Build log

pdb2pqr-1.4.0-r1:20090708-161429.log (text/plain), 22.03 KB, created by Diego Elio Pettenò (RETIRED) on 2009-07-08 16:32:31 UTC

 [32;01m*[0m You need one of these Fortran Compilers: g77 gfortran
 [32;01m*[0m Installed are:  gfortran
>>> Unpacking source...
>>> Unpacking pdb2pqr-1.4.0.tar.gz to /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work
 [32;01m*[0m Applying pdb2pqr-1.4.0-ldflags.patch ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying pdb2pqr-1.4.0-automagic.patch ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying pdb2pqr-1.4.0-install.patch ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying pdb2pqr-1.4.0-gcc44.patch ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0' ...
 [32;01m*[0m Running aclocal ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running elibtoolize in: pdb2pqr-1.4.0/config
 [32;01m*[0m   Applying install-sh-1.5.patch ...
 [32;01m*[0m   Applying portage-1.5.10.patch ...
 [32;01m*[0m   Applying sed-1.5.6.patch ...
 [32;01m*[0m   Applying as-needed-1.5.26.patch ...
 [32;01m*[0m   Applying uclibc-ltconf-1.3.0.patch ...
 [32;01m*[0m Running elibtoolize in: pdb2pqr-1.4.0/propka/config
 [32;01m*[0m   Applying install-sh-1.5.patch ...
 [32;01m*[0m   Applying ltmain-1.5.patch ...
 [32;01m*[0m   Applying portage-1.5.10.patch ...
 [33;01m*[0m   Could not apply relink.patch!
 [32;01m*[0m   Applying sed-1.5.6.patch ...
 [32;01m*[0m   Applying as-needed-1.5.patch ...
 [32;01m*[0m   Applying uclibc-ltconf-1.3.0.patch ...
>>> Source unpacked in /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work
 [33;01m*[0m 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:
 [33;01m*[0m 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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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 <module>
    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
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-chemistry/pdb2pqr-1.4.0-r1 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_test
 [31;01m*[0m             environment, line 3722:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake -j1 test && F77="${FORTRANC}" emake -j1 adv-test || die "test failed"
 [31;01m*[0m  The die message:
 [31;01m*[0m   test failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
 [31;01m*[0m A complete build log is located at '/var/log/portage/sci-chemistry/pdb2pqr-1.4.0-r1:20090708-161429.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/temp/environment'.
 [31;01m*[0m 

>>> 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
 [32;01m*[0m Removing /usr/share/doc
 [32;01m*[0m Removing /usr/share/man
 [32;01m*[0m Removing /usr/share/info