printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild pdb2pqr 2>&1 The package 'pdb2pqr' will be built without being installed. Reading build dependency for pdb2pqr-1.7-4... Reading dependency for pdb2pqr-1.7-4... Reading build conflict for pdb2pqr-1.7-4... WARNING: While resolving conflict "g77" for package "pdb2pqr-1.7-4", package "g77" was not found. WARNING: While resolving conflict "g95" for package "pdb2pqr-1.7-4", package "g95" was not found. The package 'python' will be installed. Reading dependency for python-2.7.8-1... Reading runtime dependency for python-2.7.8-1... The package 'python27' will be installed. Reading dependency for python27-2.7.8-1... Reading runtime dependency for python27-2.7.8-1... The package 'gcc48' will be installed. Reading dependency for gcc48-4.8.3-1000... Reading runtime dependency for gcc48-4.8.3-1000... The package 'gcc48-shlibs' will be installed. Reading dependency for gcc48-shlibs-4.8.3-1000... Reading runtime dependency for gcc48-shlibs-4.8.3-1000... The package 'numpy-py27' will be installed. Reading dependency for numpy-py27-1.8.1-1... Reading runtime dependency for numpy-py27-1.8.1-1... The package 'python27-shlibs' will be installed. Reading dependency for python27-shlibs-2.7.8-1... Reading runtime dependency for python27-shlibs-2.7.8-1... The package 'blt-shlibs' will be installed. Reading dependency for blt-shlibs-2.4z-160... Reading runtime dependency for blt-shlibs-2.4z-160... The package 'db53-aes-shlibs' will be installed. Reading dependency for db53-aes-shlibs-5.3.21-2... Reading runtime dependency for db53-aes-shlibs-5.3.21-2... The package 'expat1-shlibs' will be installed. Reading dependency for expat1-shlibs-2.1.0-1... Reading runtime dependency for expat1-shlibs-2.1.0-1... The package 'gdbm3-shlibs' will be installed. Reading dependency for gdbm3-shlibs-1.8.3-4... Reading runtime dependency for gdbm3-shlibs-1.8.3-4... The package 'libffi6-shlibs' will be installed. Reading dependency for libffi6-shlibs-3.1-1... Reading runtime dependency for libffi6-shlibs-3.1-1... The package 'libncursesw5-shlibs' will be installed. Reading dependency for libncursesw5-shlibs-5.9-20110507-1... Reading runtime dependency for libncursesw5-shlibs-5.9-20110507-1... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The package 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... The package 'sqlite3-shlibs' will be installed. Reading dependency for sqlite3-shlibs-3.8.3.1-1... Reading runtime dependency for sqlite3-shlibs-3.8.3.1-1... The package 'tcltk' will be installed. Reading dependency for tcltk-8.6.1-104... Reading runtime dependency for tcltk-8.6.1-104... The package 'gcc48-compiler' will be installed. Reading dependency for gcc48-compiler-4.8.3-1000... Reading runtime dependency for gcc48-compiler-4.8.3-1000... The package 'nose-py27' will be installed. Reading dependency for nose-py27-1.3.0-1... Reading runtime dependency for nose-py27-1.3.0-1... The package 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... The package 'tcltk-shlibs' will be installed. Reading dependency for tcltk-shlibs-8.6.1-104... Reading runtime dependency for tcltk-shlibs-8.6.1-104... The package 'fontconfig2-shlibs' will be installed. Reading dependency for fontconfig2-shlibs-2.10.2-1... Reading runtime dependency for fontconfig2-shlibs-2.10.2-1... The package 'freetype219-shlibs' will be installed. Reading dependency for freetype219-shlibs-2.4.12-1... Reading runtime dependency for freetype219-shlibs-2.4.12-1... The package 'xft2-shlibs' will be installed. Reading dependency for xft2-shlibs-2.2.0-3... Reading runtime dependency for xft2-shlibs-2.2.0-3... The package 'gmp5-shlibs' will be installed. Reading dependency for gmp5-shlibs-6.0.0a-1... Reading runtime dependency for gmp5-shlibs-6.0.0a-1... The package 'libgmpxx5-shlibs' will be installed. Reading dependency for libgmpxx5-shlibs-6.0.0a-1... Reading runtime dependency for libgmpxx5-shlibs-6.0.0a-1... The package 'libmpfr4-shlibs' will be installed. Reading dependency for libmpfr4-shlibs-3.1.2-1... Reading runtime dependency for libmpfr4-shlibs-3.1.2-1... The package 'cloog-org2-shlibs' will be installed. Reading dependency for cloog-org2-shlibs-0.18.2-1... Reading runtime dependency for cloog-org2-shlibs-0.18.2-1... The package 'isl-shlibs' will be installed. Reading dependency for isl-shlibs-0.12.2-2... Reading runtime dependency for isl-shlibs-0.12.2-2... The package 'libmpc3-shlibs' will be installed. Reading dependency for libmpc3-shlibs-1.0.2-1... Reading runtime dependency for libmpc3-shlibs-1.0.2-1... The package 'setuptools-tng-py27' will be installed. Reading dependency for setuptools-tng-py27-5.1-1... Reading runtime dependency for setuptools-tng-py27-5.1-1... The package 'fontconfig-config' will be installed. Reading dependency for fontconfig-config-2.10.2-1... Reading runtime dependency for fontconfig-config-2.10.2-1... The following package will be rebuilt: pdb2pqr The following 31 additional packages will be installed: blt-shlibs cloog-org2-shlibs db53-aes-shlibs expat1-shlibs fontconfig-config fontconfig2-shlibs freetype219-shlibs gcc48 gcc48-compiler gcc48-shlibs gdbm3-shlibs gmp5-shlibs isl-shlibs libffi6-shlibs libgmpxx5-shlibs libjpeg9-shlibs libmpc3-shlibs libmpfr4-shlibs libncursesw5-shlibs nose-py27 numpy-py27 openssl100-shlibs python python27 python27-shlibs readline6-shlibs setuptools-tng-py27 sqlite3-shlibs tcltk tcltk-shlibs xft2-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/pdb2pqr-1.7.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 6744k 1 99668 0 0 54880 0 0:02:05 0:00:01 0:02:04 54883 15 6744k 15 1073k 0 0 386k 0 0:00:17 0:00:02 0:00:15 386k 36 6744k 36 2485k 0 0 658k 0 0:00:10 0:00:03 0:00:07 658k 62 6744k 62 4207k 0 0 865k 0 0:00:07 0:00:04 0:00:03 865k 63 6744k 63 4311k 0 0 728k 0 0:00:09 0:00:05 0:00:04 837k 88 6744k 88 5988k 0 0 884k 0 0:00:07 0:00:06 0:00:01 1188k 100 6744k 100 6744k 0 0 939k 0 0:00:07 0:00:07 --:--:-- 1286k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/crypto/db53-aes-shlibs_5.3.21-2_darwin-x86_64.deb Selecting previously deselected package db53-aes-shlibs. (Reading database ... 4296 files and directories currently installed.) Unpacking db53-aes-shlibs (from .../db53-aes-shlibs_5.3.21-2_darwin-x86_64.deb) ... Setting up db53-aes-shlibs (5.3.21-2) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/expat1-shlibs_2.1.0-1_darwin-x86_64.deb Selecting previously deselected package expat1-shlibs. (Reading database ... 4306 files and directories currently installed.) Unpacking expat1-shlibs (from .../expat1-shlibs_2.1.0-1_darwin-x86_64.deb) ... Setting up expat1-shlibs (2.1.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/freetype219-shlibs_2.4.12-1_darwin-x86_64.deb Selecting previously deselected package freetype219-shlibs. (Reading database ... 4311 files and directories currently installed.) Unpacking freetype219-shlibs (from .../freetype219-shlibs_2.4.12-1_darwin-x86_64.deb) ... Setting up freetype219-shlibs (2.4.12-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb Selecting previously deselected package gdbm3-shlibs. (Reading database ... 4322 files and directories currently installed.) Unpacking gdbm3-shlibs (from .../gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb) ... Setting up gdbm3-shlibs (1.8.3-4) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libffi6-shlibs_3.1-1_darwin-x86_64.deb Selecting previously deselected package libffi6-shlibs. (Reading database ... 4330 files and directories currently installed.) Unpacking libffi6-shlibs (from .../libffi6-shlibs_3.1-1_darwin-x86_64.deb) ... Setting up libffi6-shlibs (3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb Selecting previously deselected package libgmpxx5-shlibs. (Reading database ... 4331 files and directories currently installed.) Unpacking libgmpxx5-shlibs (from .../libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Selecting previously deselected package gmp5-shlibs. Unpacking gmp5-shlibs (from .../gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Setting up gmp5-shlibs (6.0.0a-1) ... Setting up libgmpxx5-shlibs (6.0.0a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/libjpeg9-shlibs_9a-1_darwin-x86_64.deb Selecting previously deselected package libjpeg9-shlibs. (Reading database ... 4360 files and directories currently installed.) Unpacking libjpeg9-shlibs (from .../libjpeg9-shlibs_9a-1_darwin-x86_64.deb) ... Setting up libjpeg9-shlibs (9a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb Selecting previously deselected package libmpfr4-shlibs. (Reading database ... 4363 files and directories currently installed.) Unpacking libmpfr4-shlibs (from .../libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb) ... Setting up libmpfr4-shlibs (3.1.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncursesw5-shlibs. (Reading database ... 4376 files and directories currently installed.) Unpacking libncursesw5-shlibs (from .../libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncursesw5-shlibs (5.9-20110507-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb Selecting previously deselected package openssl100-shlibs. (Reading database ... 4387 files and directories currently installed.) Unpacking openssl100-shlibs (from .../openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb) ... Setting up openssl100-shlibs (1.0.1h-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/readline6-shlibs_6.3.6-1_darwin-x86_64.deb Selecting previously deselected package readline6-shlibs. (Reading database ... 4408 files and directories currently installed.) Unpacking readline6-shlibs (from .../readline6-shlibs_6.3.6-1_darwin-x86_64.deb) ... Setting up readline6-shlibs (6.3.6-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/database/sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb Selecting previously deselected package sqlite3-shlibs. (Reading database ... 4419 files and directories currently installed.) Unpacking sqlite3-shlibs (from .../sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb) ... Setting up sqlite3-shlibs (3.8.3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig-config_2.10.2-1_darwin-x86_64.deb Selecting previously deselected package fontconfig2-shlibs. (Reading database ... 4423 files and directories currently installed.) Unpacking fontconfig2-shlibs (from .../fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb) ... Selecting previously deselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.10.2-1_darwin-x86_64.deb) ... Setting up fontconfig-config (2.10.2-1) ... Setting up fontconfig2-shlibs (2.10.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/isl-shlibs_0.12.2-2_darwin-x86_64.deb Selecting previously deselected package isl-shlibs. (Reading database ... 4508 files and directories currently installed.) Unpacking isl-shlibs (from .../isl-shlibs_0.12.2-2_darwin-x86_64.deb) ... Setting up isl-shlibs (0.12.2-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpc3-shlibs_1.0.2-1_darwin-x86_64.deb Selecting previously deselected package libmpc3-shlibs. (Reading database ... 4509 files and directories currently installed.) Unpacking libmpc3-shlibs (from .../libmpc3-shlibs_1.0.2-1_darwin-x86_64.deb) ... Setting up libmpc3-shlibs (1.0.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/xft2-shlibs_2.2.0-3_darwin-x86_64.deb Selecting previously deselected package xft2-shlibs. (Reading database ... 4512 files and directories currently installed.) Unpacking xft2-shlibs (from .../xft2-shlibs_2.2.0-3_darwin-x86_64.deb) ... Setting up xft2-shlibs (2.2.0-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/cloog-org2-shlibs_0.18.2-1_darwin-x86_64.deb Selecting previously deselected package cloog-org2-shlibs. (Reading database ... 4521 files and directories currently installed.) Unpacking cloog-org2-shlibs (from .../cloog-org2-shlibs_0.18.2-1_darwin-x86_64.deb) ... Setting up cloog-org2-shlibs (0.18.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/gcc48_4.8.3-1000_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc48-compiler_4.8.3-1000_darwin-x86_64.deb Selecting previously deselected package gcc48. (Reading database ... 4522 files and directories currently installed.) Unpacking gcc48 (from .../gcc48_4.8.3-1000_darwin-x86_64.deb) ... Selecting previously deselected package gcc48-shlibs. Unpacking gcc48-shlibs (from .../gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb) ... Selecting previously deselected package gcc48-compiler. Unpacking gcc48-compiler (from .../gcc48-compiler_4.8.3-1000_darwin-x86_64.deb) ... Setting up gcc48-shlibs (4.8.3-1000) ... Clearing dependency_libs of .la files being installed Setting up gcc48-compiler (4.8.3-1000) ... Clearing dependency_libs of .la files being installed Setting up gcc48 (4.8.3-1000) ... * Classpath Tools: (cp-tools). GNU Classpath Tools Guide install-info(/sw/share/info/cp-tools.info): creating new section `GNU Libraries' * gcc: (gcc). The GNU Compiler Collection. install-info(/sw/share/info/gcc.info): replacing existing dir entry for `gcc' * gfortran: (gfortran). The GNU Fortran Compiler. * Cpp: (cpp). The GNU C preprocessor. * gccinstall: (gccinstall). Installing the GNU Compiler Collection. * libgomp: (libgomp). GNU OpenMP runtime library * Cpplib: (cppinternals). Cpplib internals. * gccint: (gccint). Internals of the GNU Compiler Collection. * Gcj: (gcj). Ahead-of-time compiler for the Java language Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/tcltk_8.6.1-104_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/tcltk-shlibs_8.6.1-104_darwin-x86_64.deb Selecting previously deselected package tcltk. (Reading database ... 10010 files and directories currently installed.) Unpacking tcltk (from .../tcltk_8.6.1-104_darwin-x86_64.deb) ... Selecting previously deselected package tcltk-shlibs. Unpacking tcltk-shlibs (from .../tcltk-shlibs_8.6.1-104_darwin-x86_64.deb) ... Setting up tcltk-shlibs (8.6.1-104) ... Setting up tcltk (8.6.1-104) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/blt-shlibs_2.4z-160_darwin-x86_64.deb Selecting previously deselected package blt-shlibs. (Reading database ... 10486 files and directories currently installed.) Unpacking blt-shlibs (from .../blt-shlibs_2.4z-160_darwin-x86_64.deb) ... Setting up blt-shlibs (2.4z-160) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python_2.7.8-1_darwin-x86_64.deb /sw/fink/debs/python27_2.7.8-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python27-shlibs_2.7.8-1_darwin-x86_64.deb Selecting previously deselected package python. (Reading database ... 10492 files and directories currently installed.) Unpacking python (from .../python_2.7.8-1_darwin-x86_64.deb) ... Selecting previously deselected package python27. Unpacking python27 (from .../python27_2.7.8-1_darwin-x86_64.deb) ... Selecting previously deselected package python27-shlibs. Unpacking python27-shlibs (from .../python27-shlibs_2.7.8-1_darwin-x86_64.deb) ... Setting up python27-shlibs (2.7.8-1) ... Setting up python27 (2.7.8-1) ... Setting up python (2.7.8-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/setuptools-tng-py27_5.1-1_darwin-x86_64.deb Selecting previously deselected package setuptools-tng-py27. (Reading database ... 17717 files and directories currently installed.) Unpacking setuptools-tng-py27 (from .../setuptools-tng-py27_5.1-1_darwin-x86_64.deb) ... Setting up setuptools-tng-py27 (5.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/nose-py27_1.3.0-1_darwin-x86_64.deb Selecting previously deselected package nose-py27. (Reading database ... 17888 files and directories currently installed.) Unpacking nose-py27 (from .../nose-py27_1.3.0-1_darwin-x86_64.deb) ... Setting up nose-py27 (1.3.0-1) ... Checking available versions of nosetests, updating links in /sw/etc/alternatives ... (You may modify the symlinks there yourself if desired - see `man ln'.) Updating nosetests (/sw/bin/nosetests) to point to /sw/bin/nosetests2.7. Updating nosetests.1 (/sw/share/man/man1/nosetests.1) to point to /sw//share/man/man1/nosetests-py27.1. Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/numpy-py27_1.8.1-1_darwin-x86_64.deb Selecting previously deselected package numpy-py27. (Reading database ... 18073 files and directories currently installed.) Unpacking numpy-py27 (from .../numpy-py27_1.8.1-1_darwin-x86_64.deb) ... Setting up numpy-py27 (1.8.1-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-pdb2pqr-1.7-4 /sw/build.build dpkg-deb: building package `fink-buildlock-pdb2pqr-1.7-4' in `/sw/build.build/fink-buildlock-pdb2pqr-1.7-4_2014.07.28-19.45.29_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-pdb2pqr-1.7-4_2014.07.28-19.45.29_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-pdb2pqr-1.7-4. (Reading database ... 18851 files and directories currently installed.) Unpacking fink-buildlock-pdb2pqr-1.7-4 (from .../fink-buildlock-pdb2pqr-1.7-4_2014.07.28-19.45.29_darwin-x86_64.deb) ... Setting up fink-buildlock-pdb2pqr-1.7-4 (2014.07.28-19.45.29) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.5DFAG env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/pdb2pqr-1.7.tar.gz pdb2pqr-1.7/ pdb2pqr-1.7/examples/ pdb2pqr-1.7/examples/pdb2pqr_web_interface_tutorial-03.png pdb2pqr-1.7/examples/ligands/ pdb2pqr-1.7/examples/ligands/LIG_1HPV.mol2 pdb2pqr-1.7/examples/ligands/LIG_1QBS.mol2 pdb2pqr-1.7/examples/ligands/README pdb2pqr-1.7/examples/ligands/LIG_1ABF.mol2 pdb2pqr-1.7/examples/ligands/LIG_1XL5.mol2 pdb2pqr-1.7/examples/ligands/LIG_1HPX.mol2 pdb2pqr-1.7/examples/pdb2pqr_web_interface_tutorial-01.png pdb2pqr-1.7/examples/index.html pdb2pqr-1.7/examples/pdb2pqr_web_interface_tutorial-04.png pdb2pqr-1.7/examples/pdb2pqr_web_interface_tutorial-02.png pdb2pqr-1.7/examples/1a1p/ pdb2pqr-1.7/examples/1a1p/README pdb2pqr-1.7/examples/1a1p/1a1p.pdb pdb2pqr-1.7/examples/pdb2pqr_web_interface_tutorial-05.png pdb2pqr-1.7/configure.ac pdb2pqr-1.7/apbs_cgi.py pdb2pqr-1.7/doc/ pdb2pqr-1.7/doc/userguide.html pdb2pqr-1.7/doc/license.txt pdb2pqr-1.7/doc/images/ pdb2pqr-1.7/doc/images/flowchart.png pdb2pqr-1.7/doc/pydoc/ pdb2pqr-1.7/doc/pydoc/src.quatfit.html pdb2pqr-1.7/doc/pydoc/copy.html pdb2pqr-1.7/doc/pydoc/src.hydrogens.html pdb2pqr-1.7/doc/pydoc/index.html pdb2pqr-1.7/doc/pydoc/src.psize.html pdb2pqr-1.7/doc/pydoc/src.na.html pdb2pqr-1.7/doc/pydoc/src.protein.html pdb2pqr-1.7/doc/pydoc/src.server.html pdb2pqr-1.7/doc/pydoc/sys.html pdb2pqr-1.7/doc/pydoc/src.forcefield.html pdb2pqr-1.7/doc/pydoc/time.html pdb2pqr-1.7/doc/pydoc/math.html pdb2pqr-1.7/doc/pydoc/xml.sax.html pdb2pqr-1.7/doc/pydoc/src.aa.html pdb2pqr-1.7/doc/pydoc/pdb2pqr.html pdb2pqr-1.7/doc/pydoc/src.routines.html pdb2pqr-1.7/doc/pydoc/string.html pdb2pqr-1.7/doc/pydoc/.htaccess pdb2pqr-1.7/doc/pydoc/re.html pdb2pqr-1.7/doc/pydoc/getopt.html pdb2pqr-1.7/doc/pydoc/src.structures.html pdb2pqr-1.7/doc/pydoc/src.inputgen.html pdb2pqr-1.7/doc/pydoc/src.utilities.html pdb2pqr-1.7/doc/pydoc/src.pdb.html pdb2pqr-1.7/doc/pydoc/os.html pdb2pqr-1.7/doc/pydoc/src.html pdb2pqr-1.7/doc/pydoc/src.definitions.html pdb2pqr-1.7/doc/programmerguide.html pdb2pqr-1.7/doc/genpydoc.sh pdb2pqr-1.7/doc/template pdb2pqr-1.7/pdb2pka/ pdb2pqr-1.7/pdb2pka/pMC_mult.py pdb2pqr-1.7/pdb2pka/apbs.py pdb2pqr-1.7/pdb2pka/pMC_mult.h pdb2pqr-1.7/pdb2pka/substruct/ pdb2pqr-1.7/pdb2pka/substruct/Makefile.in pdb2pqr-1.7/pdb2pka/substruct/Algorithms.cpp pdb2pqr-1.7/pdb2pka/substruct/__init__.py pdb2pqr-1.7/pdb2pka/substruct/clique/ pdb2pqr-1.7/pdb2pka/substruct/clique/set.h pdb2pqr-1.7/pdb2pka/substruct/clique/README pdb2pqr-1.7/pdb2pka/substruct/clique/clique.h pdb2pqr-1.7/pdb2pka/substruct/clique/bk.h pdb2pqr-1.7/pdb2pka/substruct/clique/util.h pdb2pqr-1.7/pdb2pka/substruct/clique/COPYING pdb2pqr-1.7/pdb2pka/substruct/Makefile.am pdb2pqr-1.7/pdb2pka/pMC_mult.cpp pdb2pqr-1.7/pdb2pka/Makefile.in pdb2pqr-1.7/pdb2pka/__init__.py pdb2pqr-1.7/pdb2pka/pka_help.py pdb2pqr-1.7/pdb2pka/pKa_base.py pdb2pqr-1.7/pdb2pka/NEWligand_topology.py pdb2pqr-1.7/pdb2pka/pka.py pdb2pqr-1.7/pdb2pka/ligand_topology.py pdb2pqr-1.7/pdb2pka/ligandclean/ pdb2pqr-1.7/pdb2pka/ligandclean/templates.py pdb2pqr-1.7/pdb2pka/ligandclean/ligff.py pdb2pqr-1.7/pdb2pka/ligandclean/lookuptable.py pdb2pqr-1.7/pdb2pka/ligandclean/__init__.py pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/ pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/carvedilol.mol2 pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/1qbs_clean.pdb pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/acetacid3.mol2 pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/1qbs_test.pdb pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/lig1b_h.mol2 pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/1qbs_lig_clean.mol2 pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/IDD594.mol2 pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/1us0_ASP43.pdb pdb2pqr-1.7/pdb2pka/ligandclean/testcomplexes/1us0_lig_clean.mol2 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pdb2pqr-1.7/config/depcomp pdb2pqr-1.7/config/mkinstalldirs pdb2pqr-1.7/config/install-sh pdb2pqr-1.7/config/ltconfig pdb2pqr-1.7/pdb2pqr-opal.py pdb2pqr-1.7/main.py pdb2pqr-1.7/AppService_types.py pdb2pqr-1.7/tests/ pdb2pqr-1.7/tests/Makefile.in pdb2pqr-1.7/tests/test/ pdb2pqr-1.7/tests/test/test.cpp.in pdb2pqr-1.7/tests/test/Makefile.in pdb2pqr-1.7/tests/test/test-output-correct.pqr pdb2pqr-1.7/tests/test/test.sh.in pdb2pqr-1.7/tests/test/Makefile.am pdb2pqr-1.7/tests/adv-test/ pdb2pqr-1.7/tests/adv-test/test.cpp.in pdb2pqr-1.7/tests/adv-test/Makefile.in pdb2pqr-1.7/tests/adv-test/test-output-correct.pqr pdb2pqr-1.7/tests/adv-test/test-output-correct.propka pdb2pqr-1.7/tests/adv-test/test.sh.in pdb2pqr-1.7/tests/adv-test/LIG_1HPX.mol2 pdb2pqr-1.7/tests/adv-test/Makefile.am pdb2pqr-1.7/tests/local-test/ pdb2pqr-1.7/tests/local-test/test.cpp.in pdb2pqr-1.7/tests/local-test/Makefile.in pdb2pqr-1.7/tests/local-test/test-output-correct.pqr pdb2pqr-1.7/tests/local-test/1AFS.pdb pdb2pqr-1.7/tests/local-test/test.sh.in pdb2pqr-1.7/tests/local-test/Makefile.am pdb2pqr-1.7/tests/test-webserver/ pdb2pqr-1.7/tests/test-webserver/lst pdb2pqr-1.7/tests/test-webserver/Makefile.in pdb2pqr-1.7/tests/test-webserver/test.sh.in pdb2pqr-1.7/tests/test-webserver/Makefile.am pdb2pqr-1.7/tests/test-webserver/web_server_tester.py pdb2pqr-1.7/tests/test-long/ pdb2pqr-1.7/tests/test-long/lst pdb2pqr-1.7/tests/test-long/Makefile.in pdb2pqr-1.7/tests/test-long/test.py pdb2pqr-1.7/tests/test-long/out/ pdb2pqr-1.7/tests/test-long/test.sh.in pdb2pqr-1.7/tests/test-long/Makefile.am pdb2pqr-1.7/tests/Makefile.am pdb2pqr-1.7/src/ pdb2pqr-1.7/src/definitions.py pdb2pqr-1.7/src/inputgen.py pdb2pqr-1.7/src/pdb.py pdb2pqr-1.7/src/aconf.py.in pdb2pqr-1.7/src/structures.py pdb2pqr-1.7/src/aa.py pdb2pqr-1.7/src/__init__.py pdb2pqr-1.7/src/na.py pdb2pqr-1.7/src/hydrogens.py pdb2pqr-1.7/src/routines.py pdb2pqr-1.7/src/quatfit.py pdb2pqr-1.7/src/topology.py pdb2pqr-1.7/src/forcefield.py pdb2pqr-1.7/src/.cvsignore pdb2pqr-1.7/src/psize.py pdb2pqr-1.7/src/protein.py pdb2pqr-1.7/src/utilities.py pdb2pqr-1.7/src/server.py.in pdb2pqr-1.7/pdb2pqr.py.in pdb2pqr-1.7/configure pdb2pqr-1.7/ChangeLog pdb2pqr-1.7/.htaccess pdb2pqr-1.7/pdb2pqr.css pdb2pqr-1.7/aclocal.m4 pdb2pqr-1.7/NEWS pdb2pqr-1.7/querystatus.py pdb2pqr-1.7/jmol/ pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_pt.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersMore.jar pdb2pqr-1.7/jmol/apbstransp.gif pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_fr.jar pdb2pqr-1.7/jmol/Jmol.js pdb2pqr-1.7/jmol/JmolAppletSigned0_MultiTouch.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_sv.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_Console.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ShapeBio.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersMolXyz.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_et.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_es.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_Smiles.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_ar.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_pl.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_cs.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_de.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersXtal.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_ko.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_Minimize.jar pdb2pqr-1.7/jmol/JmolAppletSigned0.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_hu.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersSimple.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_tr.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersQuantum.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_zh_CN.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_ca.jar pdb2pqr-1.7/jmol/apbsjmol.js pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_id.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_en_GB.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_Popup.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_uk.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersXml.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_sl.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_zh_TW.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_Symmetry.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ShapeSurface.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_ru.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_ta.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_pt_BR.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ShapeSpecial.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_nb.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_oc.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_ReadersCifPdb.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_el.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_da.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_it.jar pdb2pqr-1.7/jmol/JmolAppletSigned0_i18n_nl.jar pdb2pqr-1.7/AUTHORS pdb2pqr-1.7/contrib/ pdb2pqr-1.7/contrib/numpy-1.1.0/ pdb2pqr-1.7/contrib/numpy-1.1.0/DEV_README.txt pdb2pqr-1.7/contrib/numpy-1.1.0/THANKS.txt pdb2pqr-1.7/contrib/numpy-1.1.0/site.cfg.example pdb2pqr-1.7/contrib/numpy-1.1.0/MANIFEST.in pdb2pqr-1.7/contrib/numpy-1.1.0/COMPATIBILITY pdb2pqr-1.7/contrib/numpy-1.1.0/PKG-INFO pdb2pqr-1.7/contrib/numpy-1.1.0/setup.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/ pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/ pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/ufunclike.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/polynomial.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/arraysetops.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/utils.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/shape_base.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/info.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/__init__.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/function_base.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/index_tricks.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/setup.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/tests/ pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/tests/test_arraysetops.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/tests/test_machar.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/tests/test_shape_base.py pdb2pqr-1.7/contrib/numpy-1.1.0/numpy/lib/tests/test_financial.py 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pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/wstools/UserTuple.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/wstools/Utility.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/.cvsignore pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/address.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/writer.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/auth.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/typeinterpreter.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/digest_auth.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/version.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/parse.py pdb2pqr-1.7/contrib/ZSI-2.1-a1/ZSI/TCtimes.py pdb2pqr-1.7/AppService_client.py pdb2pqr-1.7/extensions/ pdb2pqr-1.7/extensions/README pdb2pqr-1.7/extensions/__init__.py pdb2pqr-1.7/extensions/salt.py pdb2pqr-1.7/extensions/contact.py pdb2pqr-1.7/extensions/rama.py pdb2pqr-1.7/extensions/psi.py pdb2pqr-1.7/extensions/chi.py pdb2pqr-1.7/extensions/phi.py pdb2pqr-1.7/extensions/hbond.py pdb2pqr-1.7/extensions/template pdb2pqr-1.7/extensions/hbondwhatif.py pdb2pqr-1.7/COPYING pdb2pqr-1.7/html/ pdb2pqr-1.7/html/README pdb2pqr-1.7/html/master-index.html pdb2pqr-1.7/html/server.html.in pdb2pqr-1.7/AppService_services_types.py pdb2pqr-1.7/main_cgi.py pdb2pqr-1.7/tools/ pdb2pqr-1.7/tools/fixpqr.c pdb2pqr-1.7/dat/ pdb2pqr-1.7/dat/SWANSON.DAT pdb2pqr-1.7/dat/AA.xml pdb2pqr-1.7/dat/AMBER.names pdb2pqr-1.7/dat/PEOEPB.DAT pdb2pqr-1.7/dat/PEOEPB.names pdb2pqr-1.7/dat/HYDROGENS.xml pdb2pqr-1.7/dat/TOPOLOGY.xml pdb2pqr-1.7/dat/PARSE.names pdb2pqr-1.7/dat/AMBER.DAT pdb2pqr-1.7/dat/PARSE.DAT pdb2pqr-1.7/dat/TYL06.DAT pdb2pqr-1.7/dat/TYL06.names pdb2pqr-1.7/dat/CHARMM.DAT pdb2pqr-1.7/dat/CHARMM.names pdb2pqr-1.7/dat/SWANSON.names pdb2pqr-1.7/dat/NA.xml pdb2pqr-1.7/dat/PATCHES.xml pdb2pqr-1.7/AppService_services.py pdb2pqr-1.7/INSTALL pdb2pqr-1.7/acinclude.m4 pdb2pqr-1.7/Makefile.am pdb2pqr-1.7/visualize.py sudo -u fink-bld [ENV] sh -c /tmp/fink.CVP1V /tmp/fink.sebrS #!/bin/bash -efv #PATH=%p/bin:%p/sbin:${PATH} ; export PATH #source %p/bin/init.sh # if [[ "x86_64" != "x86_64" ]]; then export CCPFLAGS="-m32" export LDFLAGS="-m32" perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|/sw/lib/python2.7/config/libpython2.7.dylib -m32 -bundle|g' ./configure perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|/sw/lib/python2.7/config/libpython2.7.dylib -m32 -bundle|g' ./propka/configure else perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|/sw/lib/python2.7/config/libpython2.7.dylib -bundle|g' ./configure perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|/sw/lib/python2.7/config/libpython2.7.dylib -bundle|g' ./propka/configure fi perl -pi -e 's|fort xlf95 lf95 g95|gfortran|g' ./propka/configure perl -pi -e 's|/usr/bin/python|/sw/bin/python2.7|g' ./pdb2pka/pka.py perl -pi -e 's|/usr/bin/python|/sw/bin/python2.7|g' ./src/psize.py rm -fr contrib ./configure --with-max-atoms="1000000" --without-url --with-python=/sw/bin/python2.7 --with-f77=gfortran checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking target system type... i386-apple-darwin13.3.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for python include directory... -I/sw/include/python2.7 checking for --disable-propka... no ------------- Begin Processing PropKa Configure Options ----------- checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking target system type... i386-apple-darwin13.3.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for python... /sw/bin/python2.7 checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fl32... no checking for af77... no checking for fort77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... no checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking how to run the C preprocessor... gcc -E checking for python include directory... -I/sw/include/python2.7 configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands ------------- End Processing PropKa Configure Options ----------- checking for--disable-pdb2pka... no ------------- Begin Processing pdb2pka Configure Options ----------- checking whether you defined Numeric or Numpy... no checking for Numeric include files... no checking whether you defined numpy... no checking for numpy includes files... -I/sw/lib/python2.7/site-packages/numpy/core/include/numpy ------------- End Processing pdb2ka Configure Options ----------- checking for tmp/... no checking for OpenBabel... OpenBabel not found. ------------- End Processing PDB2PQR Configure Options ----------- configure: creating ./config.status config.status: creating Makefile config.status: creating pdb2pka/Makefile config.status: creating pdb2pka/substruct/Makefile config.status: creating tests/Makefile config.status: creating tests/test/Makefile config.status: creating tests/adv-test/Makefile config.status: creating tests/test-long/Makefile config.status: creating tests/test-webserver/Makefile config.status: creating tests/local-test/Makefile config.status: executing depfiles commands --------------------------------------------------------------------------------------- Please run "make" followed by "make install" to complete the installation. You may also run "make test" or "make adv-test". ======================== Configuration Parameters ======================== User ID: fink-bld Version: 1.7 Install Dir: /tmp/fink-build-HOME.4t16UcUHc0/pdb2pqr/ propka: enable pdb2pka: enable PY_CFLAGS: -I/sw/include/python2.7 -I/sw/lib/python2.7/site-packages/numpy/core/include/numpy WEBSITE (path to the website directory): http://no/ (WEBSITE can be changed with the --with-url option) PDB2PQR_CGI (path to pdb2pqr.cgi): http://no/pdb2pqr.cgi PDB2PQR jobs will be forked on the server MAX_ATOMS (max number of atoms in a protein): 1000000 As a regular user, you must ask your system administrator to create a symbolic link that enables you to view http://no/ after you run "make install" if [[ "x86_64" != "x86_64" ]]; then perl -pi -e 's|-DPACKAGE|-m32 -DPACKAGE|g' Makefile pdb2pka/substruct/Makefile tests/Makefile tests/test/Makefile pdb2pka/Makefile propka/Makefile tests/adv-test/Makefile fi make cd . && : cd . && : --gnu Making all in propka cd . && \ : --gnu Makefile gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen@uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" -I. -I. -I/sw/include/python2.7 -g -O2 -c `test -f 'propkalib.c' || echo './'`propkalib.c gfortran -g -O2 -c -o propka.o `test -f 'propka.f' || echo './'`propka.f propka.f:90.34: CALL RUNPROPKA(NATOM, PDB, 'PROPKATMP3') 1 Warning: Character length of actual argument shorter than of dummy argument 'outname' (10/100) at (1) gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen@uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" -I. -I. -I/sw/include/python2.7 -g -O2 -c `test -f 'propkac.c' || echo './'`propkac.c gfortran -o _propkalib.so propkalib.o propka.o propkac.o /sw/lib/python2.7/config/libpython2.7.dylib -bundle gfortran -g -O2 -o propka propka.o Making all in pdb2pka cd .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in substruct cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I. -I/sw/include/python2.7 -I/sw/lib/python2.7/site-packages/numpy/core/include/numpy -g -O2 -c -o Algorithms.o Algorithms.cpp In file included from Algorithms.cpp:43: In file included from /sw/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /sw/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17: In file included from /sw/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761: /sw/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ 1 warning generated. g++ -o Algorithms.so Algorithms.o /sw/lib/python2.7/config/libpython2.7.dylib -bundle cd .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I. -I/sw/include/python2.7 -I/sw/lib/python2.7/site-packages/numpy/core/include/numpy -g -O2 -c -o pMC_mult.o pMC_mult.cpp g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I. -I/sw/include/python2.7 -I/sw/lib/python2.7/site-packages/numpy/core/include/numpy -g -O2 -c -o pMC_mult_wrap.o pMC_mult_wrap.cpp pMC_mult_wrap.cpp:864:38: warning: format string is not a string literal (potentially insecure) [-Wformat-security] PyErr_Format(PyExc_RuntimeError, mesg); ^~~~ 1 warning generated. g++ -o _pMC_mult.so pMC_mult.o pMC_mult_wrap.o /sw/lib/python2.7/config/libpython2.7.dylib -bundle Making all in tests cd .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in test cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in . cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I. -g -O2 -MT test.o -MD -MP -MF .deps/test.Tpo -c -o test.o test.cpp test.cpp:36:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("test-output-correct.pqr could not be opened"); ^ test.cpp:39:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("test-output-user.pqr could not be opened"); ^ test.cpp:52:21: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Found a difference in REMARK in the PQR files"); ^ test.cpp:103:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Simple test failed because the user's PQR output file contains the wrong number of data items"); ^ test.cpp:106:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Simple test failed because the numbers in the user PQR output file and the expected values are too big"); ^ 5 warnings generated. mv -f .deps/test.Tpo .deps/test.Po g++ -g -O2 -o simpletest test.o Making all in adv-test cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in . cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I. -g -O2 -MT test.o -MD -MP -MF .deps/test.Tpo -c -o test.o test.cpp test.cpp:43:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("test-output-user.pqr could not be opened"); ^ test.cpp:46:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("test-output-user.propka could not be opened"); ^ test.cpp:58:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Found a difference in REMARK in the PQR files"); ^ test.cpp:83:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Advanced test failed because the user's PQR output file contains the wrong number of data items"); ^ test.cpp:86:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Advanced test failed because the numbers in the user PQR output file and the expected values are too big"); ^ test.cpp:97:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Propka files produced different numbers of fields"); ^ test.cpp:116:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Advanced test failed because the numbers in the user PROPKA output file and the expected values are too big"); ^ test.cpp:119:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Advanced test failed because the size ofyour propka output file is different from the expected size"); ^ 8 warnings generated. mv -f .deps/test.Tpo .deps/test.Po g++ -g -O2 -o advtest test.o Making all in test-long cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in . cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu make[3]: Nothing to be done for `all-am'. Making all in local-test cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in . cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I. -g -O2 -MT test.o -MD -MP -MF .deps/test.Tpo -c -o test.o test.cpp test.cpp:36:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("test-output-correct.pqr could not be opened"); ^ test.cpp:39:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("test-output-user.pqr could not be opened"); ^ test.cpp:52:21: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Found a difference in REMARK in the PQR files"); ^ test.cpp:103:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Local test failed because the user's PQR output file contains the wrong number of data items"); ^ test.cpp:106:15: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] error_msg("Local test failed because the numbers in the user PQR output file and the expected values are too big"); ^ 5 warnings generated. mv -f .deps/test.Tpo .deps/test.Po g++ -g -O2 -o localtest test.o Making all in test-webserver cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu Making all in . cd ../.. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu make[3]: Nothing to be done for `all-am'. Making all in . cd .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make am--refresh cd . && : cd . && : --gnu cd . && : cd . && : --gnu make[2]: Nothing to be done for `all-am'. cd . && : cd . && : --gnu make[1]: Nothing to be done for `all-am'. rm -f pdb2pka/pMC_mult.o pdb2pka/substruct/Algorithms.o propka/propkac.o tests/adv-test/test.o rm -r pdb2pka/pMC_mult_wrap.o propka/propka.o propka/propkalib.o tests/test/test.o /bin/rm -rf /sw/build.build/root-pdb2pqr-1.7-4 /bin/mkdir -p /sw/build.build/root-pdb2pqr-1.7-4/sw /bin/mkdir -p /sw/build.build/root-pdb2pqr-1.7-4/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-pdb2pqr-1.7-4 sudo -u fink-bld [ENV] sh -c /tmp/fink.Ls3MV /tmp/fink.gU6Ln # system-wide environment settings for zsh(1) if [ -x /usr/libexec/path_helper ]; then eval `/usr/libexec/path_helper -s` fi #!/bin/zsh -efv source /sw/bin/init.sh # init.sh # # to use the Fink hierarchy, put the following in your .profile: # # . /sw/bin/init.sh # # # Fink - a package manager that downloads source and installs it # Copyright (c) 2001 Christoph Pfisterer # Copyright (c) 2001-2013 The Fink Team # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110, USA. # # define append_path and prepend_path to add directory paths, e.g. PATH, MANPATH. # add to end of path append_path() { if ! eval test -z "\"\${$1##*:$2:*}\"" -o -z "\"\${$1%%*:$2}\"" -o -z "\"\${$1##$2:*}\"" -o -z "\"\${$1##$2}\"" ; then eval "$1=\$$1:$2" fi } # add to front of path prepend_path() { if ! eval test -z "\"\${$1##*:$2:*}\"" -o -z "\"\${$1%%*:$2}\"" -o -z "\"\${$1##$2:*}\"" -o -z "\"\${$1##$2}\"" ; then eval "$1=$2:\$$1" fi } # setup fink related paths. we assume that the fink directories exist. if [ -z "$PATH" ]; then PATH=/sw/bin:/sw/sbin:/bin:/sbin:/usr/bin:/usr/sbin else prepend_path PATH /sw/bin:/sw/sbin fi export PATH osMajorVer=`uname -r | cut -d. -f1` osMinorVer=`uname -r | cut -d. -f2` if [ -z "$MANPATH" ]; then if [ $osMajorVer -gt 7 ]; then MANPATH=`/usr/bin/manpath` else MANPATH=`/usr/bin/manpath -q` fi fi prepend_path MANPATH /sw/share/man perlversion=`/usr/bin/perl -e 'printf("%vd\n", $^V)'` append_path MANPATH /sw/lib/perl5/$perlversion/man export MANPATH if [ -z "$INFOPATH" ]; then INFOPATH=/sw/share/info:/sw/info:/usr/share/info else prepend_path INFOPATH /sw/share/info:/sw/info fi export INFOPATH if [ -r /sw/share/java/classpath ]; then if [ -z "$CLASSPATH" ]; then CLASSPATH=`cat /sw/share/java/classpath`:. else add2classpath=`cat /sw/share/java/classpath` prepend_path CLASSPATH $add2classpath fi export CLASSPATH fi if [ -z "$PERL5LIB" ]; then PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin else prepend_path PERL5LIB /sw/lib/perl5:/sw/lib/perl5/darwin fi export PERL5LIB # Add X11 paths (but only if the directories are readable) # Don't add /usr/X11R6/bin if it or another X11 executable path is already # available if [ -r /usr/X11R6/bin ] && [ "`echo $PATH | grep 'X11.*/bin'`x" = "x" ]; then append_path PATH /usr/X11R6/bin export PATH fi if [ -r /usr/X11R6/man ]; then append_path MANPATH /usr/X11R6/man export MANPATH fi # On Mac OS X 10.4.{x|x<3} there is a dyld bug (rdar://problem/4139432) # where a library will not load if a library with a matching basename # is already loaded from one of the system paths, # the workaround is to set DYLD_FALLBACK_LIBRARY_PATH to : if [ -z "$DYLD_FALLBACK_LIBRARY_PATH" ]; then if [ $osMajorVer -eq 8 -a $osMinorVer -lt 3 ]; then DYLD_FALLBACK_LIBRARY_PATH=: export DYLD_FALLBACK_LIBRARY_PATH fi fi PROXYHTTP=`grep ProxyHTTP /sw/etc/fink.conf | grep -v "#" | cut -d " " -f2` if [ "$PROXYHTTP" != "" ]; then HTTP_PROXY=$PROXYHTTP http_proxy=$PROXYHTTP export HTTP_PROXY http_proxy fi PROXYFTP=`grep ProxyFTP /sw/etc/fink.conf | grep -v "#" | cut -d " " -f2` if [ "$PROXYFTP" != "" ]; then FTP_PROXY=$PROXYFTP ftp_proxy=$PROXYFTP export FTP_PROXY ftp_proxy fi # read per-package scripts from /sw/etc/profile.d if [ -d /sw/etc/profile.d ]; then for i in /sw/etc/profile.d/*.sh ; do if [ -r $i -a -x $i ]; then . $i fi done unset i fi # eof PATH=/sw/bin:/sw/sbin:${PATH} ; export PATH mkdir -p /sw/build.build/root-pdb2pqr-1.7-4/sw/share/pdb2pqr cp -R * /sw/build.build/root-pdb2pqr-1.7-4/sw/share/pdb2pqr # mkdir -p /sw/build.build/root-pdb2pqr-1.7-4/sw/bin echo "#!/bin/zsh -f" >| /sw/build.build/root-pdb2pqr-1.7-4/sw/bin/pdb2pqr echo "/sw/share/pdb2pqr/pdb2pqr.py \"\$@\" " >>| /sw/build.build/root-pdb2pqr-1.7-4/sw/bin/pdb2pqr chmod a+x /sw/build.build/root-pdb2pqr-1.7-4/sw/bin/pdb2pqr # echo "#!/bin/zsh -f" >| /sw/build.build/root-pdb2pqr-1.7-4/sw/bin/propka echo "/sw/share/pdb2pqr/propka/propka \"\$@\" " >>| /sw/build.build/root-pdb2pqr-1.7-4/sw/bin/propka chmod a+x /sw/build.build/root-pdb2pqr-1.7-4/sw/bin/propka sudo -u fink-bld [ENV] sh -c /tmp/fink.oqG41 /bin/rm -f /sw/build.build/root-pdb2pqr-1.7-4/sw/info/dir /sw/build.build/root-pdb2pqr-1.7-4/sw/info/dir.old /sw/build.build/root-pdb2pqr-1.7-4/sw/share/info/dir /sw/build.build/root-pdb2pqr-1.7-4/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-pdb2pqr-1.7-4 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `pdb2pqr' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/pdb2pqr_1.7-4_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-pdb2pqr-1.7-4 (Reading database ... 18852 files and directories currently installed.) Removing fink-buildlock-pdb2pqr-1.7-4 ...