* You need one of these Fortran Compilers: g77 gfortran * Installed are: gfortran >>> Unpacking source... >>> Unpacking pdb2pqr-1.4.0.tar.gz to /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work * Applying pdb2pqr-1.4.0-ldflags.patch ...  [ ok ] * Applying pdb2pqr-1.4.0-automagic.patch ...  [ ok ] * Applying pdb2pqr-1.4.0-install.patch ...  [ ok ] * Applying pdb2pqr-1.4.0-gcc44.patch ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] * Running elibtoolize in: pdb2pqr-1.4.0/config * Applying install-sh-1.5.patch ... * Applying portage-1.5.10.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-1.5.26.patch ... * Applying uclibc-ltconf-1.3.0.patch ... * Running elibtoolize in: pdb2pqr-1.4.0/propka/config * Applying install-sh-1.5.patch ... * Applying ltmain-1.5.patch ... * Applying portage-1.5.10.patch ... * Could not apply relink.patch! * Applying sed-1.5.6.patch ... * Applying as-needed-1.5.patch ... * Applying uclibc-ltconf-1.3.0.patch ... >>> Source unpacked in /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work * Flameeyes QA Warning! AC_CANONICAL_TARGET used /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/propka/configure.ac:17:AC_CANONICAL_TARGET: * Flameeyes QA Warning (end)! AC_CANONICAL_TARGET used >>> Compiling source in /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0 ... * econf: updating pdb2pqr-1.4.0/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating pdb2pqr-1.4.0/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating pdb2pqr-1.4.0/propka/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating pdb2pqr-1.4.0/propka/config/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --without-opal configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for i686-pc-linux-gnu-g++... i686-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 i686-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking for python... /usr/bin/python checking for python include directory... -I/usr/include/python2.6 checking for --disable-propka... no ------------- Begin Processing PropKa Configure Options ----------- checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-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 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/python2.6 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... checking whether you defined numpy... yes ------------- End Processing pdb2ka Configure Options ----------- ZSI is installed 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: 1.4.0 Install Dir: /usr/ propka: enable pdb2pka: enable PY_CFLAGS: -I/usr/include/python2.6 -I/usr/lib/python2.6/site-packages/Numeric/Numeric_headers/Numeric WEBSITE (path to the website directory): http://yamato/pdb2pqr/ (WEBSITE can be changed with the --with-url option) PDB2PQR_CGI (path to pdb2pqr.cgi): http://yamato/pdb2pqr/pdb2pqr.cgi PDB2PQR_OPAL_URL (url to the pdb2pqr opal service): no *** Warning: The install directory is not inside /var/www/html/ A symbolic link will be created when you run "make install" make -j14 Making all in propka make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/propka' 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/python2.6 -O2 -pipe -fPIC -c `test -f 'propkalib.c' || echo './'`propkalib.c gfortran -fPIC -fPIC -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/python2.6 -O2 -pipe -fPIC -c `test -f 'propkac.c' || echo './'`propkac.c gfortran -Wl,-O1 -o _propkalib.so -shared propkalib.o propka.o propkac.o gfortran -fPIC -fPIC -Wl,-O1 -o propka propka.o make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/propka' Making all in pdb2pka make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' Making all in substruct make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/substruct' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.4.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.4.0\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.4.0\" -I. -I/usr/include/python2.6 -I/usr/lib/python2.6/site-packages/Numeric/Numeric_headers/Numeric -O2 -pipe -fPIC -c -o Algorithms.o Algorithms.cpp In file included from /usr/include/python2.6/Python.h:8, from Algorithms.cpp:40: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.0/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.0/include/g++-v4/iostream:39, from Algorithms.cpp:37: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from Algorithms.cpp:40: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.0/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.0/include/g++-v4/iostream:39, from Algorithms.cpp:37: /usr/include/features.h:160:1: warning: this is the location of the previous definition i686-pc-linux-gnu-g++ -Wl,-O1 -o Algorithms.so -shared Algorithms.o make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/substruct' make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.4.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.4.0\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.4.0\" -I. -I/usr/include/python2.6 -I/usr/lib/python2.6/site-packages/Numeric/Numeric_headers/Numeric -O2 -pipe -fPIC -c -o pMC_mult.o pMC_mult.cpp i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.4.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.4.0\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.4.0\" -I. -I/usr/include/python2.6 -I/usr/lib/python2.6/site-packages/Numeric/Numeric_headers/Numeric -O2 -pipe -fPIC -c -o pMC_mult_wrap.o pMC_mult_wrap.cpp pMC_mult_wrap.cpp: In function 'void SWIG_Python_AddErrorMsg(const char*)': pMC_mult_wrap.cpp:864: warning: format not a string literal and no format arguments i686-pc-linux-gnu-g++ -Wl,-O1 -o _pMC_mult.so -shared pMC_mult.o pMC_mult_wrap.o make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' Making all in tests make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' Making all in test make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' Making all in . make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.4.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.4.0\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.4.0\" -I. -O2 -pipe -fPIC -MT test.o -MD -MP -MF .deps/test.Tpo -c -o test.o test.cpp test.cpp: In function 'int main()': test.cpp:36: warning: deprecated conversion from string constant to 'char*' test.cpp:39: warning: deprecated conversion from string constant to 'char*' test.cpp:52: warning: deprecated conversion from string constant to 'char*' test.cpp:103: warning: deprecated conversion from string constant to 'char*' test.cpp:106: warning: deprecated conversion from string constant to 'char*' mv -f .deps/test.Tpo .deps/test.Po i686-pc-linux-gnu-g++ -O2 -pipe -fPIC -Wl,-O1 -o simpletest test.o make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' Making all in adv-test make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' Making all in . make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.4.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.4.0\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.4.0\" -I. -O2 -pipe -fPIC -MT test.o -MD -MP -MF .deps/test.Tpo -c -o test.o test.cpp test.cpp: In function 'int main()': test.cpp:43: warning: deprecated conversion from string constant to 'char*' test.cpp:46: warning: deprecated conversion from string constant to 'char*' test.cpp:58: warning: deprecated conversion from string constant to 'char*' test.cpp:83: warning: deprecated conversion from string constant to 'char*' test.cpp:86: warning: deprecated conversion from string constant to 'char*' test.cpp:97: warning: deprecated conversion from string constant to 'char*' test.cpp:116: warning: deprecated conversion from string constant to 'char*' test.cpp:119: warning: deprecated conversion from string constant to 'char*' mv -f .deps/test.Tpo .deps/test.Po i686-pc-linux-gnu-g++ -O2 -pipe -fPIC -Wl,-O1 -o advtest test.o make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' Making all in . make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' >>> Source compiled. make -j14 -j1 test tests/test/test.sh ---------------------------------------------------------------------------------- This is a simple command line test. Running pdb2pqr with forcefield=AMBER and path=1AFS -------------------------- PDB2PQR - a Python-based structural conversion utility -------------------------- Please cite your use of PDB2PQR as: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). Simple test passed for PQR files You may also run make adv-test to test propka and pdb2pka. make -j14 -j1 adv-test tests/adv-test/test.sh ---------------------------------------------------------------------------------- Running pdb2pqr with pH = 7.00, ligand = /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test/LIG_1HPX.mol2, force field = AMBER, and path = 1H -------------------------- PDB2PQR - a Python-based structural conversion utility -------------------------- Please cite your use of PDB2PQR as: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py:8: DeprecationWarning: the sets module is deprecated from sets import Set Traceback (most recent call last): File "/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pqr.py", line 63, in mainCommand(sys.argv) File "/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/main.py", line 567, in mainCommand header, lines, missedligands = runPDB2PQR(pdblist, ff, options) File "/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/main.py", line 267, in runPDB2PQR myProtein, myDefinition, Lig = ligff.initialize(myDefinition, options["ligand"], pdblist, verbose) File "/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/ligandclean/ligff.py", line 73, in initialize ligand_titratable_groups=X.find_titratable_groups() File "/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py", line 557, in find_titratable_groups output = match(templates[current_template],atoms) File "/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py", line 544, in match allcliques = Algorithms.find_cliques(AGL) TypeError: argument 1 must be array, not numpy.ndarray ERORR! test-output-user.pqr could not be opened make: *** [adv-test] Error 1 * * ERROR: sci-chemistry/pdb2pqr-1.4.0-r1 failed. * Call stack: * ebuild.sh, line 49: Called src_test * environment, line 3722: Called die * The specific snippet of code: * emake -j1 test && F77="${FORTRANC}" emake -j1 adv-test || die "test failed" * The die message: * test failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-chemistry/pdb2pqr-1.4.0-r1:20090708-161429.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/temp/environment'. * >>> Install pdb2pqr-1.4.0-r1 into /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/image/ category sci-chemistry make -j14 -j1 DESTDIR=/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/image//usr/lib/python2.6/site-packages/pdb2pqr PREFIX= install make make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' Making all in propka make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/propka' cd . && : make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/propka' Making all in pdb2pka make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' Making all in substruct make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/substruct' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka/substruct' make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/pdb2pka' Making all in tests make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' Making all in test make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' Making all in . make[4]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/test' Making all in adv-test make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' Making all in . make[4]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests/adv-test' Making all in . make[3]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/tests' make[2]: Entering directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' Creating tmp/ Adding __init__.py Adding pdb2pqr.py Adding dat/ Adding extensions Adding python files from src/ Adding propka Adding pdb2pka PDB2PQR has been installed in /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/image//usr/lib/python2.6/site-packages/pdb2pqr/ >>> Completed installing pdb2pqr-1.4.0-r1 into /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/image/ strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/lib/python2.6/site-packages/pdb2pqr/propka/_propkalib.so usr/lib/python2.6/site-packages/pdb2pqr/propka/propka usr/lib/python2.6/site-packages/pdb2pqr/pdb2pka/_pMC_mult.so usr/lib/python2.6/site-packages/pdb2pqr/pdb2pka/substruct/Algorithms.so * Removing /usr/share/doc * Removing /usr/share/man * Removing /usr/share/info