diff options
author | 2015-08-07 11:03:58 +0000 | |
---|---|---|
committer | 2015-08-07 11:03:58 +0000 | |
commit | ee68772f2b54b5c47b169a1a2a2febd57ba44e49 (patch) | |
tree | 53a435b016fcf49dd7a5e57178daf3ce75ec032e /sci-chemistry | |
parent | Stable for x86, wrt bug #534696 (diff) | |
download | historical-ee68772f2b54b5c47b169a1a2a2febd57ba44e49.tar.gz historical-ee68772f2b54b5c47b169a1a2a2febd57ba44e49.tar.bz2 historical-ee68772f2b54b5c47b169a1a2a2febd57ba44e49.zip |
Drop old, fixes bug #478592
Signed-off-by: Justin Lecher <jlec@gentoo.org>
Package-Manager: portage-2.2.20/cvs/Linux x86_64
Manifest-Sign-Key: 0xE9402A79B03529A2!
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/pdb2pqr/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/Manifest | 42 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/files/1.7.0-install.patch | 131 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch | 105 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch | 134 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch | 33 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch | 75 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch | 30 | ||||
-rw-r--r-- | sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild | 159 |
9 files changed, 25 insertions, 692 deletions
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 <jlec@gentoo.org> -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 <ago@gentoo.org> 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 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$(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} -} |