* You need one of these Fortran Compilers: g77 gfortran * Installed are: gfortran >>> Unpacking source... >>> Unpacking pdb2pqr-1.3.0.tar.gz to /var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work >>> Source unpacked. >>> Compiling source in /var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0 ... * econf: updating pdb2pqr-1.3.0/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating pdb2pqr-1.3.0/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating pdb2pqr-1.3.0/propka/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating pdb2pqr-1.3.0/propka/config/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --build=x86_64-pc-linux-gnu checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-g++... gcc3 checking for python... /usr/bin/python checking for python include directory... -I/usr/include/python2.5 checking for --disable-propka... no ------------- Begin Processing PropKa Configure Options ----------- checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for python... /usr/bin/python checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking how to run the C preprocessor... gcc -E checking for python include directory... -I/usr/include/python2.5 configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands ------------- End Processing PropKa Configure Options ----------- checking for--disable-pdb2pka... no ------------- Begin Processing pdb2pka Configure Options ----------- checking whether you defined Numeric or Numpy... no checking for Numeric include files... -I/usr/include/python2.5/Numeric checking whether you defined numpy... no ------------- End Processing pdb2ka Configure Options ----------- checking for tmp/... no ------------- End Processing PDB2PQR Configure Options ----------- configure: creating ./config.status config.status: creating Makefile config.status: creating pdb2pka/Makefile config.status: creating pdb2pka/substruct/Makefile config.status: creating tests/Makefile config.status: creating tests/test/Makefile config.status: creating tests/adv-test/Makefile config.status: executing depfiles commands --------------------------------------------------------------------------------------- Please run "make" followed by "make install" to complete the installation. You may also run "make test" or "make adv-test". ======================== Configuration Parameters ======================== User ID: root Version: 1.3.0 Install Dir: /usr/ propka: enable pdb2pka: enable PY_CFLAGS: -I/usr/include/python2.5 -I/usr/include/python2.5/Numeric WEBSITE (path to the website directory): http://calculator/pdb2pqr/ (WEBSITE can be changed with the --with-url option) PDB2PQR_CGI (path to pdb2pqr.cgi): http://calculator/pdb2pqr/pdb2pqr.cgi PDB2PQR jobs will be forked on the server MAX_ATOMS (max number of atoms in a protein): 10000 *** Warning: The install directory is not inside /var/www/html/ A symbolic link will be created when you run "make install" Making all in propka make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/propka' cd . && \ : --gnu Makefile cd . && : gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen@uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" -I. -I. -I/usr/include/python2.5 -fPIC -O3 -pipe -march=native -mtune=native -ftree-vectorize -fPIC -c `test -f 'propkalib.c' || echo './'`propkalib.c gfortran -fPIC -g -O2 -c -o propka.o `test -f 'propka.f' || echo './'`propka.f gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen@uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" -I. -I. -I/usr/include/python2.5 -fPIC -O3 -pipe -march=native -mtune=native -ftree-vectorize -fPIC -c `test -f 'propkac.c' || echo './'`propkac.c gfortran -fPIC -g -O2 -Wl,-O1 -Wl,--sort-common -o propka propka.o gfortran -o _propkalib.so -shared propkalib.o propka.o propkac.o make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/propka' Making all in pdb2pka make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/pdb2pka' Making all in substruct make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/pdb2pka/substruct' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.3.0\" -DPACKAGE_BUGREPORT=\"todd@ccb.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.3.0\" -I. -I. -I/usr/include/python2.5 -I/usr/include/python2.5/Numeric -fPIC -O3 -pipe -march=native -mtune=native -ftree-vectorize -fPIC -c -o Algorithms.o Algorithms.cpp x86_64-pc-linux-gnu-g++ -o Algorithms.so -shared Algorithms.o make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/pdb2pka/substruct' make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/pdb2pka' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.3.0\" -DPACKAGE_BUGREPORT=\"todd@ccb.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.3.0\" -I. -I. -I/usr/include/python2.5 -I/usr/include/python2.5/Numeric -fPIC -O3 -pipe -march=native -mtune=native -ftree-vectorize -fPIC -c -o pMC_mult.o pMC_mult.cpp x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.3.0\" -DPACKAGE_BUGREPORT=\"todd@ccb.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.3.0\" -I. -I. -I/usr/include/python2.5 -I/usr/include/python2.5/Numeric -fPIC -O3 -pipe -march=native -mtune=native -ftree-vectorize -fPIC -c -o pMC_mult_wrap.o pMC_mult_wrap.cpp pMC_mult.cpp: In member function ‘std::vector > MC::calc_charge(float)’: pMC_mult.cpp:226: error: ‘srand’ was not declared in this scope pMC_mult.cpp:234: error: ‘rand’ was not declared in this scope pMC_mult.cpp:288: error: ‘rand’ was not declared in this scope pMC_mult.cpp:305: error: ‘abs’ was not declared in this scope pMC_mult.cpp:325: error: ‘RAND_MAX’ was not declared in this scope make[2]: *** [pMC_mult.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/pdb2pka' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/work/pdb2pqr-1.3.0/pdb2pka' make: *** [all-recursive] Error 1 * * ERROR: sci-chemistry/pdb2pqr-1.3.0 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3332: Called die * The specific snippet of code: * emake || die "emake failed" * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/temp/environment'. *