RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux komainu 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_119~0.IS.08.04 python-lpbuildd_119~0.IS.08.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 27 Dec 03:59:37 ntpdate[12126]: adjust time server 10.211.37.1 offset 0.000084 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5386987', '/home/buildd/filecache-default/85437d411726979c3d865ddb70b8896a411f3906'] Unpacking chroot for build PACKAGEBUILD-5386987 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5386987'] Mounting chroot for build PACKAGEBUILD-5386987 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5386987', 'deb http://ftpmaster.internal/ubuntu trusty main universe', 'deb http://ftpmaster.internal/ubuntu trusty-security main universe', 'deb http://ftpmaster.internal/ubuntu trusty-updates main universe', 'deb http://ftpmaster.internal/ubuntu trusty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-5386987 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5386987', 'i386'] Updating debian chroot for build PACKAGEBUILD-5386987 Ign http://ftpmaster.internal trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty-updates InRelease Ign http://ftpmaster.internal trusty-proposed InRelease Ign http://archive-team.internal trusty Release.gpg Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Get:2 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:3 http://archive-team.internal trusty Release [723 B] Get:4 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal trusty Release [58.5 kB] Get:7 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:8 http://ftpmaster.internal trusty-updates Release [58.5 kB] Get:9 http://archive-team.internal trusty/main i386 Packages Get:10 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Ign http://archive-team.internal trusty/main Translation-en Get:11 http://ftpmaster.internal trusty/main i386 Packages [1263 kB] Get:12 http://ftpmaster.internal trusty/universe i386 Packages [5816 kB] Get:13 http://ftpmaster.internal trusty/main Translation-en [727 kB] Get:14 http://ftpmaster.internal trusty/universe Translation-en [4002 kB] Get:15 http://ftpmaster.internal trusty-security/main i386 Packages [14 B] Get:16 http://ftpmaster.internal trusty-security/universe i386 Packages [14 B] Get:17 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal trusty-updates/main i386 Packages [14 B] Get:20 http://ftpmaster.internal trusty-updates/universe i386 Packages [14 B] Get:21 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal trusty-proposed/main i386 Packages [30.7 kB] Get:24 http://ftpmaster.internal trusty-proposed/universe i386 Packages [275 kB] Get:25 http://ftpmaster.internal trusty-proposed/main Translation-en [14.8 kB] Get:26 http://ftpmaster.internal trusty-proposed/universe Translation-en [152 kB] Fetched 12.5 MB in 6s (1854 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5386987', 'i386', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '-A', '--purpose=PRIMARY', '--architecture=i386', '--comp=universe', 'autodocksuite_4.2.5.1-3ubuntu1.dsc'] Initiating build PACKAGEBUILD-5386987 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 i686 Automatic build of autodocksuite_4.2.5.1-3ubuntu1 on komainu by sbuild/i386 1.170.5 Build started at 20131227-0359 ****************************************************************************** autodocksuite_4.2.5.1-3ubuntu1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7), automake, csh, autotools-dev Checking for already installed source dependencies... debhelper: missing automake: missing csh: missing autotools-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper automake csh autotools-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof autoconf bsdmainutils dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libbsd0 libcroco3 libexpat1 libglib2.0-0 libmagic1 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libsigsegv2 libssl1.0.0 libunistring0 libxml2 m4 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof autoconf automake autotools-dev bsdmainutils csh debhelper dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libbsd0 libcroco3 libexpat1 libglib2.0-0 libmagic1 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libsigsegv2 libssl1.0.0 libunistring0 libxml2 m4 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 12.0 MB of archives. After this operation, 46.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libbsd0 i386 0.6.0-1ubuntu1 [32.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1 i386 2.1.0-4ubuntu1 [71.4 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libmagic1 i386 1:5.14-2ubuntu1 [184 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libssl1.0.0 i386 1.0.1e-4ubuntu4 [782 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-minimal i386 3.3.3-4 [396 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-stdlib i386 3.3.3-4 [2028 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main python3.3-minimal i386 3.3.3-4 [1307 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libasprintf0c2 i386 0.18.3.1-1ubuntu2 [6618 B] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libglib2.0-0 i386 2.39.2-0ubuntu1 [1016 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 i386 1.2.6-1 [23.3 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libxml2 i386 2.9.1+dfsg1-3ubuntu3 [555 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main groff-base i386 1.22.2-3 [705 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils i386 9.0.5ubuntu1 [197 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main man-db i386 2.6.5-2 [704 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 i386 0.6.8-2ubuntu1 [81.1 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libsigsegv2 i386 2.10-2 [14.8 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 i386 0.9.3-5ubuntu3 [272 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main python3.3 i386 3.3.3-4 [129 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main python3-minimal i386 3.3.2-17ubuntu1 [23.5 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main libpython3-stdlib i386 3.3.2-17ubuntu1 [7124 B] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main python3 i386 3.3.2-17ubuntu1 [8680 B] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main dh-python all 1.20131021-1ubuntu6 [50.2 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main file i386 1:5.14-2ubuntu1 [18.4 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main gettext-base i386 0.18.3.1-1ubuntu2 [47.9 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main m4 i386 1.4.17-2ubuntu1 [191 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main autoconf all 2.69-2 [573 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main automake all 1:1.14-2ubuntu1 [580 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/universe csh i386 20110502-2ubuntu2 [237 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main gettext i386 0.18.3.1-1ubuntu2 [815 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu35 [20.1 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu35 [7300 B] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131127ubuntu1 [604 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.0 MB in 0s (14.5 MB/s) Selecting previously unselected package libbsd0:i386. (Reading database ... 11989 files and directories currently installed.) Unpacking libbsd0:i386 (from .../libbsd0_0.6.0-1ubuntu1_i386.deb) ... Selecting previously unselected package libexpat1:i386. Unpacking libexpat1:i386 (from .../libexpat1_2.1.0-4ubuntu1_i386.deb) ... Selecting previously unselected package libmagic1:i386. Unpacking libmagic1:i386 (from .../libmagic1_1%3a5.14-2ubuntu1_i386.deb) ... Selecting previously unselected package libssl1.0.0:i386. Unpacking libssl1.0.0:i386 (from .../libssl1.0.0_1.0.1e-4ubuntu4_i386.deb) ... Selecting previously unselected package libpython3.3-minimal:i386. Unpacking libpython3.3-minimal:i386 (from .../libpython3.3-minimal_3.3.3-4_i386.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.54ubuntu1_all.deb) ... Selecting previously unselected package libpython3.3-stdlib:i386. Unpacking libpython3.3-stdlib:i386 (from .../libpython3.3-stdlib_3.3.3-4_i386.deb) ... 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Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython3.3-stdlib:i386 (3.3.3-4) ... Setting up python3.3-minimal (3.3.3-4) ... Setting up libasprintf0c2:i386 (0.18.3.1-1ubuntu2) ... Setting up libglib2.0-0:i386 (2.39.2-0ubuntu1) ... No schema files found: doing nothing. Setting up libpipeline1:i386 (1.2.6-1) ... Setting up libxml2:i386 (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:i386 (0.6.8-2ubuntu1) ... Setting up libsigsegv2:i386 (2.10-2) ... Setting up libunistring0:i386 (0.9.3-5ubuntu3) ... Setting up python3.3 (3.3.3-4) ... Setting up python3-minimal (3.3.2-17ubuntu1) ... Setting up libpython3-stdlib:i386 (3.3.2-17ubuntu1) ... Setting up file (1:5.14-2ubuntu1) ... Setting up gettext-base (0.18.3.1-1ubuntu2) ... Setting up m4 (1.4.17-2ubuntu1) ... Setting up autoconf (2.69-2) ... Setting up autotools-dev (20130810.1) ... Setting up automake (1:1.14-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode Setting up csh (20110502-2ubuntu2) ... update-alternatives: using /bin/bsd-csh to provide /bin/csh (csh) in auto mode Setting up gettext (0.18.3.1-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-python (1.20131021-1ubuntu6) ... Setting up python3 (3.3.2-17ubuntu1) ... running python rtupdate hooks for python3.3... running python post-rtupdate hooks for python3.3... Setting up apparmor-easyprof (2.8.0-0ubuntu35) ... Setting up dh-apparmor (2.8.0-0ubuntu35) ... Setting up debhelper (9.20131127ubuntu1) ... Processing triggers for libc-bin ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.18-0ubuntu2 make_3.81-8.2ubuntu3 dpkg-dev_1.17.1ubuntu1 gcc-4.8_4.8.2-10ubuntu2 g++-4.8_4.8.2-10ubuntu2 binutils_2.24-2ubuntu2 libstdc++-4.8-dev_4.8.2-10ubuntu2 libstdc++6_4.8.2-10ubuntu2 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Fri Dec 27 03:52:54 2013 UTC using RSA key ID EA330543 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./autodocksuite_4.2.5.1-3ubuntu1.dsc dpkg-source: info: extracting autodocksuite in autodocksuite-4.2.5.1 dpkg-source: info: unpacking autodocksuite_4.2.5.1.orig.tar.gz dpkg-source: info: unpacking autodocksuite_4.2.5.1-3ubuntu1.debian.tar.gz dpkg-source: info: applying make.patch dpkg-buildpackage: source package autodocksuite dpkg-buildpackage: source version 4.2.5.1-3ubuntu1 dpkg-buildpackage: source distribution trusty dpkg-source --before-build autodocksuite-4.2.5.1 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh_testdir dh_testroot rm -f build-arch-stamp build-indep-stamp configure-stamp for d in autodock autogrid; \ do \ if [ -r $d/Makefile ]; then /usr/bin/make -C $d distclean; fi \ done dh_autotools-dev_restoreconfig dh_clean configure-stamp debian/rules build dh_testdir dh_autotools-dev_updateconfig set -e; \ for d in autodock autogrid; do \ ( cd $d && autoreconf -i && ./configure CC="gcc" CXX="g++" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro "-Wl,--as-needed"" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions" CPPFLAGS="-D_FORTIFY_SOURCE=2" --prefix=/usr ) \ done configure.ac:30: installing './compile' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /build/buildd/autodocksuite-4.2.5.1/autodock/missing: Unknown `--is-lightweight' option Try `/build/buildd/autodocksuite-4.2.5.1/autodock/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 ranlib... ranlib checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for gethostname... yes checking for getpid... yes checking for GetProcessId... no checking for fchmod... yes checking for setlinebuf... yes checking for sysconf... yes checking for times... yes checking for getrusage... yes checking for pow... no checking for sqrt... no checking for strncasecmp... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands configure.ac:18: installing './compile' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /build/buildd/autodocksuite-4.2.5.1/autogrid/missing: Unknown `--is-lightweight' option Try `/build/buildd/autodocksuite-4.2.5.1/autogrid/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for sqrt in -lm... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for gethostname... yes checking for getpid... yes checking for GetProcessId... no checking for fchmod... yes checking for setlinebuf... yes checking for sysconf... yes checking for times... yes checking for getrusage... yes checking for pow... yes checking for sqrt... yes checking for strncasecmp... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands touch configure-stamp set -e; \ pwd; \ for d in autodock autogrid; do /usr/bin/make -C $d; done /build/buildd/autodocksuite-4.2.5.1 make[1]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autodock' rm -f default_parameters.h csh ./paramdat2h.csh ./AD4_parameters.dat ./AD4.1_bound.dat > default_parameters.h /usr/bin/make all-am make[2]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autodock' g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cc main.cc: In function 'int main(int, const char**)': main.cc:284:6: warning: variable 'etotal' set but not used [-Wunused-but-set-variable] Real etotal = 0.0; ^ In file included from gs.h:37:0, from hybrids.h:40, from main.cc:98: ls.h:210:8: warning: inlining failed in call to 'Solis_Wets_Base::~Solis_Wets_Base()': call is unlikely and code size would grow [-Winline] inline Solis_Wets_Base::~Solis_Wets_Base(void) ^ ls.h:278:68: warning: called from here [-Winline] rho(init_rho), lower_bound_on_rho(init_lb_on_rho) ^ mv -f .deps/main.Tpo .deps/main.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT alea.o -MD -MP -MF .deps/alea.Tpo -c -o alea.o alea.cc mv -f .deps/alea.Tpo .deps/alea.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT analysis.o -MD -MP -MF .deps/analysis.Tpo -c -o analysis.o analysis.cc mv -f .deps/analysis.Tpo .deps/analysis.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT atom_parameter_manager.o -MD -MP -MF .deps/atom_parameter_manager.Tpo -c -o atom_parameter_manager.o atom_parameter_manager.cc mv -f .deps/atom_parameter_manager.Tpo .deps/atom_parameter_manager.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT banner.o -MD -MP -MF .deps/banner.Tpo -c -o banner.o banner.cc mv -f .deps/banner.Tpo .deps/banner.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT bestpdb.o -MD -MP -MF .deps/bestpdb.Tpo -c -o bestpdb.o bestpdb.cc mv -f .deps/bestpdb.Tpo .deps/bestpdb.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT calculateEnergies.o -MD -MP -MF .deps/calculateEnergies.Tpo -c -o calculateEnergies.o calculateEnergies.cc mv -f .deps/calculateEnergies.Tpo .deps/calculateEnergies.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT call_glss.o -MD -MP -MF .deps/call_glss.Tpo -c -o call_glss.o call_glss.cc In file included from gs.h:36:0, from call_glss.cc:40: support.h: In function 'Individual random_ind(int, const GridMapSetInfo*)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ cc1plus: warning: called from here [-Winline] support.h: In function 'Individual set_ind(int, const GridMapSetInfo*, State)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ cc1plus: warning: called from here [-Winline] support.h: In function 'State call_glss(Global_Search*, Local_Search*, const State&, unsigned int, unsigned int, int, const Output_pop_stats&, Molecule*, Boole, Boole, Boole, const GridMapSetInfo*, const char*, int*)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ cc1plus: warning: called from here [-Winline] support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ call_glss.cc:297:24: warning: called from here [-Winline] thisPop[i] = random_ind( sInit.ntor, info ); ^ mv -f .deps/call_glss.Tpo .deps/call_glss.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT call_ls.o -MD -MP -MF .deps/call_ls.Tpo -c -o call_ls.o call_ls.cc mv -f .deps/call_ls.Tpo .deps/call_ls.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT center_ligand.o -MD -MP -MF .deps/center_ligand.Tpo -c -o center_ligand.o center_ligand.cc mv -f .deps/center_ligand.Tpo .deps/center_ligand.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT changeState.o -MD -MP -MF .deps/changeState.Tpo -c -o changeState.o changeState.cc mv -f .deps/changeState.Tpo .deps/changeState.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT check_header_float.o -MD -MP -MF .deps/check_header_float.Tpo -c -o check_header_float.o check_header_float.cc mv -f .deps/check_header_float.Tpo .deps/check_header_float.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT check_header_int.o -MD -MP -MF .deps/check_header_int.Tpo -c -o check_header_int.o check_header_int.cc mv -f .deps/check_header_int.Tpo .deps/check_header_int.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT check_header_line.o -MD -MP -MF .deps/check_header_line.Tpo -c -o check_header_line.o check_header_line.cc mv -f .deps/check_header_line.Tpo .deps/check_header_line.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT cluster_analysis.o -MD -MP -MF .deps/cluster_analysis.Tpo -c -o cluster_analysis.o cluster_analysis.cc mv -f .deps/cluster_analysis.Tpo .deps/cluster_analysis.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT clmode.o -MD -MP -MF .deps/clmode.Tpo -c -o clmode.o clmode.cc mv -f .deps/clmode.Tpo .deps/clmode.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT cnv_state_to_coords.o -MD -MP -MF .deps/cnv_state_to_coords.Tpo -c -o cnv_state_to_coords.o cnv_state_to_coords.cc mv -f .deps/cnv_state_to_coords.Tpo .deps/cnv_state_to_coords.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT com.o -MD -MP -MF .deps/com.Tpo -c -o com.o com.cc mv -f .deps/com.Tpo .deps/com.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT conformation_sampler.o -MD -MP -MF .deps/conformation_sampler.Tpo -c -o conformation_sampler.o conformation_sampler.cc conformation_sampler.cc: In constructor 'ConformationSampler::ConformationSampler(const State&, int, int, FILE*)': conformation_sampler.cc:99:10: warning: variable 'base_q' set but not used [-Wunused-but-set-variable] Quat base_q = probe_point.readQuat(); ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h: In destructor 'ConformationSampler::~ConformationSampler()': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:150:47: warning: called from here [-Winline] ConformationSampler::~ConformationSampler(void) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:150:47: warning: called from here [-Winline] ConformationSampler::~ConformationSampler(void) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h: In function 'Individual set_ind(GridMapSetInfo*, State)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ cc1plus: warning: called from here [-Winline] support.h: In constructor 'ConformationSampler::ConformationSampler(const State&, int, int, FILE*)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:76:11: warning: called from here [-Winline] base_ind = set_ind(info, init_state); ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:74:50: warning: called from here [-Winline] int true_ligand_atoms, int outlev, FILE *logFile) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:74:50: warning: called from here [-Winline] int true_ligand_atoms, int outlev, FILE *logFile) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h: In function 'void systematic_conformation_sampler(const State*, int, Real (*)[3], Real (*)[3], int (*)[2048], Real*, int, int*, GridMapSetInfo*, int, int, FILE*)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:150:47: warning: called from here [-Winline] ConformationSampler::~ConformationSampler(void) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:150:47: warning: called from here [-Winline] ConformationSampler::~ConformationSampler(void) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h: In function 'void random_conformation_sampler(const State*, int, int, Real (*)[3], Real (*)[3], int (*)[2048], Real*, int, int*, GridMapSetInfo*, int, int, FILE*)': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:150:47: warning: called from here [-Winline] ConformationSampler::~ConformationSampler(void) { ^ In file included from conformation_sampler.h:29:0, from conformation_sampler.cc:27: support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ conformation_sampler.cc:150:47: warning: called from here [-Winline] ConformationSampler::~ConformationSampler(void) { ^ mv -f .deps/conformation_sampler.Tpo .deps/conformation_sampler.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT dimLibrary.o -MD -MP -MF .deps/dimLibrary.Tpo -c -o dimLibrary.o dimLibrary.cc mv -f .deps/dimLibrary.Tpo .deps/dimLibrary.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT distdepdiel.o -MD -MP -MF .deps/distdepdiel.Tpo -c -o distdepdiel.o distdepdiel.cc mv -f .deps/distdepdiel.Tpo .deps/distdepdiel.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT stateLibrary.o -MD -MP -MF .deps/stateLibrary.Tpo -c -o stateLibrary.o stateLibrary.cc mv -f .deps/stateLibrary.Tpo .deps/stateLibrary.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT readfield.o -MD -MP -MF .deps/readfield.Tpo -c -o readfield.o readfield.cc readfield.cc: In function 'void readfield(GridMapSetInfo*, char*, const clock_t&, const tms&, int, FILE*)': readfield.cc:83:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] (void) fgets(inputline, LINE_LEN, fldFile); ^ readfield.cc:108:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] (void) fgets(inputline, LINE_LEN, fldFile); ^ readfield.cc:116:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] (void) fgets(inputline, LINE_LEN, fldFile); ^ readfield.cc:123:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] (void) fgets(inputline, LINE_LEN, fldFile); ^ mv -f .deps/readfield.Tpo .deps/readfield.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT readmap.o -MD -MP -MF .deps/readmap.Tpo -c -o readmap.o readmap.cc mv -f .deps/readmap.Tpo .deps/readmap.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT readPDBQT.o -MD -MP -MF .deps/readPDBQT.Tpo -c -o readPDBQT.o readPDBQT.cc readPDBQT.cc: In function 'Molecule readPDBQT(char*, int, int*, Real (*)[3], Real*, Boole*, int*, int*, char (*)[5], char*, char*, Boole, char (*)[128], int*, int*, Boole*, int*, int*, Real*, Real*, int*, int*, int (*)[2048], Real (*)[3], int*, int*, NonbondParam*, const clock_t&, const tms&, const char*, int*, int*, int, char (*)[256], int*, int, int, FILE*)': readPDBQT.cc:132:18: warning: variable 'B_has_conect_records' set but not used [-Wunused-but-set-variable] Boole B_has_conect_records = FALSE; ^ mv -f .deps/readPDBQT.Tpo .deps/readPDBQT.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT read_parameter_library.o -MD -MP -MF .deps/read_parameter_library.Tpo -c -o read_parameter_library.o read_parameter_library.cc mv -f .deps/read_parameter_library.Tpo .deps/read_parameter_library.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT eval.o -MD -MP -MF .deps/eval.Tpo -c -o eval.o eval.cc mv -f .deps/eval.Tpo .deps/eval.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT gencau.o -MD -MP -MF .deps/gencau.Tpo -c -o gencau.o gencau.cc mv -f .deps/gencau.Tpo .deps/gencau.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT getrms.o -MD -MP -MF .deps/getrms.Tpo -c -o getrms.o getrms.cc mv -f .deps/getrms.Tpo .deps/getrms.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT get_atom_type.o -MD -MP -MF .deps/get_atom_type.Tpo -c -o get_atom_type.o get_atom_type.cc get_atom_type.cc: In function 'int get_atom_type(const char*)': get_atom_type.cc:53:9: warning: variable 'bond_index' set but not used [-Wunused-but-set-variable] int bond_index = -1; ^ mv -f .deps/get_atom_type.Tpo .deps/get_atom_type.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT getInitialState.o -MD -MP -MF .deps/getInitialState.Tpo -c -o getInitialState.o getInitialState.cc mv -f .deps/getInitialState.Tpo .deps/getInitialState.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT getpdbcrds.o -MD -MP -MF .deps/getpdbcrds.Tpo -c -o getpdbcrds.o getpdbcrds.cc mv -f .deps/getpdbcrds.Tpo .deps/getpdbcrds.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -DCHECK_ISNAN -c ./gs.cc g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT initautodock.o -MD -MP -MF .deps/initautodock.Tpo -c -o initautodock.o initautodock.cc mv -f .deps/initautodock.Tpo .deps/initautodock.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT input_state.o -MD -MP -MF .deps/input_state.Tpo -c -o input_state.o input_state.cc input_state.cc: In function 'int input_state(State*, FILE*, const char*, int, int*, Real*, Real*, char*)': input_state.cc:70:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] (void) fgets(myline, LINELEN, fp); ^ mv -f .deps/input_state.Tpo .deps/input_state.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT investigate.o -MD -MP -MF .deps/investigate.Tpo -c -o investigate.o investigate.cc mv -f .deps/investigate.Tpo .deps/investigate.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT linpack.o -MD -MP -MF .deps/linpack.Tpo -c -o linpack.o linpack.cc mv -f .deps/linpack.Tpo .deps/linpack.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT ls.o -MD -MP -MF .deps/ls.Tpo -c -o ls.o ls.cc mv -f .deps/ls.Tpo .deps/ls.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT mapping.o -MD -MP -MF .deps/mapping.Tpo -c -o mapping.o mapping.cc mv -f .deps/mapping.Tpo .deps/mapping.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT mingw_getrusage.o -MD -MP -MF .deps/mingw_getrusage.Tpo -c -o mingw_getrusage.o mingw_getrusage.cc mv -f .deps/mingw_getrusage.Tpo .deps/mingw_getrusage.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT minmeanmax.o -MD -MP -MF .deps/minmeanmax.Tpo -c -o minmeanmax.o minmeanmax.cc minmeanmax.cc: In function 'void minmeanmax(FILE*, const Population&, int, const GridMapSetInfo*)': minmeanmax.cc:56:76: warning: variable 'best' set but not used [-Wunused-but-set-variable] double minimum[ 7+MAX_TORS ], sum[ 7+MAX_TORS ], maximum[ 7+MAX_TORS ], best[ 7+MAX_TORS ]; ^ mv -f .deps/minmeanmax.Tpo .deps/minmeanmax.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT mkNewState.o -MD -MP -MF .deps/mkNewState.Tpo -c -o mkNewState.o mkNewState.cc mv -f .deps/mkNewState.Tpo .deps/mkNewState.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT mkTorTree.o -MD -MP -MF .deps/mkTorTree.Tpo -c -o mkTorTree.o mkTorTree.cc mv -f .deps/mkTorTree.Tpo .deps/mkTorTree.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT mkRandomState.o -MD -MP -MF .deps/mkRandomState.Tpo -c -o mkRandomState.o mkRandomState.cc mv -f .deps/mkRandomState.Tpo .deps/mkRandomState.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT nonbonds.o -MD -MP -MF .deps/nonbonds.Tpo -c -o nonbonds.o nonbonds.cc In file included from nonbonds.cc:35:0: mdist.h: In function 'void mdist()': mdist.h:32:76: warning: operation on 'mindist[0][0]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:89:5: note: in expansion of macro 'set_minmax' set_minmax(C, C, 1.20, 1.545); // mindist[C][C] = 1.20, p. 3510 ; maxdist[C][C] = 1.545, p. 3511 ^ mdist.h:89:34: warning: operation on 'maxdist[0][0]' may be undefined [-Wsequence-point] set_minmax(C, C, 1.20, 1.545); // mindist[C][C] = 1.20, p. 3510 ; maxdist[C][C] = 1.545, p. 3511 ^ mdist.h:32:76: warning: operation on 'mindist[1][1]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:96:5: note: in expansion of macro 'set_minmax' set_minmax(N, N, 1.0974, 1.128); // mindist[N][N] = 1.0974, p. 3513 ; maxdist[N][N] = 1.128, p. 3515 ^ mdist.h:96:36: warning: operation on 'maxdist[1][1]' may be undefined [-Wsequence-point] set_minmax(N, N, 1.0974, 1.128); // mindist[N][N] = 1.0974, p. 3513 ; maxdist[N][N] = 1.128, p. 3515 ^ mdist.h:32:76: warning: operation on 'mindist[2][2]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:102:5: note: in expansion of macro 'set_minmax' set_minmax(O, O, 1.208, 1.51); // p.3513, p.3515 ^ In file included from nonbonds.cc:35:0: mdist.h:102:34: warning: operation on 'maxdist[2][2]' may be undefined [-Wsequence-point] set_minmax(O, O, 1.208, 1.51); // p.3513, p.3515 ^ In file included from nonbonds.cc:35:0: mdist.h:32:76: warning: operation on 'mindist[3][3]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:107:5: note: in expansion of macro 'set_minmax' set_minmax(H, H, 100.,-100.); // impossible values to prevent such bonds from forming. ^ In file included from nonbonds.cc:35:0: mdist.h:107:33: warning: operation on 'maxdist[3][3]' may be undefined [-Wsequence-point] set_minmax(H, H, 100.,-100.); // impossible values to prevent such bonds from forming. ^ In file included from nonbonds.cc:35:0: mdist.h:32:76: warning: operation on 'mindist[4][4]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:111:5: note: in expansion of macro 'set_minmax' set_minmax(XX, XX, 0.9, 2.1); // AutoDock 3 defaults ^ In file included from nonbonds.cc:35:0: mdist.h:111:33: warning: operation on 'maxdist[4][4]' may be undefined [-Wsequence-point] set_minmax(XX, XX, 0.9, 2.1); // AutoDock 3 defaults ^ In file included from nonbonds.cc:35:0: mdist.h:32:76: warning: operation on 'mindist[5][5]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:114:5: note: in expansion of macro 'set_minmax' set_minmax(P, P, 2.18, 2.23); // mindist[P][P] = 2.18, p. 3513 ; maxdist[P][P] = 2.23, p. 3513 ^ In file included from nonbonds.cc:35:0: mdist.h:114:33: warning: operation on 'maxdist[5][5]' may be undefined [-Wsequence-point] set_minmax(P, P, 2.18, 2.23); // mindist[P][P] = 2.18, p. 3513 ; maxdist[P][P] = 2.23, p. 3513 ^ In file included from nonbonds.cc:35:0: mdist.h:32:76: warning: operation on 'mindist[6][6]' may be undefined [-Wsequence-point] mindist[(a1)][(a2)] = mindist[(a2)][(a1)] = (min)-BOND_LENGTH_TOLERANCE;\ ^ mdist.h:116:5: note: in expansion of macro 'set_minmax' set_minmax(S, S, 2.03, 2.05); // mindist[S][S] = 2.03, p. 3515 ; maxdist[S][S] = 2.05, p. 3515 ^ In file included from nonbonds.cc:35:0: mdist.h:116:33: warning: operation on 'maxdist[6][6]' may be undefined [-Wsequence-point] set_minmax(S, S, 2.03, 2.05); // mindist[S][S] = 2.03, p. 3515 ; maxdist[S][S] = 2.05, p. 3515 ^ mv -f .deps/nonbonds.Tpo .deps/nonbonds.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT openfile.o -MD -MP -MF .deps/openfile.Tpo -c -o openfile.o openfile.cc mv -f .deps/openfile.Tpo .deps/openfile.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT output_state.o -MD -MP -MF .deps/output_state.Tpo -c -o output_state.o output_state.cc mv -f .deps/output_state.Tpo .deps/output_state.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT parse_dpf_line.o -MD -MP -MF .deps/parse_dpf_line.Tpo -c -o parse_dpf_line.o parse_dpf_line.cc mv -f .deps/parse_dpf_line.Tpo .deps/parse_dpf_line.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT parse_param_line.o -MD -MP -MF .deps/parse_param_line.Tpo -c -o parse_param_line.o parse_param_line.cc mv -f .deps/parse_param_line.Tpo .deps/parse_param_line.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT parse_PDBQT_line.o -MD -MP -MF .deps/parse_PDBQT_line.Tpo -c -o parse_PDBQT_line.o parse_PDBQT_line.cc mv -f .deps/parse_PDBQT_line.Tpo .deps/parse_PDBQT_line.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT parse_trj_line.o -MD -MP -MF .deps/parse_trj_line.Tpo -c -o parse_trj_line.o parse_trj_line.cc mv -f .deps/parse_trj_line.Tpo .deps/parse_trj_line.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT parsetypes.o -MD -MP -MF .deps/parsetypes.Tpo -c -o parsetypes.o parsetypes.cc mv -f .deps/parsetypes.Tpo .deps/parsetypes.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT print_2x.o -MD -MP -MF .deps/print_2x.Tpo -c -o print_2x.o print_2x.cc mv -f .deps/print_2x.Tpo .deps/print_2x.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT print_atomic_energies.o -MD -MP -MF .deps/print_atomic_energies.Tpo -c -o print_atomic_energies.o print_atomic_energies.cc mv -f .deps/print_atomic_energies.Tpo .deps/print_atomic_energies.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT print_avsfld.o -MD -MP -MF .deps/print_avsfld.Tpo -c -o print_avsfld.o print_avsfld.cc mv -f .deps/print_avsfld.Tpo .deps/print_avsfld.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT writePDBQT.o -MD -MP -MF .deps/writePDBQT.Tpo -c -o writePDBQT.o writePDBQT.cc writePDBQT.cc: In function 'void writePDBQT(int, const FourByteLong*, const char*, const char*, const Real*, State, int, Real*, Real*, int, const char (*)[128], Real (*)[3], EnergyComponent*, const Real*, const Real*, const Real*, int, Real, const Real (*)[3], const int (*)[2048], const Real (*)[3], const NonbondParam*, const EnergyTables*, const int*, int, int*, GroupEnergy*, int, Boole, MapType*, const int*, Boole, Real, const ParameterEntry*, Real, const GridMapSetInfo*, int, const char (*)[256], Boole, Boole, Unbound_Model, int, FILE*)': writePDBQT.cc:104:10: warning: variable 'e_inter' set but not used [-Wunused-but-set-variable] Real e_inter = 0.0; // total intermolecular energy = (1) + (4) ^ writePDBQT.cc:105:10: warning: variable 'e_intra_lig' set but not used [-Wunused-but-set-variable] Real e_intra_lig = 0.0; // ligand intramolecular energy = (3) ^ writePDBQT.cc:106:10: warning: variable 'e_intra_rec' set but not used [-Wunused-but-set-variable] Real e_intra_rec = 0.0; // receptor intramolecular energy = (2) + (5) ^ mv -f .deps/writePDBQT.Tpo .deps/writePDBQT.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT print_rem.o -MD -MP -MF .deps/print_rem.Tpo -c -o print_rem.o print_rem.cc mv -f .deps/print_rem.Tpo .deps/print_rem.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT printdate.o -MD -MP -MF .deps/printdate.Tpo -c -o printdate.o printdate.cc mv -f .deps/printdate.Tpo .deps/printdate.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT printEnergies.o -MD -MP -MF .deps/printEnergies.Tpo -c -o printEnergies.o printEnergies.cc mv -f .deps/printEnergies.Tpo .deps/printEnergies.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT printhms.o -MD -MP -MF .deps/printhms.Tpo -c -o printhms.o printhms.cc mv -f .deps/printhms.Tpo .deps/printhms.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT prClusterHist.o -MD -MP -MF .deps/prClusterHist.Tpo -c -o prClusterHist.o prClusterHist.cc mv -f .deps/prClusterHist.Tpo .deps/prClusterHist.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT prInitialState.o -MD -MP -MF .deps/prInitialState.Tpo -c -o prInitialState.o prInitialState.cc mv -f .deps/prInitialState.Tpo .deps/prInitialState.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT prTorConList.o -MD -MP -MF .deps/prTorConList.Tpo -c -o prTorConList.o prTorConList.cc mv -f .deps/prTorConList.Tpo .deps/prTorConList.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT pso.o -MD -MP -MF .deps/pso.Tpo -c -o pso.o pso.cc mv -f .deps/pso.Tpo .deps/pso.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT qmultiply.o -MD -MP -MF .deps/qmultiply.Tpo -c -o qmultiply.o qmultiply.cc qmultiply.cc: In function 'Quat randomQuatByAmount(const Real&)': qmultiply.cc:325:15: warning: variable 'aa' set but not used [-Wunused-but-set-variable] AxisAngle aa = QuatToAxisAngle( q ); // will not be 3-element normalized ^ mv -f .deps/qmultiply.Tpo .deps/qmultiply.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT qtransform.o -MD -MP -MF .deps/qtransform.Tpo -c -o qtransform.o qtransform.cc mv -f .deps/qtransform.Tpo .deps/qtransform.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT quicksort.o -MD -MP -MF .deps/quicksort.Tpo -c -o quicksort.o quicksort.cc mv -f .deps/quicksort.Tpo .deps/quicksort.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT ranlib.o -MD -MP -MF .deps/ranlib.Tpo -c -o ranlib.o ranlib.cc mv -f .deps/ranlib.Tpo .deps/ranlib.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT rep.o -MD -MP -MF .deps/rep.Tpo -c -o rep.o rep.cc mv -f .deps/rep.Tpo .deps/rep.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT scauchy.o -MD -MP -MF .deps/scauchy.Tpo -c -o scauchy.o scauchy.cc mv -f .deps/scauchy.Tpo .deps/scauchy.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT setflags.o -MD -MP -MF .deps/setflags.Tpo -c -o setflags.o setflags.cc mv -f .deps/setflags.Tpo .deps/setflags.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT simanneal.o -MD -MP -MF .deps/simanneal.Tpo -c -o simanneal.o simanneal.cc mv -f .deps/simanneal.Tpo .deps/simanneal.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT sort_enrg.o -MD -MP -MF .deps/sort_enrg.Tpo -c -o sort_enrg.o sort_enrg.cc mv -f .deps/sort_enrg.Tpo .deps/sort_enrg.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT stack.o -MD -MP -MF .deps/stack.Tpo -c -o stack.o stack.cc mv -f .deps/stack.Tpo .deps/stack.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT stop.o -MD -MP -MF .deps/stop.Tpo -c -o stop.o stop.cc mv -f .deps/stop.Tpo .deps/stop.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT strindex.o -MD -MP -MF .deps/strindex.Tpo -c -o strindex.o strindex.cc mv -f .deps/strindex.Tpo .deps/strindex.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT success.o -MD -MP -MF .deps/success.Tpo -c -o success.o success.cc mv -f .deps/success.Tpo .deps/success.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT support.o -MD -MP -MF .deps/support.Tpo -c -o support.o support.cc In file included from support.cc:35:0: support.h: In member function 'void Population::swap(Individual&, Individual&) const': support.h:472:8: warning: inlining failed in call to 'Individual::~Individual()': call is unlikely and code size would grow [-Winline] inline Individual::~Individual(void) ^ support.cc:89:22: warning: called from here [-Winline] individual2 = temp; ^ mv -f .deps/support.Tpo .deps/support.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT swap.o -MD -MP -MF .deps/swap.Tpo -c -o swap.o swap.cc mv -f .deps/swap.Tpo .deps/swap.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT timesys.o -MD -MP -MF .deps/timesys.Tpo -c -o timesys.o timesys.cc mv -f .deps/timesys.Tpo .deps/timesys.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT timesyshms.o -MD -MP -MF .deps/timesyshms.Tpo -c -o timesyshms.o timesyshms.cc mv -f .deps/timesyshms.Tpo .deps/timesyshms.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT torNorVec.o -MD -MP -MF .deps/torNorVec.Tpo -c -o torNorVec.o torNorVec.cc mv -f .deps/torNorVec.Tpo .deps/torNorVec.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT torsion.o -MD -MP -MF .deps/torsion.Tpo -c -o torsion.o torsion.cc mv -f .deps/torsion.Tpo .deps/torsion.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT trilinterp.o -MD -MP -MF .deps/trilinterp.Tpo -c -o trilinterp.o trilinterp.cc trilinterp.cc: In function 'Real trilinterp(int, int, const Real (*)[3], const Real*, const Real*, const int*, MapType*, const GridMapSetInfo*, const int*, EnergyComponent*, EnergyComponent*, EnergyComponent*)': trilinterp.cc:199:29: warning: narrowing conversion of 'p1u' from 'double' to 'MapType {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing] MapType pu[2] = { p1u, p0u }; ^ trilinterp.cc:199:29: warning: narrowing conversion of 'p0u' from 'double' to 'MapType {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing] trilinterp.cc:200:29: warning: narrowing conversion of 'p1v' from 'double' to 'MapType {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing] MapType pv[2] = { p1v, p0v }; ^ trilinterp.cc:200:29: warning: narrowing conversion of 'p0v' from 'double' to 'MapType {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing] trilinterp.cc:201:29: warning: narrowing conversion of 'p1w' from 'double' to 'MapType {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing] MapType pw[2] = { p1w, p0w }; ^ trilinterp.cc:201:29: warning: narrowing conversion of 'p0w' from 'double' to 'MapType {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing] trilinterp.cc:98:22: warning: variable 'u1' set but not used [-Wunused-but-set-variable] register int u1, v1, w1; ^ trilinterp.cc:98:27: warning: variable 'v1' set but not used [-Wunused-but-set-variable] register int u1, v1, w1; ^ trilinterp.cc:98:32: warning: variable 'w1' set but not used [-Wunused-but-set-variable] register int u1, v1, w1; ^ mv -f .deps/trilinterp.Tpo .deps/trilinterp.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT usage.o -MD -MP -MF .deps/usage.Tpo -c -o usage.o usage.cc mv -f .deps/usage.Tpo .deps/usage.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT weedbonds.o -MD -MP -MF .deps/weedbonds.Tpo -c -o weedbonds.o weedbonds.cc mv -f .deps/weedbonds.Tpo .deps/weedbonds.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT warn_bad_file.o -MD -MP -MF .deps/warn_bad_file.Tpo -c -o warn_bad_file.o warn_bad_file.cc mv -f .deps/warn_bad_file.Tpo .deps/warn_bad_file.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT coliny.o -MD -MP -MF .deps/coliny.Tpo -c -o coliny.o coliny.cc mv -f .deps/coliny.Tpo .deps/coliny.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT eintcal.o -MD -MP -MF .deps/eintcal.Tpo -c -o eintcal.o eintcal.cc mv -f .deps/eintcal.Tpo .deps/eintcal.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT eintcalPrint.o -MD -MP -MF .deps/eintcalPrint.Tpo -c -o eintcalPrint.o eintcalPrint.cc mv -f .deps/eintcalPrint.Tpo .deps/eintcalPrint.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT intnbtable.o -MD -MP -MF .deps/intnbtable.Tpo -c -o intnbtable.o intnbtable.cc mv -f .deps/intnbtable.Tpo .deps/intnbtable.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.5.1\" -DPACKAGE_STRING=\"autodock\ 4.2.5.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.5.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DASSERTQUATOK -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE -I./../acro/include -D_FORTIFY_SOURCE=2 -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT nbe.o -MD -MP -MF .deps/nbe.Tpo -c -o nbe.o nbe.cc mv -f .deps/nbe.Tpo .deps/nbe.Po g++ -O3 -Wall -Wno-write-strings -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--as-needed -o autodock4 main.o alea.o analysis.o atom_parameter_manager.o banner.o bestpdb.o calculateEnergies.o call_glss.o call_ls.o center_ligand.o changeState.o check_header_float.o check_header_int.o check_header_line.o cluster_analysis.o clmode.o cnv_state_to_coords.o com.o conformation_sampler.o dimLibrary.o distdepdiel.o stateLibrary.o readfield.o readmap.o readPDBQT.o read_parameter_library.o eval.o gencau.o getrms.o get_atom_type.o getInitialState.o getpdbcrds.o gs.o initautodock.o input_state.o investigate.o linpack.o ls.o mapping.o mingw_getrusage.o minmeanmax.o mkNewState.o mkTorTree.o mkRandomState.o nonbonds.o openfile.o output_state.o parse_dpf_line.o parse_param_line.o parse_PDBQT_line.o parse_trj_line.o parsetypes.o print_2x.o print_atomic_energies.o print_avsfld.o writePDBQT.o print_rem.o printdate.o printEnergies.o printhms.o prClusterHist.o prInitialState.o prTorConList.o pso.o qmultiply.o qtransform.o quicksort.o ranlib.o rep.o scauchy.o setflags.o simanneal.o sort_enrg.o stack.o stop.o strindex.o success.o support.o swap.o timesys.o timesyshms.o torNorVec.o torsion.o trilinterp.o usage.o weedbonds.o warn_bad_file.o coliny.o eintcal.o eintcalPrint.o intnbtable.o nbe.o -lm make[2]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autodock' make[1]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autodock' make[1]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' rm -f default_parameters.h csh ./../autodock/paramdat2h.csh ./../autodock/AD4_parameters.dat ./../autodock/AD4.1_bound.dat > default_parameters.h sh ./copyfilesfromAD # copying from src dir , not build dir /usr/bin/make all-am make[2]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-main.o -MD -MP -MF .deps/autogrid4-main.Tpo -c -o autogrid4-main.o `test -f 'main.cpp' || echo './'`main.cpp main.cpp: In function 'int main(int, char**)': main.cpp:213:5: warning: variable 'parameter_library_found' set but not used [-Wunused-but-set-variable] int parameter_library_found = 0; ^ main.cpp:262:8: warning: variable 'maptypeptr' set but not used [-Wunused-but-set-variable] char * maptypeptr; /*ptr for current map->type*/ ^ main.cpp:300:44: warning: variable 'nitrogen' set but not used [-Wunused-but-set-variable] int hydrogen, carbon, arom_carbon, oxygen, nitrogen; ^ main.cpp:301:21: warning: variable 'nonHB_nitrogen' set but not used [-Wunused-but-set-variable] int nonHB_hydrogen, nonHB_nitrogen, sulphur, nonHB_sulphur; ^ main.cpp:301:46: warning: variable 'nonHB_sulphur' set but not used [-Wunused-but-set-variable] int nonHB_hydrogen, nonHB_nitrogen, sulphur, nonHB_sulphur; ^ main.cpp:304:5: warning: variable 'chlorine' set but not used [-Wunused-but-set-variable] int chlorine, bromine, fluorine, iodine; ^ main.cpp:304:15: warning: variable 'bromine' set but not used [-Wunused-but-set-variable] int chlorine, bromine, fluorine, iodine; ^ main.cpp:304:24: warning: variable 'fluorine' set but not used [-Wunused-but-set-variable] int chlorine, bromine, fluorine, iodine; ^ main.cpp:304:34: warning: variable 'iodine' set but not used [-Wunused-but-set-variable] int chlorine, bromine, fluorine, iodine; ^ main.cpp:306:5: warning: variable 'map_hydrogen' set but not used [-Wunused-but-set-variable] int map_hydrogen, map_carbon, map_arom_carbon, map_oxygen, map_nitrogen; ^ main.cpp:306:19: warning: variable 'map_carbon' set but not used [-Wunused-but-set-variable] int map_hydrogen, map_carbon, map_arom_carbon, map_oxygen, map_nitrogen; ^ main.cpp:306:31: warning: variable 'map_arom_carbon' set but not used [-Wunused-but-set-variable] int map_hydrogen, map_carbon, map_arom_carbon, map_oxygen, map_nitrogen; ^ main.cpp:306:48: warning: variable 'map_oxygen' set but not used [-Wunused-but-set-variable] int map_hydrogen, map_carbon, map_arom_carbon, map_oxygen, map_nitrogen; ^ main.cpp:306:60: warning: variable 'map_nitrogen' set but not used [-Wunused-but-set-variable] int map_hydrogen, map_carbon, map_arom_carbon, map_oxygen, map_nitrogen; ^ main.cpp:307:5: warning: variable 'map_nonHB_hydrogen' set but not used [-Wunused-but-set-variable] int map_nonHB_hydrogen, map_nonHB_nitrogen, map_sulphur, map_nonHB_sulphur; ^ main.cpp:307:25: warning: variable 'map_nonHB_nitrogen' set but not used [-Wunused-but-set-variable] int map_nonHB_hydrogen, map_nonHB_nitrogen, map_sulphur, map_nonHB_sulphur; ^ main.cpp:307:45: warning: variable 'map_sulphur' set but not used [-Wunused-but-set-variable] int map_nonHB_hydrogen, map_nonHB_nitrogen, map_sulphur, map_nonHB_sulphur; ^ main.cpp:307:58: warning: variable 'map_nonHB_sulphur' set but not used [-Wunused-but-set-variable] int map_nonHB_hydrogen, map_nonHB_nitrogen, map_sulphur, map_nonHB_sulphur; ^ main.cpp:308:5: warning: variable 'map_chlorine' set but not used [-Wunused-but-set-variable] int map_chlorine, map_bromine, map_fluorine, map_iodine; ^ main.cpp:308:19: warning: variable 'map_bromine' set but not used [-Wunused-but-set-variable] int map_chlorine, map_bromine, map_fluorine, map_iodine; ^ main.cpp:308:32: warning: variable 'map_fluorine' set but not used [-Wunused-but-set-variable] int map_chlorine, map_bromine, map_fluorine, map_iodine; ^ main.cpp:308:46: warning: variable 'map_iodine' set but not used [-Wunused-but-set-variable] int map_chlorine, map_bromine, map_fluorine, map_iodine; ^ main.cpp:2616:112: warning: 'Hramp' may be used uninitialized in this function [-Wmaybe-uninitialized] gridmap[map_index].energy += et.e_vdW_Hb[indx_n][atom_type[ia]][map_index] * Hramp * (racc + (1. - racc)*rsph); ^ main.cpp:2641:105: warning: 'rdon' may be used uninitialized in this function [-Wmaybe-uninitialized] temp_hbond_enrg = et.e_vdW_Hb[indx_n][atom_type[ia]][map_index] * (rdon + (1. - rdon)*rsph); ^ main.cpp:2629:133: warning: 'racc' may be used uninitialized in this function [-Wmaybe-uninitialized] hbondmin[map_index] = min( hbondmin[map_index],et.e_vdW_Hb[indx_n][atom_type[ia]][map_index] * (racc+(1.-racc)*rsph)); ^ mv -f .deps/autogrid4-main.Tpo .deps/autogrid4-main.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-check_size.o -MD -MP -MF .deps/autogrid4-check_size.Tpo -c -o autogrid4-check_size.o `test -f 'check_size.cpp' || echo './'`check_size.cpp mv -f .deps/autogrid4-check_size.Tpo .deps/autogrid4-check_size.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-setflags.o -MD -MP -MF .deps/autogrid4-setflags.Tpo -c -o autogrid4-setflags.o `test -f 'setflags.cpp' || echo './'`setflags.cpp mv -f .deps/autogrid4-setflags.Tpo .deps/autogrid4-setflags.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-timesys.o -MD -MP -MF .deps/autogrid4-timesys.Tpo -c -o autogrid4-timesys.o `test -f 'timesys.cpp' || echo './'`timesys.cpp mv -f .deps/autogrid4-timesys.Tpo .deps/autogrid4-timesys.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-timesyshms.o -MD -MP -MF .deps/autogrid4-timesyshms.Tpo -c -o autogrid4-timesyshms.o `test -f 'timesyshms.cpp' || echo './'`timesyshms.cpp mv -f .deps/autogrid4-timesyshms.Tpo .deps/autogrid4-timesyshms.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-printhms.o -MD -MP -MF .deps/autogrid4-printhms.Tpo -c -o autogrid4-printhms.o `test -f 'printhms.cpp' || echo './'`printhms.cpp mv -f .deps/autogrid4-printhms.Tpo .deps/autogrid4-printhms.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-prHMSfixed.o -MD -MP -MF .deps/autogrid4-prHMSfixed.Tpo -c -o autogrid4-prHMSfixed.o `test -f 'prHMSfixed.cpp' || echo './'`prHMSfixed.cpp mv -f .deps/autogrid4-prHMSfixed.Tpo .deps/autogrid4-prHMSfixed.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-printdate.o -MD -MP -MF .deps/autogrid4-printdate.Tpo -c -o autogrid4-printdate.o `test -f 'printdate.cpp' || echo './'`printdate.cpp mv -f .deps/autogrid4-printdate.Tpo .deps/autogrid4-printdate.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-strindex.o -MD -MP -MF .deps/autogrid4-strindex.Tpo -c -o autogrid4-strindex.o `test -f 'strindex.cpp' || echo './'`strindex.cpp mv -f .deps/autogrid4-strindex.Tpo .deps/autogrid4-strindex.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-banner.o -MD -MP -MF .deps/autogrid4-banner.Tpo -c -o autogrid4-banner.o `test -f 'banner.cpp' || echo './'`banner.cpp mv -f .deps/autogrid4-banner.Tpo .deps/autogrid4-banner.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-gpfparser.o -MD -MP -MF .deps/autogrid4-gpfparser.Tpo -c -o autogrid4-gpfparser.o `test -f 'gpfparser.cpp' || echo './'`gpfparser.cpp mv -f .deps/autogrid4-gpfparser.Tpo .deps/autogrid4-gpfparser.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-parsetypes.o -MD -MP -MF .deps/autogrid4-parsetypes.Tpo -c -o autogrid4-parsetypes.o `test -f 'parsetypes.cpp' || echo './'`parsetypes.cpp mv -f .deps/autogrid4-parsetypes.Tpo .deps/autogrid4-parsetypes.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-atom_parameter_manager.o -MD -MP -MF .deps/autogrid4-atom_parameter_manager.Tpo -c -o autogrid4-atom_parameter_manager.o `test -f 'atom_parameter_manager.cpp' || echo './'`atom_parameter_manager.cpp mv -f .deps/autogrid4-atom_parameter_manager.Tpo .deps/autogrid4-atom_parameter_manager.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-read_parameter_library.o -MD -MP -MF .deps/autogrid4-read_parameter_library.Tpo -c -o autogrid4-read_parameter_library.o `test -f 'read_parameter_library.cpp' || echo './'`read_parameter_library.cpp mv -f .deps/autogrid4-read_parameter_library.Tpo .deps/autogrid4-read_parameter_library.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-parse_param_line.o -MD -MP -MF .deps/autogrid4-parse_param_line.Tpo -c -o autogrid4-parse_param_line.o `test -f 'parse_param_line.cpp' || echo './'`parse_param_line.cpp mv -f .deps/autogrid4-parse_param_line.Tpo .deps/autogrid4-parse_param_line.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-distdepdiel.o -MD -MP -MF .deps/autogrid4-distdepdiel.Tpo -c -o autogrid4-distdepdiel.o `test -f 'distdepdiel.cpp' || echo './'`distdepdiel.cpp mv -f .deps/autogrid4-distdepdiel.Tpo .deps/autogrid4-distdepdiel.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-mingw_getrusage.o -MD -MP -MF .deps/autogrid4-mingw_getrusage.Tpo -c -o autogrid4-mingw_getrusage.o `test -f 'mingw_getrusage.cpp' || echo './'`mingw_getrusage.cpp mv -f .deps/autogrid4-mingw_getrusage.Tpo .deps/autogrid4-mingw_getrusage.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-calc_vina_potential.o -MD -MP -MF .deps/autogrid4-calc_vina_potential.Tpo -c -o autogrid4-calc_vina_potential.o `test -f 'calc_vina_potential.cpp' || echo './'`calc_vina_potential.cpp calc_vina_potential.cpp: In function 'int calc_vina_potential(int, const char (*)[3], int, const char (*)[3], EnergyTables*)': calc_vina_potential.cpp:110:9: warning: variable 'hydrogen' set but not used [-Wunused-but-set-variable] int hydrogen=-1; ^ calc_vina_potential.cpp:113:9: warning: variable 'oxygen' set but not used [-Wunused-but-set-variable] int oxygen=-1; ^ calc_vina_potential.cpp:114:9: warning: variable 'nitrogen' set but not used [-Wunused-but-set-variable] int nitrogen=-1; ^ calc_vina_potential.cpp:115:9: warning: variable 'fluorine' set but not used [-Wunused-but-set-variable] int fluorine=-1; ^ calc_vina_potential.cpp:116:9: warning: variable 'chlorine' set but not used [-Wunused-but-set-variable] int chlorine=-1; ^ calc_vina_potential.cpp:117:9: warning: variable 'bromine' set but not used [-Wunused-but-set-variable] int bromine=-1; ^ calc_vina_potential.cpp:118:9: warning: variable 'iodine' set but not used [-Wunused-but-set-variable] int iodine=-1; ^ mv -f .deps/autogrid4-calc_vina_potential.Tpo .deps/autogrid4-calc_vina_potential.Po g++ -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.5\" -DPACKAGE_STRING=\"autogrid\ 4.2.5\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.5\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -MT autogrid4-stop.o -MD -MP -MF .deps/autogrid4-stop.Tpo -c -o autogrid4-stop.o `test -f 'stop.cpp' || echo './'`stop.cpp mv -f .deps/autogrid4-stop.Tpo .deps/autogrid4-stop.Po g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -g -O2 -Winline -finline-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--as-needed -o autogrid4 autogrid4-main.o autogrid4-check_size.o autogrid4-setflags.o autogrid4-timesys.o autogrid4-timesyshms.o autogrid4-printhms.o autogrid4-prHMSfixed.o autogrid4-printdate.o autogrid4-strindex.o autogrid4-banner.o autogrid4-gpfparser.o autogrid4-parsetypes.o autogrid4-atom_parameter_manager.o autogrid4-read_parameter_library.o autogrid4-parse_param_line.o autogrid4-distdepdiel.o autogrid4-mingw_getrusage.o autogrid4-calc_vina_potential.o autogrid4-stop.o -lm make[2]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' make[1]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' touch build-arch-stamp # Add here commands to compile the indep part of the package. touch build-indep-stamp /usr/bin/fakeroot debian/rules binary dh_testdir dh_testroot dh_prep -s dh_installdirs -s for d in autodock autogrid; do \ /usr/bin/make -C $d DESTDIR=/build/buildd/autodocksuite-4.2.5.1/debian/$d install; \ done make[1]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autodock' /usr/bin/make install-am make[2]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autodock' make[3]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autodock' /bin/mkdir -p '/build/buildd/autodocksuite-4.2.5.1/debian/autodock/usr/bin' /usr/bin/install -c autodock4 '/build/buildd/autodocksuite-4.2.5.1/debian/autodock/usr/bin' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autodock' make[2]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autodock' make[1]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autodock' make[1]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' /usr/bin/make install-am make[2]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' make[3]: Entering directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' /bin/mkdir -p '/build/buildd/autodocksuite-4.2.5.1/debian/autogrid/usr/bin' /usr/bin/install -c autogrid4 '/build/buildd/autodocksuite-4.2.5.1/debian/autogrid/usr/bin' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' make[2]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' make[1]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1/autogrid' dh_install -s /usr/bin/make -f debian/rules DH_OPTIONS=-s binary-common make[1]: Entering directory `/build/buildd/autodocksuite-4.2.5.1' dh_testdir dh_testroot dh_lintian dh_installchangelogs autodock/RELEASENOTES dh_installdocs dh_installexamples dh_installman dh_link dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: autodock autogrid dh_strip debug symbol extraction: packages to act on: autodock autogrid dh_strip debug symbol extraction: ignored packages: dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: warning: '/build/buildd/autodocksuite-4.2.5.1/debian/autodock-dbgsym/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autodock-dbgsym' in `../autodock-dbgsym_4.2.5.1-3ubuntu1_i386.ddeb'. dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: warning: '/build/buildd/autodocksuite-4.2.5.1/debian/autogrid-dbgsym/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autogrid-dbgsym' in `../autogrid-dbgsym_4.2.5.1-3ubuntu1_i386.ddeb'. dh_compress dh_fixperms dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums dh_builddeb INFO: pkgstriptranslations version 118 pkgstriptranslations: processing autodock (in debian/autodock); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/autodock/DEBIAN/control, package autodock, directory debian/autodock .. removing usr/share/doc/autodock/changelog.gz pkgstripfiles: Truncating usr/share/doc/autodock/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package autodock took 0 s dpkg-deb: warning: 'debian/autodock/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autodock' in `../autodock_4.2.5.1-3ubuntu1_i386.deb'. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing autogrid (in debian/autogrid); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/autogrid/DEBIAN/control, package autogrid, directory debian/autogrid .. removing usr/share/doc/autogrid/changelog.gz pkgstripfiles: Truncating usr/share/doc/autogrid/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package autogrid took 0 s dpkg-deb: warning: 'debian/autogrid/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autogrid' in `../autogrid_4.2.5.1-3ubuntu1_i386.deb'. make[1]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1' dh_testdir dh_testroot dh_prep -i dh_installdirs -i dh_install -i rm -rf /build/buildd/autodocksuite-4.2.5.1/debian/autodock-test/usr/share/autodock/Tests/AutoDockTools rm -rf /build/buildd/autodocksuite-4.2.5.1/debian/autogrid-test/usr/share/autogrid/Tests/CVS/ rm -rf /build/buildd/autodocksuite-4.2.5.1/debian/autodock-test/usr/share/autodock/Tests/CVS/ chmod 644 /build/buildd/autodocksuite-4.2.5.1/debian/autodock-test/usr/share/autodock/Tests/* chmod 644 /build/buildd/autodocksuite-4.2.5.1/debian/autogrid-test/usr/share/autogrid/Tests/* /usr/bin/make -f debian/rules DH_OPTIONS=-i binary-common make[1]: Entering directory `/build/buildd/autodocksuite-4.2.5.1' dh_testdir dh_testroot dh_lintian dh_installchangelogs autodock/RELEASENOTES dh_installdocs dh_installexamples dh_installman dh_link dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: autodock autogrid dh_strip debug symbol extraction: packages to act on: dh_strip debug symbol extraction: ignored packages: dh_compress dh_fixperms dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums dh_builddeb INFO: pkgstriptranslations version 118 pkgstriptranslations: processing autodock-test (in debian/autodock-test); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/autodock-test/DEBIAN/control, package autodock-test, directory debian/autodock-test .. removing usr/share/doc/autodock-test/changelog.gz pkgstripfiles: Truncating usr/share/doc/autodock-test/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package autodock-test took 0 s dpkg-deb: warning: 'debian/autodock-test/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autodock-test' in `../autodock-test_4.2.5.1-3ubuntu1_all.deb'. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing autogrid-test (in debian/autogrid-test); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/autogrid-test/DEBIAN/control, package autogrid-test, directory debian/autogrid-test .. removing usr/share/doc/autogrid-test/changelog.gz pkgstripfiles: Truncating usr/share/doc/autogrid-test/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package autogrid-test took 0 s dpkg-deb: warning: 'debian/autogrid-test/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autogrid-test' in `../autogrid-test_4.2.5.1-3ubuntu1_all.deb'. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing autodock-getdata (in debian/autodock-getdata); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/autodock-getdata/DEBIAN/control, package autodock-getdata, directory debian/autodock-getdata .. removing usr/share/doc/autodock-getdata/changelog.gz pkgstripfiles: Truncating usr/share/doc/autodock-getdata/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package autodock-getdata took 0 s dpkg-deb: warning: 'debian/autodock-getdata/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `autodock-getdata' in `../autodock-getdata_4.2.5.1-3ubuntu1_all.deb'. make[1]: Leaving directory `/build/buildd/autodocksuite-4.2.5.1' dpkg-genchanges -b -mUbuntu/amd64 Build Daemon >../autodocksuite_4.2.5.1-3ubuntu1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build autodocksuite-4.2.5.1 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20131227-0401 Publishing debug debs. chroot-autobuild/build/buildd/autodock_4.2.5.1-3ubuntu1_i386.deb: new debian package, version 2.0. size 159894 bytes: control archive= 1593 bytes. 1048 bytes, 22 lines control 680 bytes, 10 lines md5sums 1068 bytes, 42 lines * postinst #!/bin/sh Package: autodock Source: autodocksuite Version: 4.2.5.1-3ubuntu1 Architecture: i386 Maintainer: Ubuntu Developers Installed-Size: 491 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.1.1) Suggests: autogrid, autodocktools Section: science Priority: optional Homepage: http://autodock.scripps.edu/ Description: analysis of ligand binding to protein structure AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account. . The AutoDock program performs the docking of the ligand to a set of grids describing the target protein. AutoGrid pre-calculates these grids. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/autogrid_4.2.5.1-3ubuntu1_i386.deb: new debian package, version 2.0. size 35300 bytes: control archive= 939 bytes. 936 bytes, 22 lines control 458 bytes, 7 lines md5sums Package: autogrid Source: autodocksuite Version: 4.2.5.1-3ubuntu1 Architecture: i386 Maintainer: Ubuntu Developers Installed-Size: 131 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.1.1) Suggests: autodock, autodocktools Enhances: autodock Section: science Priority: optional Homepage: http://autodock.scripps.edu/ Description: pre-calculate binding of ligands to their receptor The AutoDockSuite addresses the molecular analysis of the docking of a smaller chemical compounds to their receptors of known three-dimensional structure. . The AutoGrid program performs pre-calculations for the docking of a ligand to a set of grids that describe the effect that the protein has on point charges. The effect of these forces on the ligand is then analysed by the AutoDock program. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/autodock-test_4.2.5.1-3ubuntu1_all.deb: new debian package, version 2.0. size 3198784 bytes: control archive= 3780 bytes. 865 bytes, 20 lines control 8691 bytes, 107 lines md5sums Package: autodock-test Source: autodocksuite Version: 4.2.5.1-3ubuntu1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 11466 Suggests: autodock Section: science Priority: optional Homepage: http://autodock.scripps.edu/ Description: test files for AutoDock AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account. . This package contain the test files for the AutoDock program. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/autogrid-test_4.2.5.1-3ubuntu1_all.deb: new debian package, version 2.0. size 53480 bytes: control archive= 1287 bytes. 628 bytes, 17 lines control 1844 bytes, 24 lines md5sums Package: autogrid-test Source: autodocksuite Version: 4.2.5.1-3ubuntu1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 386 Suggests: autogrid Section: science Priority: optional Homepage: http://autodock.scripps.edu/ Description: test files for AutoGrid The AutoDockSuite addresses the molecular analysis of the docking of a smaller chemical compounds to their receptors of known three-dimensional structure. . This package contain the test files for the AutoGrid program. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/autodock-getdata_4.2.5.1-3ubuntu1_all.deb: new debian package, version 2.0. size 4690 bytes: control archive= 1009 bytes. 42 bytes, 1 lines conffiles 1235 bytes, 33 lines control 239 bytes, 3 lines md5sums Package: autodock-getdata Source: autodocksuite Version: 4.2.5.1-3ubuntu1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 49 Recommends: getdata Suggests: autodock, autogrid, autodocktools Section: science Priority: optional Homepage: http://autodock.scripps.edu/ Description: instructions for getData to collect compounds This package provides instructions for getData to retrieve descriptions for sets of molecular compounds that can be used directly as input for autodock. The data is not provided direclty by this package. Only the instructions for the download are maintained here. . The FightAids@Home project of the World Community Grid publicly provides the input sets of their runs. The original structures come from the ZINC database and have been processed from the mol2 to pdbqt format by the Scripps institute: * asinex * chembridge_buildingblocks_pdbqt_1000split * drugbank_nutraceutics * drugbank_smallmol * fda_approved * human_metabolome_pdbqt_1000split * otava * zinc_natural_products . Please cite the ZINC database when using that data. 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./usr/share/doc/autodock-getdata/ -rw-r--r-- root/root 1360 2013-12-27 04:01 ./usr/share/doc/autodock-getdata/changelog.Debian.gz -rw-r--r-- root/root 479 2012-04-02 08:12 ./usr/share/doc/autodock-getdata/README.Debian -rw-r--r-- root/root 2071 2013-02-18 07:34 ./usr/share/doc/autodock-getdata/copyright drwxr-xr-x root/root 0 2013-12-27 04:01 ./etc/ drwxr-xr-x root/root 0 2013-12-27 04:01 ./etc/getData.conf.d/ -rw-r--r-- root/root 1008 2012-04-02 08:12 ./etc/getData.conf.d/autodock-zinc.getData autodocksuite_4.2.5.1-3ubuntu1_i386.changes: Format: 1.8 Date: Thu, 26 Dec 2013 22:52:16 -0500 Source: autodocksuite Binary: autodock autogrid autodock-test autogrid-test autodock-getdata Architecture: i386 all Version: 4.2.5.1-3ubuntu1 Distribution: trusty-proposed Urgency: medium Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Logan Rosen Description: autodock - analysis of ligand binding to protein structure autodock-getdata - instructions for getData to collect compounds autodock-test - test files for AutoDock autogrid - pre-calculate binding of ligands to their receptor autogrid-test - test files for AutoGrid Changes: autodocksuite (4.2.5.1-3ubuntu1) trusty; urgency=medium . * Use autotools-dev to update config.{sub,guess} for new arches. Checksums-Sha1: f5a737578c4fd375df662538030451e283805dfb 159894 autodock_4.2.5.1-3ubuntu1_i386.deb 63544b3c6ba94a1106f7776481b8b8a6e3551aac 35300 autogrid_4.2.5.1-3ubuntu1_i386.deb f429f7b3e09518a6b3441e91ff39a18c8f30f7e0 3198784 autodock-test_4.2.5.1-3ubuntu1_all.deb 5c6522780b9b2cc0e7070c95c203f609957234a1 53480 autogrid-test_4.2.5.1-3ubuntu1_all.deb d8f646f3be18fa20245148423d0a9468375dd971 4690 autodock-getdata_4.2.5.1-3ubuntu1_all.deb Checksums-Sha256: a7c1fd301a264d88fe43d2bb20c90ac2ff8378a8ab6e34ee3c74f184b7bf2d93 159894 autodock_4.2.5.1-3ubuntu1_i386.deb b68ca399155982168568f3d2c64e3eb81460d78424104ffcb8d079b5ab433071 35300 autogrid_4.2.5.1-3ubuntu1_i386.deb 7f8b49fddcb3c0669001c7bc91f27b9fe81803212e5ef6e5b46ac17023b82fc6 3198784 autodock-test_4.2.5.1-3ubuntu1_all.deb 394ad76f40ddcefc5d5452ce03d61a9ded5ab11b8ca45188a510de3c05118a86 53480 autogrid-test_4.2.5.1-3ubuntu1_all.deb 52e401dc76a02d370597b86ccbbb68bf0bad9af28e0f323e70eab2821cb2f265 4690 autodock-getdata_4.2.5.1-3ubuntu1_all.deb Files: d48b62cbaa3e733c1cc3c0cf0c9cb44e 159894 science optional autodock_4.2.5.1-3ubuntu1_i386.deb 4175feea4bc150c34e5484723043be7a 35300 science optional autogrid_4.2.5.1-3ubuntu1_i386.deb 233b50e58dcdbee0cd9e36d6ce2c4eb2 3198784 science optional autodock-test_4.2.5.1-3ubuntu1_all.deb 3dc5315535db5586605d767e9e530fe8 53480 science optional autogrid-test_4.2.5.1-3ubuntu1_all.deb ad5b59242b86110b5de8d9d7f89b70b4 4690 science optional autodock-getdata_4.2.5.1-3ubuntu1_all.deb Original-Maintainer: Debian Med Packaging Team ****************************************************************************** Built successfully ****************************************************************************** Finished at 20131227-0401 Build needed 00:01:11, 42804k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5386987'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5386987/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5386987'] Unmounting chroot for build PACKAGEBUILD-5386987... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5386987'] Removing build PACKAGEBUILD-5386987