete mode 100644 sci-chemistry/pdb2pqr/files/1.7.0-install.patch delete mode 100644 sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch delete mode 100644 sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch delete mode 100644 sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch delete mode 100644 sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch delete mode 100644 sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch delete mode 100644 sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog index a1a3589acb8a..2231d93962da 100644 --- a/sci-chemistry/pdb2pqr/ChangeLog +++ b/sci-chemistry/pdb2pqr/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/pdb2pqr # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.50 2015/08/07 10:36:03 ago Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.51 2015/08/07 11:03:57 jlec Exp $ + + 07 Aug 2015; Justin Lecher -files/1.7.0-install.patch, + -files/pdb2pqr-1.4.0-automagic.patch, -files/pdb2pqr-1.4.0-install.patch, + -files/pdb2pqr-1.4.0-ldflags.patch, -files/pdb2pqr-1.8.0-automagic.patch, + -files/pdb2pqr-1.8.0-ldflags.patch, -pdb2pqr-1.5.0-r2.ebuild: + Drop old, fixes bug #478592 07 Aug 2015; Agostino Sarubbo pdb2pqr-1.9.0-r1.ebuild: Stable for x86, wrt bug #534696 diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest index 4cf1dfb86726..f60b680dc530 100644 --- a/sci-chemistry/pdb2pqr/Manifest +++ b/sci-chemistry/pdb2pqr/Manifest @@ -1,36 +1,30 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -AUX 1.7.0-install.patch 5165 SHA256 965c0bf8077eebc733c60d4e80d05167ce31d7188b01ca43c0fb5c0b27ede22b SHA512 72f290d8df7051f0fc2d42543f0d09fef4350656194f5013f132abb7edbe4dc11f18a3329bbd41b86f9a582b170fea53d472be320f5e08a2f0d84d42b4f4639c WHIRLPOOL ea71e6271c0dd491a7778cf3c0f54ebce79f35680abb49eadfbb6208379b1d5c69b18eacde92183bd005ffad26db115b05f69b7cbcf5256fa72d94caab9509c4 AUX pdb2pka 270 SHA256 ae1112d6b793b10399a4ae14dc5cfd0518c463121d98e00ab08b2827db061303 SHA512 c6e66fa73a3119ea84a9bf304c9c8701a6eaf32870ba8c1755bfd8f2055e20af2f2ebc01fd2bf6a663e5873f3d6da7387a439efac3dcb7d4a415c176cb2f761b WHIRLPOOL ef5d1fac1bacd6403219e36955701b2a2d33a2aa9936b2334ed7ea48346b1cae74481bb634ba67f9250e7bac73723ce2e4da6c759b87c57111fad166624f0b82 AUX pdb2pqr 263 SHA256 f07b197ec4903125e9566b394ed6a620f56511413bf14ba5fdd3484302d166e2 SHA512 5f8c963fc5addf782579b9312f601ec4547573c7ab88df5a6e38c71c9e31e7b7eea3cde99bdac8f8270f3646d933a0b510a94046e3a30736f75953af5d160b8d WHIRLPOOL 8e4889677ec874a88f3d485b133d3e92a3618d0ed90f4199d05add55f1819df94be762d3950ef9bd21db1112fa75adf26f909d04fdc57c4686cccb3244687fd2 -AUX pdb2pqr-1.4.0-automagic.patch 3526 SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a SHA512 dfb5a219fabe4b57da82098c80eb6556e6826cd91d3db2da2e858964180cfe3268314562320159b82dc811a08714ca3a0e78881244949ff7ffeef2f797397237 WHIRLPOOL 03061ecbab813a572f18a794609655aa9ad9a16d6ed10c421437dddac589de750adacdfe2f89b17e022cccf0ffe0018a40bbe2e7f37c692d025f6998088364af -AUX pdb2pqr-1.4.0-install.patch 5372 SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643 SHA512 615e984335d67668689423d4ab37be996cb178450a2ae0782432d47d7be2cfa8aaeb18776e604c706df743d2a30b93bc1febc28722ef7b5b2480545ca3ccd510 WHIRLPOOL c054c12d1c9ed4ad093326736fd74c6af54d7124ef6455120e5bf37a1a683cf1a5d1a9faec7ff323c7512c4bdbd53c703ee305daf6c76847e87aa2b9a58f7b59 -AUX pdb2pqr-1.4.0-ldflags.patch 1293 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726 SHA512 4edf74ae59b5ca99e2c492103d16769f300293df07f833d78d8e7d24d85c10531ac7907c5444b65507952f4622608459952ae57835f52af8b0f7e09637f1fcf5 WHIRLPOOL 359a84ecaa55cadfa7cf1bb3c116105c486f1fa737d74b6f2ba2f399147dfcd15d088682c75efee7a69394a3f7adf7dc0c978c060ad64c105b3e96a0b75f49d5 -AUX pdb2pqr-1.8.0-automagic.patch 2544 SHA256 135cfe03fc38a7bef028452010dedab3cc90c1f554cef1139b1d9836824520e9 SHA512 65dc03368909a9378ecda6c8357e9119bd76311b5fd6dc0ce00ff7d5b948190ad9f07ac3626dad04915928558f911f4deea5f44725e6cf029ca26dcb2e54b76c WHIRLPOOL 8462f3288722bcaca651845242b3354f365a9686a6400d3fae9c8ca69e3fa55d9282a62bdc2a3374eb468fbfae2611f8fa700ddecc404943c2a08080fad34b06 -AUX pdb2pqr-1.8.0-ldflags.patch 1098 SHA256 b9ab2740e062b130c4b61d385b762d4ce54ec3d6a040f37b8b501b4f107890b8 SHA512 0bd250efd74c70096011ed6f9f6fd2f22a987bbe0355f5ba33ad4675141d1d7b02e9eaa90bc1c7328454da2225183a56dae6acbaae97a929b2455430ca55ab4e WHIRLPOOL 75b4110d4259454551256c3a647b1981aa4ee040f73baf8f3e5ce1f0a4b01b54cdf2879030265dde4c7dbc0a5c60bd400a0d498f00446c88125d147c291ef107 AUX pdb2pqr-1.9.0-flags.patch 1392 SHA256 478b86cf3871e39b9d231a10474abbcade07eceb32db2a83c0e68bbd2c1f5f32 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b WHIRLPOOL 7280c677dbfeb309c6c66d495c857a581fbac80801f9241c20ff17a2c6f4e051929f675807ec30f8dce1fd5337937c76e857b955570f2c1f134855a2b7c0ec2c AUX pdb2pqr-1.9.0-install-py.patch 578 SHA256 c82c11eb421a839710d40bfb3de4d99852ef69dc9b35b1ac31f7b51b36ff512d SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 WHIRLPOOL 94348fe88a1910e916ca0d428a78636e5fe8371582a80dbbbda07d433d1fb8a35157a73d525eac88bd9dac6dc1c3a913288fdb7bd06f7584553b0b5c17aa17da -DIST pdb2pqr-1.5.tar.gz 5747178 SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5 DIST pdb2pqr-src-1.9.0.tar.gz 9051969 SHA256 d9d91bf27a023732be33d1d780ef283ae28d3b0e256c53e86c37ac001dd7ef53 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f WHIRLPOOL 4a4b883200dad3e7467392e508c2372ad6876e78005da14e5747f3b7b12d0e3d5695e3cc590812b835ae67703819b201620809dff05af0a7c363c23d22046bae -EBUILD pdb2pqr-1.5.0-r2.ebuild 3668 SHA256 09b59ed6461c60ca7fdcdca1604306579f054db992b1833226cce00566f05a7a SHA512 2d1ce04378e15d814dfc73d407149465e61b04d646710b918708e4f8eb1a6f1973c85cfca0d63dfa8f85aa6cf1e61b3a950c82833ff7853e2d6d3bc223890f6d WHIRLPOOL 3e4da41f599befa813ec693c8fd2b42ffda163047a43ecbe8f83a3fd63e1066a61e05e56993b2fa3fcc507e652ad60ad3aeca7c6fbb1e967edcc1ead362b943d EBUILD pdb2pqr-1.9.0-r1.ebuild 3030 SHA256 bebe2059a75043ec8634b6c9130e19f2f1b2ea8a001d83d137e7daca15d8d4f3 SHA512 f0dc8a0464d84e72e595817b17aaa703346666a1f0e07e098eea810cf1b0c039485c0542d7bbe4cf32e06263f5e0bdf4819f0bf951bee70be5945732a3d2f618 WHIRLPOOL 617ac375dacaa0f473adec511ab9d8d02256ac415fee584d3273b37edfd27b52a939c656474d009feea3a538f217f673710c77b7fb8d1e807dc601208a71ef7f -MISC ChangeLog 7834 SHA256 bed1e46ddeccb2ecdde0e78af7f30e9550ccf68b21851ca8902c93b46e7fbe47 SHA512 f012e61047aacc2b115a9c238dd1fad6489ac6890b3e602cd9d582b0088e144168958d1d2ad15d1accec0b4a19a27d08507c8604c7ff54ffc83505237fe68a27 WHIRLPOOL 8d87d9a8bbf8678a35e248103b3a5f6c245b4b4fd48c56e5c20961d354ae7b88703c9f417406f3c63efd7bd41af5476c8bb32162d63d70065ee74e01d67dfb0a +MISC ChangeLog 8157 SHA256 c05694b5d9f6956e9beb4ef67234f8f8807c0f707696deafcd58dffbb48ec23c SHA512 515f7a96bd3a1b80b11f46d20d3865c5aab7975ff0c8c77266dbf26b5e54dc0718fc006a6d733bbd4f1946e6975df9dfd98232e6393bf38b7891392f57ffc4aa WHIRLPOOL 660a27a3c807e7a445e54ebba830cb0c84b1ab6d5ae9c20d7a9dafcea45af8f343cd608a4103f560a061cd7081b9b76a50cd0a4cfdd9c4be1b22333c341aaa09 MISC metadata.xml 408 SHA256 a835ee092251d931dd23459814c2689bfddeb1682c4baffe05ecccc0e5ebe1ff SHA512 16fec7aa9c078b4221412efc4406a78b840f773bd765682a1eb090306db018d68a266d6f2e0a78c1d86bc7b55d7ec61a6d1bb338f385825956750bfe41a693f5 WHIRLPOOL 5bac81102bacccd18fa3b7322e860fb8de8b6e74c9c79502719345bac650da764876e2be3465a50f9bf29d8dda53e1d07de8ba34bbcd3fa23504e27e2e1f162f -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2 +Version: GnuPG v2.1 -iQIcBAEBCAAGBQJVxIoUAAoJELp701BxlEWfOfMQAKawKibqi8y5yVhCFN8IdOEz -T0xoPUjTaQTIz+ifTzEL0k9Jc3FuEZ+y6IJxDtmzWK+wAoIa8Nukki8rpVxHr0vr -xZlwQZzdpFD8S92OlLQqE+7Wjbx5d8hFeAsWCb/TItHd1zkXSfyThXn2XZVvYpSj -RtxJa4b8WEd0uWdv2wGmbPtz5GOqgY1XGOdK5se0udEWRDpyxqz4jUnpbIUjTPzD -5RezHyY/uUJVeT1KlOmXsc4ItSJAwf+2oTPgPoa3+CwKhOvDZE+T+1oNEi4jb1ZQ -Xy979hv9zezJ6Fmpkheff50viiQ4G2UiXxXinE1yPRVU6x8cJepBdTEuV3+mGkRw -rXY48GOWlT0H8OelAvIY//IRkZi497HKH0BFbL4aGkgkgCa5hSm0wxzG0K1cQSNF -YESRlCbJE0BdukTNviatBfYQLhs4z+nilw5bBsYtzxI7pi9wgvBn7pQN86u02i+X -xU5CRL1N5nh4OeGO+bMd0Bp9fKjUZe+TTE8QYN2Se9Asuvs9VJZCkeD5cXd9h4MI -p3AJ/cHyQbsElsQWey7+A6J5KuYp7qb9uqKfbg2dAQ90wZNfiUfN7S1XXGpTgx2c -kWn7mmYtVJTap+sR3GpnXr3UAJ5wq12ESqepJVTLq1ATa4ARpLRQYK4pJGyYrGo6 -OBYh6aA4lFYpMXBqGGf4 -=HRw3 +iQJ8BAEBCgBmBQJVxJCeXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQ0QUU0N0I4NzFERUI0MTJFN0EyODE0NUFF +OTQwMkE3OUIwMzUyOUEyAAoJEOlAKnmwNSmipJAQAL0WrfXMhUbxpW3wfGzLVBp5 +KhSi8d9MdAi67Xt4boW97z3rTvyrxog9143kWo9vKJyqPcGmj1ycrz84QX06yS7d +Tlu4tOoPiYJs6PYerbskpJvOdFGOTPVpFGU4v1EO661DxZRCjgwCHY+HBpiqFKzB +D0aeUhKz3rT/RW2qEMoLOnW/kQJJGr1Q0wH92VUIi3RgpvtF2NkqIe2PF89HzIzI +RnVqeqWXokLwn/Aute8pb1oEGPueJr6x8d6JVbuKatl6BeAwKGpic8NqkZamxeHs ++D5FzTUocbtnU64tiBBFy2Igl91wpermjjhY2u+IFYtyayDgHRx33DqBfXCVAc3q +iLzACsNJRbAok/dcJqEhDkWFHRERCXDGq3T3DvGMBtBIlBQKmL4XLuq/5ouJrk4j +4iGF3U1jXGQCdSPks01s0lESpp3MZlHHDVeXyNoISRS6ItpnRhU/sjzHZiRPH41O +JDlQBTUDz7Y03jwL5uhmP2WL529XWEqFzxYOLzamSmwJpib4KSGuSr3/IMB4VVLs +Ziw0Ju6ovOANdtMHIVhgoyuguJXQv9JKwGGWfUkIJRhEdDnMNq8doWNx+S/ZZtIC +XPi3S94hFzdCVf3Yz4pSjaGBuZXJzjAf6o3CCEhwtveF9afNYsM2KYbr6873rMnC +DKnl2grjn9xw8HwwJFcm +=SIa8 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch deleted file mode 100644 index 77ee077937dc..000000000000 --- a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch +++ /dev/null @@ -1,131 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index d5d020d..550d52a 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -113,24 +113,11 @@ install: - mkdir $(CWD)/$$dir/tmp ; \ - fi ; \ - chmod 777 $(CWD)/$$dir/tmp ; \ -- echo "Adding server.html" ; \ -- cp $$c/html/server.html $(CWD)/$$dir/index.html ; \ -- echo "Adding python files" ; \ -- cp $$c/*.py* $(CWD)/$$dir/. ; \ -+ cp $$c/main*.py $(CWD)/$$dir/. ; \ - echo "Adding __init__.py" ; \ - cp $$c/__init__.py $(CWD)/$$dir/__init__.py ; \ - echo "Adding pdb2pqr.py" ; \ - cp $$c/pdb2pqr.py $(CWD)/$$dir/. ; \ -- echo "Adding pdb2pqr.cgi" ; \ -- cp $$c/pdb2pqr.cgi $(CWD)/$$dir/. ; \ -- echo "Adding pdb2pqr.css" ; \ -- cp $$c/apbs_cgi.cgi $(CWD)/$$dir/. ; \ -- echo "Adding apbs_cgi.cgi" ; \ -- cp $$c/visualize.cgi $(CWD)/$$dir/. ; \ -- echo "Adding visualize.cgi" ; \ -- cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \ -- echo "Adding querystatus.cgi" ; \ -- cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \ - if ! test -d $(CWD)/$$dir/dat ; then \ - mkdir $(CWD)/$$dir/dat ; \ - fi ; \ -@@ -138,49 +125,12 @@ install: - cp $$c/dat/*.xml $(CWD)/$$dir/dat/. ; \ - cp $$c/dat/*.DAT $(CWD)/$$dir/dat/. ; \ - cp $$c/dat/*.names $(CWD)/$$dir/dat/. ; \ -- if ! test -d $(CWD)/$$dir/doc ; then \ -- mkdir $(CWD)/$$dir/doc ; \ -- fi ; \ -- echo "Adding doc/" ; \ -- cp $$c/doc/*.html $(CWD)/$$dir/doc/. ; \ -- cp $$c/doc/*.sh $(CWD)/$$dir/doc/. ; \ -- if ! test -d $(CWD)/$$dir/doc/images ; then \ -- mkdir $(CWD)/$$dir/doc/images ; \ -- fi ; \ -- cp $$c/doc/images/*.png $(CWD)/$$dir/doc/images/. ; \ -- if ! test -d $(CWD)/$$dir/doc/pydoc ; then \ -- mkdir $(CWD)/$$dir/doc/pydoc ; \ -- fi ; \ -- cp $$c/doc/pydoc/*.html $(CWD)/$$dir/doc/pydoc/. ; \ -- if ! test -d $(CWD)/$$dir/examples ; then \ -- mkdir $(CWD)/$$dir/examples ; \ -- fi ; \ -- echo "Adding examples/" ; \ -- cp $$c/examples/*.html $(CWD)/$$dir/examples/. ; \ -- if ! test -d $(CWD)/$$dir/examples/1a1p ; then \ -- mkdir $(CWD)/$$dir/examples/1a1p ; \ -- fi ; \ -- cp $$c/examples/1a1p/*.pdb $(CWD)/$$dir/examples/1a1p/. ; \ -- cp $$c/examples/1a1p/README $(CWD)/$$dir/examples/1a1p/. ; \ -- if ! test -d $(CWD)/$$dir/examples/ligands ; then \ -- mkdir $(CWD)/$$dir/examples/ligands ; \ -- fi ; \ -- cp $$c/examples/ligands/*.mol* $(CWD)/$$dir/examples/ligands/. ; \ -+ echo "Adding extensions" ; \ - if ! test -d $(CWD)/$$dir/extensions ; then \ - mkdir $(CWD)/$$dir/extensions ; \ - fi ; \ - echo "Adding extensions" ; \ - cp $$c/extensions/*.py $(CWD)/$$dir/extensions/. ; \ -- if ! test -d $(CWD)/$$dir/html ; then \ -- mkdir $(CWD)/$$dir/html ; \ -- fi ; \ -- cp $$c/html/master-index.html $(CWD)/$$dir/html/. ; \ -- cp $$c/html/server.html $(CWD)/$$dir/html/server.html ; \ -- if ! test -d $(CWD)/$$dir/jmol ; then \ -- mkdir $(CWD)/$$dir/jmol ; \ -- fi ; \ -- echo "Adding jmol/" ; \ -- cp -rf $$c/jmol/*.* $(CWD)/$$dir/jmol/. ; \ - if ! test -d $(CWD)/$$dir/src ; then \ - mkdir $(CWD)/$$dir/src ; \ - fi ; \ -@@ -229,49 +179,6 @@ install: - echo PDB2PQR has been installed in $(CWD)/$$dir ; \ - echo ; \ - cd $(CWD)/$$dir ; \ -- cd $$c; \ -- rm lastfieldfile prefixfile dir1file fieldfile ; \ -- echo $(URL) > url_file ; \ -- awk -F"/" '{print $$(NF-1)}' url_file > url_file_2 ; \ -- last_url=`cat url_file_2` ; \ -- echo $(PREFIX) > p_file ; \ -- awk -F"/" '{print $$(NF-1)}' p_file > p_file_2 ; \ -- last_p=`cat p_file_2` ; \ -- rm -f url_file* p_file* ; \ -- if test `whoami` = "root" ; then \ -- webviewable="true" ; \ -- echo ${prefix} > prefix_file_tmp ; \ -- first=`awk -F"/" '{ print $$2 }' prefix_file_tmp` ; \ -- second=`awk -F"/" '{ print $$3 }' prefix_file_tmp` ; \ -- third=`awk -F"/" '{ print $$4 }' prefix_file_tmp` ; \ -- rm -f prefix_file_tmp ; \ -- if test $$first != var || test $$second != www || test $$third != html ; then \ -- webviewable=false ; \ -- fi ; \ -- if test "$$last_url" != "$$last_p" || test "$$webviewable" = "false" ; then \ -- echo Need to make symbolic link between $(PREFIX) and /var/www/html/"$$last_url" ; \ -- if test -d "/var/www/html/$$last_url" ; then \ -- echo "***" Warning! Directory /var/www/html/"$$last_url" already exists. ; \ -- echo Do you want to overwrite this? \(Y/N\); \ -- read choice ; \ -- while (test $$choice != "Y" && test $$choice != "y" && test $$choice != "N" && test $$choice != "n") \ -- do \ -- echo You have entered $$choice. Please enter Y or N: ; \ -- read choice ; \ -- done ; \ -- if test $$choice = "N" || test $$choice = "n" ; then \ -- echo Please run configure again and specify a different --prefix ; \ -- exit 0 ; \ -- fi ; \ -- rm -rf /var/www/html/"$$last_url" ; \ -- fi ; \ -- ln -s $(PREFIX) /var/www/html/"$$last_url" ; \ -- echo "Symbolic link created." ; \ -- fi ; \ -- else \ -- echo Ask your system administrator to make a symbolic link in /var/www/html by executing the following command; \ -- echo ln -s $(PREFIX) /var/www/html/"$$last_url" ; \ -- fi ; \ - fi - - diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch deleted file mode 100644 index addb76b9b4e6..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch +++ /dev/null @@ -1,105 +0,0 @@ -diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac ---- pdb2pqr-1.4.0/configure.ac 2009-04-02 10:53:56.000000000 -0400 -+++ pdb2pqr-1.4.0.new/configure.ac 2009-09-24 19:36:47.000000000 -0400 -@@ -255,38 +255,6 @@ - - # Test for Numeric install - AC_MSG_CHECKING([whether you defined Numeric or Numpy]) -- if (test -n "${NUMERIC}") ; then -- AC_MSG_RESULT([yes]) -- NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1` -- if test "$NUMERIC_INC" = ""; then -- AC_MSG_ERROR([Please check your NUMERIC path. arrayobject.h cannot be found in ${NUMERIC}]) -- fi -- NUMERIC_INC=`dirname ${NUMERIC_INC}` -- NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1` -- if test "${NUMERIC_LIB}" = ""; then -- AC_MSG_ERROR([Please check your NUMERIC path. Numeric.pth cannot be found in ${NUMERIC}]) -- fi -- NUMERIC_NAME=`cat ${NUMERIC_LIB}` -- NUMERIC_LIB=`dirname ${NUMERIC_LIB}` -- NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME} -- if test "${PACKAGE_PATH}" = ""; then -- PACKAGE_PATH=${NUMERIC_LIB} -- else -- PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}" -- fi -- PY_NUMERIC="-I${NUMERIC_INC} " -- PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC" -- else -- AC_MSG_RESULT([no]) -- AC_MSG_CHECKING([for Numeric include files]) -- if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then -- PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric" -- AC_MSG_RESULT([$PY_NUMERIC]) -- PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC" -- else -- AC_MSG_RESULT([no]) -- fi -- fi - - # If failed, test for numpy - AC_MSG_CHECKING([whether you defined numpy]) -@@ -457,29 +425,14 @@ - HAVE_PDB2PQR_OPAL=1 - fi - --if test "$PDB2PQR_OPAL_URL" != ""; then -+if test "$PDB2PQR_OPAL_URL" != "no"; then - HAVE_PDB2PQR_OPAL=1 - if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then - echo ZSI is installed - else - # need to install ZSI -- echo Installing ZSI. This might take a while... -- cd contrib/ZSI-2.1-a1 -- if test `whoami` = "root"; then -- $py_path setup.py install -- else -- zsi_install="true" -- mkdir -p ${prefix}lib/python$PY_VERSION/site-packages -- export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages -- $py_path setup.py install --prefix=${prefix} -- if test -d ${prefix}ZSI ; then -- echo ZSI is installed -- else -- cp -r ./build/lib/ZSI ${prefix}ZSI -- fi -- PYTHONPATH="" -- fi -- cd ../.. -+ echo Missing ZSI -+ exit 1 - fi - fi - -diff -Naur pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py ---- pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py 2007-10-12 15:52:40.000000000 -0400 -+++ pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py 2009-09-24 19:36:07.000000000 -0400 -@@ -3,10 +3,7 @@ - # PC 2005/09/23 - # Get ligand topologies - # --try: -- import Numeric --except: -- import numpy as Numeric -+import numpy as Numeric - - from sets import Set - from ligandclean.trial_templates import * -diff -Naur pdb2pqr-1.4.0/pdb2pka/ligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py ---- pdb2pqr-1.4.0/pdb2pka/ligand_topology.py 2008-06-13 10:15:38.000000000 -0400 -+++ pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py 2009-09-24 19:36:07.000000000 -0400 -@@ -3,10 +3,7 @@ - # PC 2005/09/23 - # Get ligand topologies - # --try: -- import Numeric --except: -- import numpy as Numeric -+import numpy as Numeric - - from sets import Set - from ligandclean.trial_templates import * diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch deleted file mode 100644 index 4af9eda8e1b3..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch +++ /dev/null @@ -1,134 +0,0 @@ ---- Makefile.am 2008-08-07 04:57:43.000000000 +0200 -+++ Makefile.am.new 2009-04-22 13:45:22.000000000 +0200 -@@ -104,30 +104,11 @@ - mkdir $(CWD)/$$dir/tmp ; \ - fi ; \ - chmod 777 $(CWD)/$$dir/tmp ; \ -- echo "Adding server.html" ; \ -- cp $$c/html/server.html $(CWD)/$$dir/index.html ; \ -- echo "Adding python files" ; \ -- cp $$c/*.py* $(CWD)/$$dir/. ; \ -+ cp $$c/main*.py $(CWD)/$$dir/. ; \ - echo "Adding __init__.py" ; \ - cp $$c/__init__.py $(CWD)/$$dir/__init__.py ; \ - echo "Adding pdb2pqr.py" ; \ - cp $$c/pdb2pqr.py $(CWD)/$$dir/. ; \ -- echo "Adding pdb2pqr.cgi" ; \ -- cp $$c/pdb2pqr.cgi $(CWD)/$$dir/. ; \ -- echo "Adding pdb2pqr.css" ; \ -- cp $$c/apbs_cgi.cgi $(CWD)/$$dir/. ; \ -- echo "Adding apbs_cgi.cgi" ; \ -- cp $$c/jmol.cgi $(CWD)/$$dir/. ; \ -- echo "Adding jmol.cgi" ; \ -- cp $$c/visualize.cgi $(CWD)/$$dir/. ; \ -- echo "Adding visualize.cgi" ; \ -- cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \ -- echo "Adding querystatus.cgi" ; \ -- cp $$c/Jmol.js $(CWD)/$$dir/. ; \ -- echo "Adding Jmol.js" ; \ -- cp $$c/JmolApplet.jar $(CWD)/$$dir/. ; \ -- echo "Adding JmolApplet.jar" ; \ -- cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \ - if ! test -d $(CWD)/$$dir/dat ; then \ - mkdir $(CWD)/$$dir/dat ; \ - fi ; \ -@@ -135,44 +115,11 @@ - cp $$c/dat/*.xml $(CWD)/$$dir/dat/. ; \ - cp $$c/dat/*.DAT $(CWD)/$$dir/dat/. ; \ - cp $$c/dat/*.names $(CWD)/$$dir/dat/. ; \ -- if ! test -d $(CWD)/$$dir/doc ; then \ -- mkdir $(CWD)/$$dir/doc ; \ -- fi ; \ -- echo "Adding doc/" ; \ -- cp $$c/doc/*.html $(CWD)/$$dir/doc/. ; \ -- cp $$c/doc/*.sh $(CWD)/$$dir/doc/. ; \ -- if ! test -d $(CWD)/$$dir/doc/images ; then \ -- mkdir $(CWD)/$$dir/doc/images ; \ -- fi ; \ -- cp $$c/doc/images/*.png $(CWD)/$$dir/doc/images/. ; \ -- if ! test -d $(CWD)/$$dir/doc/pydoc ; then \ -- mkdir $(CWD)/$$dir/doc/pydoc ; \ -- fi ; \ -- cp $$c/doc/pydoc/*.html $(CWD)/$$dir/doc/pydoc/. ; \ -- if ! test -d $(CWD)/$$dir/examples ; then \ -- mkdir $(CWD)/$$dir/examples ; \ -- fi ; \ -- echo "Adding examples/" ; \ -- cp $$c/examples/*.html $(CWD)/$$dir/examples/. ; \ -- if ! test -d $(CWD)/$$dir/examples/1a1p ; then \ -- mkdir $(CWD)/$$dir/examples/1a1p ; \ -- fi ; \ -- cp $$c/examples/1a1p/*.pdb $(CWD)/$$dir/examples/1a1p/. ; \ -- cp $$c/examples/1a1p/README $(CWD)/$$dir/examples/1a1p/. ; \ -- if ! test -d $(CWD)/$$dir/examples/ligands ; then \ -- mkdir $(CWD)/$$dir/examples/ligands ; \ -- fi ; \ -- cp $$c/examples/ligands/*.mol* $(CWD)/$$dir/examples/ligands/. ; \ -- if ! test -d $(CWD)/$$dir/extensions ; then \ -- mkdir $(CWD)/$$dir/extensions ; \ -- fi ; \ - echo "Adding extensions" ; \ -+ if ! test -d $(CWD)/$$dir/extensions ; then \ -+ mkdir $(CWD)/$$dir/extensions ; \ -+ fi ; \ - cp $$c/extensions/*.py $(CWD)/$$dir/extensions/. ; \ -- if ! test -d $(CWD)/$$dir/html ; then \ -- mkdir $(CWD)/$$dir/html ; \ -- fi ; \ -- cp $$c/html/master-index.html $(CWD)/$$dir/html/. ; \ -- cp $$c/html/server.html $(CWD)/$$dir/html/server.html ; \ - if ! test -d $(CWD)/$$dir/src ; then \ - mkdir $(CWD)/$$dir/src ; \ - fi ; \ ---- Makefile.am 2009-04-22 13:48:23.000000000 +0200 -+++ Makefile.am.new 2009-04-22 13:49:52.000000000 +0200 -@@ -168,49 +168,6 @@ - echo PDB2PQR has been installed in $(CWD)/$$dir ; \ - echo ; \ - cd $(CWD)/$$dir ; \ -- cd $$c; \ -- rm lastfieldfile prefixfile dir1file fieldfile ; \ -- echo $(URL) > url_file ; \ -- awk -F"/" '{print $$(NF-1)}' url_file > url_file_2 ; \ -- last_url=`cat url_file_2` ; \ -- echo $(PREFIX) > p_file ; \ -- awk -F"/" '{print $$(NF-1)}' p_file > p_file_2 ; \ -- last_p=`cat p_file_2` ; \ -- rm -f url_file* p_file* ; \ -- if test `whoami` = "root" ; then \ -- webviewable="true" ; \ -- echo ${prefix} > prefix_file_tmp ; \ -- first=`awk -F"/" '{ print $$2 }' prefix_file_tmp` ; \ -- second=`awk -F"/" '{ print $$3 }' prefix_file_tmp` ; \ -- third=`awk -F"/" '{ print $$4 }' prefix_file_tmp` ; \ -- rm -f prefix_file_tmp ; \ -- if test $$first != var || test $$second != www || test $$third != html ; then \ -- webviewable=false ; \ -- fi ; \ -- if test "$$last_url" != "$$last_p" || test "$$webviewable" = "false" ; then \ -- echo Need to make symbolic link between $(PREFIX) and /var/www/html/"$$last_url" ; \ -- if test -d "/var/www/html/$$last_url" ; then \ -- echo "***" Warning! Directory /var/www/html/"$$last_url" already exists. ; \ -- echo Do you want to overwrite this? \(Y/N\); \ -- read choice ; \ -- while (test $$choice != "Y" && test $$choice != "y" && test $$choice != "N" && test $$choice != "n") \ -- do \ -- echo You have entered $$choice. Please enter Y or N: ; \ -- read choice ; \ -- done ; \ -- if test $$choice = "N" || test $$choice = "n" ; then \ -- echo Please run configure again and specify a different --prefix ; \ -- exit 0 ; \ -- fi ; \ -- rm -rf /var/www/html/"$$last_url" ; \ -- fi ; \ -- ln -s $(PREFIX) /var/www/html/"$$last_url" ; \ -- echo "Symbolic link created." ; \ -- fi ; \ -- else \ -- echo Ask your system administrator to make a symbolic link in /var/www/html by executing the following command; \ -- echo ln -s $(PREFIX) /var/www/html/"$$last_url" ; \ -- fi ; \ - fi - - diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch deleted file mode 100644 index ea5dc85ba07d..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- pdb2pka/Makefile.am 2008-04-24 21:44:28.000000000 +0200 -+++ pdb2pka/Makefile.am.new 2009-04-22 17:26:24.000000000 +0200 -@@ -16,7 +16,7 @@ - - noinst_PROGRAMS = _pMC_mult.so - _pMC_mult_so_SOURCES = pMC_mult.cpp pMC_mult_wrap.cpp --_pMC_mult_so_LINK = $(CXX) -o $@ $(PY_SHARED) -+_pMC_mult_so_LINK = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED) - _pMC_mult_so_LDADD = $(PY_LDFLAGS) - - #all: ---- pdb2pka/substruct/Makefile.am 2008-04-24 19:54:39.000000000 +0200 -+++ pdb2pka/substruct/Makefile.am.new 2009-04-22 17:26:57.000000000 +0200 -@@ -15,7 +15,7 @@ - - noinst_PROGRAMS = Algorithms.so - Algorithms_so_SOURCES = Algorithms.cpp --Algorithms_so_LINK = $(CXX) -o $@ $(PY_SHARED) -+Algorithms_so_LINK = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED) - Algorithms_so_LDADD = $(PY_LDFLAGS) - - distclean-local: clean-local ---- propka/Makefile.in 2007-10-12 00:26:48.000000000 +0200 -+++ propka/Makefile.in.new 2009-04-22 17:41:21.000000000 +0200 -@@ -99,7 +99,7 @@ - noinst_PROGRAMS = _propkalib.so propka - _propkalib_so_SOURCES = propkalib.c propka.f propkac.c - _propkalib_so_LINK = $(F77) --_propkalib_so_LDFLAGS = -o $@ $(PY_SHARED) -+_propkalib_so_LDFLAGS = $(LDFLAGS) -o $@ $(PY_SHARED) - _propkalib_so_LDADD = $(PY_LDFLAGS) - propka_SOURCES = propka.f - diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch deleted file mode 100644 index c218fe6a816e..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch +++ /dev/null @@ -1,75 +0,0 @@ -diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac ---- pdb2pqr-1.4.0/configure.ac 2009-04-02 10:53:56.000000000 -0400 -+++ pdb2pqr-1.4.0.new/configure.ac 2009-09-24 19:36:47.000000000 -0400 -@@ -255,38 +255,6 @@ - - # Test for Numeric install - AC_MSG_CHECKING([whether you defined Numeric or Numpy]) -- if (test -n "${NUMERIC}") ; then -- AC_MSG_RESULT([yes]) -- NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1` -- if test "$NUMERIC_INC" = ""; then -- AC_MSG_ERROR([Please check your NUMERIC path. arrayobject.h cannot be found in ${NUMERIC}]) -- fi -- NUMERIC_INC=`dirname ${NUMERIC_INC}` -- NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1` -- if test "${NUMERIC_LIB}" = ""; then -- AC_MSG_ERROR([Please check your NUMERIC path. Numeric.pth cannot be found in ${NUMERIC}]) -- fi -- NUMERIC_NAME=`cat ${NUMERIC_LIB}` -- NUMERIC_LIB=`dirname ${NUMERIC_LIB}` -- NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME} -- if test "${PACKAGE_PATH}" = ""; then -- PACKAGE_PATH=${NUMERIC_LIB} -- else -- PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}" -- fi -- PY_NUMERIC="-I${NUMERIC_INC} " -- PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC" -- else -- AC_MSG_RESULT([no]) -- AC_MSG_CHECKING([for Numeric include files]) -- if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then -- PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric" -- AC_MSG_RESULT([$PY_NUMERIC]) -- PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC" -- else -- AC_MSG_RESULT([no]) -- fi -- fi - - # If failed, test for numpy - AC_MSG_CHECKING([whether you defined numpy]) -@@ -457,29 +425,14 @@ - HAVE_PDB2PQR_OPAL=1 - fi - --if test "$PDB2PQR_OPAL_URL" != ""; then -+if test "$PDB2PQR_OPAL_URL" != "no"; then - HAVE_PDB2PQR_OPAL=1 - if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then - echo ZSI is installed - else - # need to install ZSI -- echo Installing ZSI. This might take a while... -- cd contrib/ZSI-2.1-a1 -- if test `whoami` = "root"; then -- $py_path setup.py install -- else -- zsi_install="true" -- mkdir -p ${prefix}lib/python$PY_VERSION/site-packages -- export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages -- $py_path setup.py install --prefix=${prefix} -- if test -d ${prefix}ZSI ; then -- echo ZSI is installed -- else -- cp -r ./build/lib/ZSI ${prefix}ZSI -- fi -- PYTHONPATH="" -- fi -- cd ../.. -+ echo Missing ZSI -+ exit 1 - fi - fi - diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch deleted file mode 100644 index 5a7e04419ce6..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch +++ /dev/null @@ -1,30 +0,0 @@ - pdb2pka/Makefile.am | 2 +- - pdb2pka/substruct/Makefile.am | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/pdb2pka/Makefile.am b/pdb2pka/Makefile.am -index 75f6ffd..e40a2f6 100644 ---- a/pdb2pka/Makefile.am -+++ b/pdb2pka/Makefile.am -@@ -16,7 +16,7 @@ SUBDIRS = substruct - - noinst_PROGRAMS = _pMC_mult.so - _pMC_mult_so_SOURCES = pMC_mult.cpp pMC_mult_wrap.cpp --_pMC_mult_so_LINK = $(CXX) -o $@ $(PY_SHARED) -+_pMC_mult_so_LINK = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED) - _pMC_mult_so_LDADD = $(PY_LDFLAGS) - - #all: -diff --git a/pdb2pka/substruct/Makefile.am b/pdb2pka/substruct/Makefile.am -index b1638a0..ae95e94 100644 ---- a/pdb2pka/substruct/Makefile.am -+++ b/pdb2pka/substruct/Makefile.am -@@ -15,7 +15,7 @@ CLEANFILES = Algorithms.so - - noinst_PROGRAMS = Algorithms.so - Algorithms_so_SOURCES = Algorithms.cpp --Algorithms_so_LINK = $(CXX) -o $@ $(PY_SHARED) -+Algorithms_so_LINK = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED) - Algorithms_so_LDADD = $(PY_LDFLAGS) - - distclean-local: clean-local diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild deleted file mode 100644 index baacac906039..000000000000 --- a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild +++ /dev/null @@ -1,159 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild,v 1.11 2012/10/19 10:10:18 jlec Exp $ - -EAPI="3" - -PYTHON_DEPEND="2:2.5" -SUPPORT_PYTHON_ABIS="1" -PYTHON_EXPORT_PHASE_FUNCTIONS="1" -RESTRICT_PYTHON_ABIS="2.4 3.*" - -inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs versionator - -MY_PV=$(get_version_component_range 1-2) -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations" -LICENSE="BSD" -HOMEPAGE="http://pdb2pqr.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" - -SLOT="0" -IUSE="doc examples opal" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" - -RDEPEND=" - dev-python/numpy - sci-chemistry/openbabel - opal? ( dev-python/zsi )" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -pkg_setup() { - fortran-2_pkg_setup - python_pkg_setup -} - -src_prepare() { - epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch - epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch - epatch "${FILESDIR}"/${PN}-1.4.0-install.patch - sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \ - || die "Failed to fix Makefile.am" - python_src_prepare - preparation() { - eautoreconf - } - python_execute_function -s preparation -} - -src_configure() { - # we need to compile the *.so as pic - append-flags -fPIC - FFLAGS="${FFLAGS} -fPIC" - - configuration() { - # Avoid automagic to numeric - NUMPY="${EPREFIX}/$(python_get_sitedir)" \ - F77="$(tc-getFC)" \ - econf \ - $(use_with opal) - } - python_execute_function -s configuration -} - -src_compile() { - compilation() { - emake || die - } - python_execute_function -s compilation -} - -src_test() { - testing() { - emake -j1 test \ - || die "tests failed" - } - python_execute_function -s testing -} - -src_install() { - installation() { - dodir $(python_get_sitedir)/${PN} - emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \ - PREFIX="" install || die "install failed" - - INPATH="$(python_get_sitedir)/${PN}" - - # generate pdb2pqr wrapper - cat >> "${T}"/${PN}-$(python_get_version) <<-EOF - #!/bin/sh - $(PYTHON) ${EPREFIX}/${INPATH}/${PN}.py \$* - EOF - - dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper." - - insinto "${INPATH}" - doins __init__.py || \ - die "Setting up the pdb2pqr site-package failed." - - exeinto "${INPATH}" - doexe ${PN}.py || die "Installing pdb2pqr failed." - - insinto "${INPATH}"/dat - doins dat/* || die "Installing data failed." - - exeinto "${INPATH}"/extensions - doexe extensions/* || \ - die "Failed to install extensions." - - insinto "${INPATH}"/src - doins src/*.py || die "Installing of python scripts failed." - - exeinto "${INPATH}"/propka - doexe propka/_propkalib.so || \ - die "Failed to install propka." - - insinto "${INPATH}"/propka - doins propka/propkalib.py propka/__init__.py || \ - die "Failed to install propka." - - insinto "${INPATH}"/pdb2pka - doins pdb2pka/*.{py,so,DAT,h} || \ - die "Failed to install pdb2pka." - - insinto "${INPATH}"/pdb2pka/ - doins pdb2pka/*.{py,so,DAT,h} || \ - die "Failed to install pdb2pka." - } - python_execute_function -s installation - - dosym ${PN}-$(python_get_version -f) /usr/bin/${PN} - - if use doc; then - cd doc - sh genpydoc.sh \ - || die "genpydoc failed" - dohtml -r *.html images pydoc \ - || die "failed to install html docs" - cd - - fi - - if use examples; then - insinto /usr/share/${PN}/ - doins -r examples || die "Failed to install examples." - fi - - dodoc ChangeLog NEWS README AUTHORS || \ - die "Failed to install docs" -} - -pkg_postinst() { - python_mod_optimize ${PN} -} - -pkg_postrm() { - python_mod_cleanup ${PN} -} -- cgit v1.2.3-65-gdbad