Hi,
I am unable to install PDB2PQR using Fink 0.35.2 on OS 10.8. It appears to
fails after the terminal echoes 'Configuration Parameters'. The same error
occurs if I run 'fink update PDB2PQR' and remains after running 'fink
selfpdate' and 'fink update-all'. I have appended what I think are the relevant
parts. Could you make any suggestions as to how to solve this?
Thanks for your help.
Best wishes,
Kyle
========================
Configuration Parameters
========================
User ID: fink-bld
Version: 1.7
Install Dir: /tmp/fink-build-HOME.tLSVzzOXrC/pdb2pqr/
propka: enable
pdb2pka: enable
PY_CFLAGS: -I/sw/include/python2.7
-I/tmp/fink-build-HOME.tLSVzzOXrC/pdb2pqr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy
WEBSITE (path to the website directory): http://no/
(WEBSITE can be changed with the --with-url option)
PDB2PQR_CGI (path to pdb2pqr.cgi): http://no/pdb2pqr.cgi
PDB2PQR jobs will be forked on the server
MAX_ATOMS (max number of atoms in a protein): 1000000
As a regular user, you must ask your system administrator to create a symbolic
link that enables you to view http://no/ after you run "make install"
if [[ "x86_64" != "x86_64" ]]; then
perl -pi -e 's|-DPACKAGE|-m32 -DPACKAGE|g' Makefile
pdb2pka/substruct/Makefile tests/Makefile tests/test/Makefile pdb2pka/Makefile
propka/Makefile tests/adv-test/Makefile
fi
make
cd . && :
cd . && : --gnu
Making all in propka
cd . && \
: --gnu Makefile
gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\"
-DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\"
-DPACKAGE_BUGREPORT=\"jan-jen...@uiowa.edu\" -DPACKAGE=\"PropKa\"
-DVERSION=\"1.0.0\" -I. -I. -I/sw/include/python2.7 -g -O2 -c `test -f
'propkalib.c' || echo './'`propkalib.c
gfortran -g -O2 -c -o propka.o `test -f 'propka.f' || echo './'`propka.f
propka.f:90.34:
CALL RUNPROPKA(NATOM, PDB, 'PROPKATMP3')
1
Warning: Character length of actual argument shorter than of dummy argument
'outname' (10/100) at (1)
gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\"
-DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\"
-DPACKAGE_BUGREPORT=\"jan-jen...@uiowa.edu\" -DPACKAGE=\"PropKa\"
-DVERSION=\"1.0.0\" -I. -I. -I/sw/include/python2.7 -g -O2 -c `test -f
'propkac.c' || echo './'`propkac.c
gfortran -o _propkalib.so propkalib.o propka.o propkac.o
/sw/lib/python2.7/config/libpython2.7.dylib -bundle
gfortran -g -O2 -o propka propka.o
Making all in pdb2pka
cd .. && make am--refresh
cd . && :
cd . && : --gnu
cd . && :
cd . && : --gnu
Making all in substruct
cd ../.. && make am--refresh
cd . && :
cd . && : --gnu
cd . && :
cd . && : --gnu
g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\"
-DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\"
-DPACKAGE_BUGREPORT=\"ba...@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\"
-DVERSION=\"1.7\" -I. -I/sw/include/python2.7
-I/tmp/fink-build-HOME.tLSVzzOXrC/pdb2pqr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy
-g -O2 -c -o Algorithms.o Algorithms.cpp
Algorithms.cpp:43:10: fatal error: 'arrayobject.h' file not found
#include "arrayobject.h"
^
1 error generated.
make[2]: *** [Algorithms.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
### execution of /tmp/fink.VvF8q failed, exit code 2
### execution of /tmp/fink.QQuL_ failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-pdb2pqr-1.7-3
(Reading database ... 36328 files and directories currently installed.)
Removing fink-buildlock-pdb2pqr-1.7-3 ...
Failed: phase compiling: pdb2pqr-1.7-3 failed
Before reporting any errors, please run "fink selfupdate" and try again.
If you continue to have issues, please check to see if the FAQ on Fink's
website solves the problem. If not, ask on one (not both, please) of
these mailing lists:
The Fink Users List <fink-users@lists.sourceforge.net>
The Fink Beginners List <fink-beginn...@lists.sourceforge.net>,
with a carbon copy to the maintainer:
W. G. Scott <wgsc...@users.sourceforge.net>
Note that this is preferable to emailing just the maintainer directly,
since most fink package maintainers do not have access to all possible
hardware and software configurations.
Please try to include the complete error message in your report. This
generally consists of a compiler line starting with e.g. "gcc" or "g++"
followed by the actual error output from the compiler.
Also include the following system information:
Package manager version: 0.35.2
Distribution version: selfupdate-rsync Sun Oct 6 22:03:20 2013, 10.8, x86_64
Trees: local/main stable/main
Xcode.app: 5.0
Xcode command-line tools: 5.0.0.0.1.1377666378
pdb2pqr-1.7-3 is set to build with only one job.
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