build.log

build.log (text/plain), 9.20 KB, created by Alexey Shvetsov on 2008-06-18 18:02:40 UTC

 [32;01m*[0m You need one of these Fortran Compilers: g77 gfortran
 [32;01m*[0m 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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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=\"[e-mail]\" -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<float, std::allocator<float> > 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
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-chemistry/pdb2pqr-1.3.0 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_compile
 [31;01m*[0m             environment, line 3332:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake || die "emake failed"
 [31;01m*[0m  The die message:
 [31;01m*[0m   emake 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/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.3.0/temp/environment'.
 [31;01m*[0m