[apbs-users] cannot use pre-builtl apbs 1.4.1 nor build it from source

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Mendez Giraldez, Raul

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Nov 11, 2014, 12:40:03 AM11/11/14

to apbs-...@lists.sourceforge.net

Dear all,

I have downloaded the pre-compiled version for linux of apbs 1.4.1 fron sourceforge

http://sourceforge.net/projects/apbs/files/apbs/apbs-1.4.1/APBS-1.4.1-binary-linux64.tgz

However the binary file does not link most of the needed libraries (I guess it has not been compiled statically):

ldd ./bin/apbs

./bin/apbs: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by ./bin/apbs)

./bin/apbs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./bin/apbs)

linux-vdso.so.1 => (0x00002aaaaaaab000)

libmaloc.so.1 => not found

libm.so.6 => /lib64/libm.so.6 (0x000000364d800000)

libstdc++.so.6 => /nas02/apps/gcc-4.8.1/lib64/libstdc++.so.6 (0x00002aaaaaaca000)

libamd.so.1 => not found

libpunc.so.1 => not found

libmc.so.1 => not found

libgamer.so.1 => not found

libsuperlu.so.1 => not found

libumfpack.so.1 => not found

libblas.so.1 => not found

libvf2c.so.1 => not found

libtetgen.so.1 => not found

libtriangle.so.1 => not found

libreadline.so.6 => not found

libiomp5.so => /nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/ipp/../compiler/lib/intel64/libiomp5.so (0x00002aaaaade3000)

libgcc_s.so.1 => /nas02/apps/gcc-4.8.1/lib64/libgcc_s.so.1 (0x00002aaaab0f7000)

libpthread.so.0 => /lib64/libpthread.so.0 (0x000000364e400000)

libc.so.6 => /lib64/libc.so.6 (0x000000364d400000)

libdl.so.2 => /lib64/libdl.so.2 (0x000000364dc00000)

/lib64/ld-linux-x86-64.so.2 (0x000000364d000000)

If I tried to download the latest source from GitHub:

https://github.com/Electrostatics/apbs-pdb2pqr/archive/1.4.1-binary-release.zip

Even if I try to build it with FETK support (script buildWithFETK.sh), if I finally try:

CC=icc cmake -DCMAKE_INSTALL_PREFIX=/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs -DENABLE_FETK=YES -DBUILD_SHARED_LIBS=YES ..

cd ..

make

I do not know how to make icc to be cc compiler, and at the very end I got

-- -std=c99

-- Supplemental tools enabled

-- Building mesh

-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem

-- Building manip

-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem

-- Installing maloc headers

-- Configuring done

-- Generating done

-- Build files have been written to: /nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs

[ 0%] Performing build step for 'maloc'

[ 5%] Building C object src/CMakeFiles/maloc.dir/base/maloc_base.c.o

In file included from /nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/contrib/maloc/src/base/maloc/maloc_base.h:70,

from /nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/contrib/maloc/src/base/maloc_base_p.h:37,

from /nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/contrib/maloc/src/base/maloc_base.c:34:

/nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/compiler/include/math.h:27:3: error: #error "This Intel <math.h> is for use with only the Intel compilers!"

make[5]: *** [src/CMakeFiles/maloc.dir/base/maloc_base.c.o] Error 1

make[4]: *** [src/CMakeFiles/maloc.dir/all] Error 2

make[3]: *** [all] Error 2

make[2]: *** [maloc-prefix/src/maloc-stamp/maloc-build] Error 2

make[1]: *** [CMakeFiles/maloc.dir/all] Error 2

make: *** [all] Error 2

Could anyone help provide me appropiate builts for linux 64 or help me building it from source ?

Thank you so much in advance,

Raul

Raul Mendez Giraldez, PhD

Dokholyan Lab

Dept. Biophysics & Biochemistry

Genetic Medicine

University of North Carolina

120 Mason Farm Road

Chapel Hill, NC 27599

Baker, Nathan

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Nov 11, 2014, 9:29:49 AM11/11/14

to Mendez Giraldez, Raul, apbs-...@lists.sourceforge.net, Jurrus, Elizabeth R, Star, Keith

Hi Raul --

I am sorry to hear about your problems with the build system. Keith, can you please help Raul with this?

Thank you,

--
Nathan Baker
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling
Pacific Northwest National Laboratory
+1-509-375-3997
http://www.linkedin.com/in/nathanandrewbaker

From: Mendez Giraldez, Raul [rme...@email.unc.edu]
Sent: Monday, November 10, 2014 21:22
To: apbs-...@lists.sourceforge.net
Subject: [apbs-users] cannot use pre-builtl apbs 1.4.1 nor build it from source

Mendez Giraldez, Raul

unread,

Nov 11, 2014, 10:03:00 AM11/11/14

to Baker, Nathan, apbs-...@lists.sourceforge.net, Jurrus, Elizabeth R, Star, Keith

Thank you Nathan.

Looking forward to hearing from you guys!

Raul

From: Baker, Nathan [Nathan...@pnnl.gov]
Sent: Tuesday, November 11, 2014 9:29 AM
To: Mendez Giraldez, Raul; apbs-...@lists.sourceforge.net
Cc: Star, Keith; Jurrus, Elizabeth R
Subject: RE: [apbs-users] cannot use pre-builtl apbs 1.4.1 nor build it from source

Star, Keith

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Nov 11, 2014, 11:14:19 AM11/11/14

to Baker, Nathan, Mendez Giraldez, Raul, apbs-...@lists.sourceforge.net, Jurrus, Elizabeth R

Hi Raul,

First off have a look here: https://github.com/Electrostatics/apbs-pdb2pqr/blob/1.4.1-binary-release/apbs/BUILD.md Please follow these directions in order to build from source. If you find that you are still having problems, let me know, and we will work through them.

Thanks,

- Keith

Mendez Giraldez, Raul

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Nov 11, 2014, 1:23:48 PM11/11/14

to Star, Keith, Baker, Nathan, apbs-...@lists.sourceforge.net, Jurrus, Elizabeth R

Hi Keith,

Thanks for the instruction, I got that file but I did not really realize it was the instructions. In any case I did not succeeded.

After the second step, trying to build FETK by doing

cp -r ../fetk-1.5_APBS fetk
cd fetk
LD=xild AR=xiar CC=icc CXX=icpc ./fetk-build maloc punc gamer mc

icpc -g -O2 -o MolecularMesh MolecularMesh.o -L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/lib -lgamer -ltetgen -ltriangle -L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/lib -lmaloc -lreadline -lncurses -lm

/nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/ipp/../compiler/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail

make[2]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/gamer/tools/MolecularMesh/x86_64-unknown-linux-gnu'

test -z "/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/bin" || /bin/mkdir -p "/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/bin"

/usr/bin/install -c MolecularMesh '/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/bin'

make[2]: Nothing to be done for `install-data-am'.

make[2]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/gamer/tools/MolecularMesh/x86_64-unknown-linux-gnu'

make[1]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/gamer/tools/MolecularMesh/x86_64-unknown-linux-gnu'

~/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk

---------------------- FETK-BUILD: STOPPING ----------------------

It took forever (I went to have lunch), and I am not sure whether this is the normal termination.

Then I did

cd ..

cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_BUILD_TYPE=RelWithDebInfo -DENABLE_FETK=ON -DFETK_PATH=./fetk/build/x86_64-unknown-linux-gnu -DBUILD_SHARED_LIBS=OFF -DENABLE_BEM=OFF -DBUILD_DOC=ON -DCMAKE_INSTALL_PREFIX=/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux ..

And It terminated because it does not find oxygen package installed:

-- The C compiler identification is Intel

-- The CXX compiler identification is Intel

-- Check for working C compiler: /nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/bin/intel64/icc

-- Check for working C compiler: /nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/bin/intel64/icc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working CXX compiler: /nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/bin/intel64/icpc

-- Check for working CXX compiler: /nas02/apps/intel-13.1-2/cc/composer_xe_2013.4.183/bin/intel64/icpc -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Setting project paths

-- Setting lookup paths for headers and libraries

-- Computing machine epsilon values

-- Floating point epsilon is 2.220446e-16

-- Double precision epsilon is 2.220446e-16

-- Looking for time

-- Looking for time - found

-- Looking for rand

-- Looking for rand - found

-- Looking for srand

-- Looking for srand - found

-- Found fetk: /nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu

-- External maloc library was found: /nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/lib/libmaloc.so

-- External maloc headers found

-- Checking for fetk components

-- Inline functions enabled

-- Checking for OpenMP

-- Try OpenMP C flag = [-fopenmp]

-- Performing Test OpenMP_FLAG_DETECTED

-- Performing Test OpenMP_FLAG_DETECTED - Success

-- Try OpenMP CXX flag = [-fopenmp]

-- Performing Test OpenMP_FLAG_DETECTED

-- Performing Test OpenMP_FLAG_DETECTED - Success

-- Found OpenMP: -fopenmp

-- OpenMP support enabled

libs: -L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/lib -lapbs_geoflow-lmaloc-lm-lstdc++-L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/lib-lamd-lpunc-lmc-lgamer-lsuperlu-lumfpack-lblas-lvf2c-ltetgen-ltriangle-lreadline-fopenmp

-- Adding apbs_generic

-- With source files nosh.c;mgparm.c;femparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c

-- With external header files nosh.h;mgparm.h;femparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h

-- With internal header files

-- With library dependencies -L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/lib -lapbs_geoflow;-lmaloc;-lm;-lstdc++;-L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/lib;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lblas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-fopenmp

-- Added apbs_generic

-- Adding apbs_pmgc

-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c

-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h

-- With internal header files

-- Added apbs_pmgc

-- Adding apbs_mg

-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c

-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h

-- With internal header files

-- Added apbs_mg

-- Adding apbs_geoflow

-- With source files cpbconcz2.cpp;modules.cpp;pbsolvercz.cpp;solvationsub.cpp;subfunction.cpp;surfconcz.cpp

-- With external header files cpbconcz2.h

-- With internal header files

-- Added apbs_geoflow

-- Adding apbs_fem

-- With source files vcsm.c;vfetk.c;vpee.c

-- With external header files vcsm.h;vfetk.h;vpee.h

-- With internal header files

-- Added apbs_fem

-- -L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/lib -lapbs_geoflow;-lmaloc;-lm;-lstdc++;-L/nas02/home/r/m/rmendez/Work/Software/apbs-pdb2pqr-1.4.1-binary-release/apbs/linux/fetk/build/x86_64-unknown-linux-gnu/lib;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lblas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-fopenmp apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow;apbs_fem

-- -std=c99

-- Building documentation enabled

CMake Error at /nas02/apps/cmake-2.8.4/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE):

Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)

Call Stack (most recent call first):

/nas02/apps/cmake-2.8.4/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:252 (_FPHSA_FAILURE_MESSAGE)

/nas02/apps/cmake-2.8.4/share/cmake-2.8/Modules/FindDoxygen.cmake:80 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)

doc/CMakeLists.txt:5 (find_package)

-- Configuring incomplete, errors occurred!

Then I download and install doxygen, but it failed

git clone https://github.com/doxygen/doxygen.git

cd doxygen

./configure --prefix=/nas02/home/r/m/rmendez/Work/Software/doxygen

Autodetected platform linux-g++...

Checking for GNU make tool... using /usr/bin/gmake

Checking for GNU install tool... using /usr/bin/install

Checking for dot (part of GraphViz)... not found!

Checking for python... using /nas02/apps/python-2.6.5/bin/python (version 2.6.5)

Checking for perl... using /nas02/apps/perl-5.12.0/bin/perl

Checking for flex... using /usr/bin/flex

Checking for bison... using /usr/bin/bison

Generating generated_src/doxygen/version.cpp and VERSION...

Created doxygen.spec file, for rpm generation.

Created Makefile from Makefile.in...

Created qtools/Makefile from qtools/Makefile.in...

Created src/Makefile from src/Makefile.in...

Created examples/Makefile from examples/Makefile.in...

Created doc/Makefile from doc/Makefile.in...

Created addon/doxywizard/Makefile from addon/doxywizard/Makefile.in...

Created addon/doxmlparser/src/Makefile from addon/doxmlparser/src/Makefile.in...

Created addon/doxmlparser/test/Makefile from addon/doxmlparser/test/Makefile.in...

Created addon/doxmlparser/examples/metrics/Makefile from addon/doxmlparser/examples/metrics/Makefile.in...

Created libmd5/Makefile from libmd5/Makefile.in...

Created addon/doxyapp/Makefile from addon/doxyapp/Makefile.in...

Created addon/doxysearch/Makefile from addon/doxysearch/Makefile.in...

Created vhdlparser/Makefile from vhdlparser/Makefile.in...

Created qtools/qtools.pro from qtools/qtools.pro.in...

Created src/libdoxygen.pro from src/libdoxygen.pro.in...

Created src/libdoxycfg.pro from src/libdoxycfg.pro.in...

Created src/doxygen.pro from src/doxygen.pro.in...

Created addon/doxywizard/doxywizard.pro from addon/doxywizard/doxywizard.pro.in...

Created addon/doxmlparser/src/doxmlparser.pro from addon/doxmlparser/src/doxmlparser.pro.in...

Created addon/doxmlparser/test/xmlparse.pro from addon/doxmlparser/test/xmlparse.pro.in...

Created addon/doxmlparser/examples/metrics/metrics.pro from addon/doxmlparser/examples/metrics/metrics.pro.in...

Created libmd5/libmd5.pro from libmd5/libmd5.pro.in...

Created addon/doxyapp/doxyapp.pro from addon/doxyapp/doxyapp.pro.in...

Created addon/doxysearch/doxysearch.pro from addon/doxysearch/doxysearch.pro.in...

Created addon/doxysearch/doxyindexer.pro from addon/doxysearch/doxyindexer.pro.in...

Created vhdlparser/vhdlparser.pro from vhdlparser/vhdlparser.pro.in...

Generating generated_src/doxygen/lang_cfg.h...

Generating generated_src/doxygen/settings.h...

Finished

Configuration apparently worked, but compilation failed:

make

/usr/bin/gmake -C qtools

gmake[1]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/qtools'

env TMAKEPATH="/nas02/home/r/m/rmendez/Work/Software/doxygen/tmake/lib/linux-g++" /nas02/apps/perl-5.12.0/bin/perl "/nas02/home/r/m/rmendez/Work/Software/doxygen/tmake/bin/tmake" qtools.pro >Makefile.qtools

/usr/bin/gmake -f Makefile.qtools all

gmake[2]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/qtools'

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qbuffer.o qbuffer.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qcollection.o qcollection.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qcstring.o qcstring.cpp

qcstring.cpp: In member function ‘QCString& QCString::sprintf(const char*, ...)’:

qcstring.cpp:32: warning: comparison between signed and unsigned integer expressions

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qdatastream.o qdatastream.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qdatetime.o qdatetime.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qdir.o qdir.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qfile.o qfile.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qfileinfo.o qfileinfo.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qgarray.o qgarray.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qgcache.o qgcache.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qgdict.o qgdict.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qglist.o qglist.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qglobal.o qglobal.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qgstring.o qgstring.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qgvector.o qgvector.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qiodevice.o qiodevice.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qregexp.o qregexp.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qstring.o qstring.cpp

qstring.cpp: In member function ‘QString QString::arg(const QString&, int) const’:

qstring.cpp:12553: warning: ‘pos’ may be used uninitialized in this function

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qtextstream.o qtextstream.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qtextcodec.o qtextcodec.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qstringlist.o qstringlist.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qxml.o qxml.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qmap.o qmap.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qthread.o qthread.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qmutex.o qmutex.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qutfcodec.o qutfcodec.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qfile_unix.o qfile_unix.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qdir_unix.o qdir_unix.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qfileinfo_unix.o qfileinfo_unix.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qthread_unix.o qthread_unix.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qmutex_unix.o qmutex_unix.cpp

g++ -c -pipe -fsigned-char -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -o ../objects/qtools/qwaitcondition_unix.o qwaitcondition_unix.cpp

rm -f ../lib/libqtools.a

ar cqs ../lib/libqtools.a ../objects/qtools/qbuffer.o ../objects/qtools/qcollection.o ../objects/qtools/qcstring.o ../objects/qtools/qdatastream.o ../objects/qtools/qdatetime.o ../objects/qtools/qdir.o ../objects/qtools/qfile.o ../objects/qtools/qfileinfo.o ../objects/qtools/qgarray.o ../objects/qtools/qgcache.o ../objects/qtools/qgdict.o ../objects/qtools/qglist.o ../objects/qtools/qglobal.o ../objects/qtools/qgstring.o ../objects/qtools/qgvector.o ../objects/qtools/qiodevice.o ../objects/qtools/qregexp.o ../objects/qtools/qstring.o ../objects/qtools/qtextstream.o ../objects/qtools/qtextcodec.o ../objects/qtools/qstringlist.o ../objects/qtools/qxml.o ../objects/qtools/qmap.o ../objects/qtools/qthread.o ../objects/qtools/qmutex.o ../objects/qtools/qutfcodec.o ../objects/qtools/qfile_unix.o ../objects/qtools/qdir_unix.o ../objects/qtools/qfileinfo_unix.o ../objects/qtools/qthread_unix.o ../objects/qtools/qmutex_unix.o ../objects/qtools/qwaitcondition_unix.o

gmake[2]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/qtools'

gmake[1]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/qtools'

/usr/bin/gmake -C libmd5

gmake[1]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/libmd5'

/usr/bin/gmake -f Makefile.libmd5

gmake[2]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/libmd5'

gcc -c -pipe -fsigned-char -Wall -W -O3 -o ../objects/md5/md5.o md5.c

rm -f ../lib/libmd5.a

ar cqs ../lib/libmd5.a ../objects/md5/md5.o

gmake[2]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/libmd5'

gmake[1]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/libmd5'

/usr/bin/gmake -C vhdlparser

gmake[1]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/vhdlparser'

/usr/bin/gmake -f Makefile.vhdlparser all

gmake[2]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/vhdlparser'

g++ -c -pipe -fsigned-char -w -fexceptions -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -I../src -I../qtools -Igenerated_src/doxygen -o ../objects/vhdlparser/CharStream.o CharStream.cc

g++ -c -pipe -fsigned-char -w -fexceptions -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -I../src -I../qtools -Igenerated_src/doxygen -o ../objects/vhdlparser/ParseException.o ParseException.cc

g++ -c -pipe -fsigned-char -w -fexceptions -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -I../src -I../qtools -Igenerated_src/doxygen -o ../objects/vhdlparser/Token.o Token.cc

g++ -c -pipe -fsigned-char -w -fexceptions -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -I../src -I../qtools -Igenerated_src/doxygen -o ../objects/vhdlparser/VhdlParser.o VhdlParser.cc

g++ -c -pipe -fsigned-char -w -fexceptions -DQT_LITE_UNICODE -D_LARGEFILE_SOURCE -Wall -W -O3 -I. -I../src -I../qtools -Igenerated_src/doxygen -o ../objects/vhdlparser/VhdlParserIF.o VhdlParserIF.cpp

rm -f ../lib/libvhdlparser.a

ar cqs ../lib/libvhdlparser.a ../objects/vhdlparser/CharStream.o ../objects/vhdlparser/ParseException.o ../objects/vhdlparser/Token.o ../objects/vhdlparser/TokenMgrError.o ../objects/vhdlparser/VhdlParser.o ../objects/vhdlparser/VhdlParserTokenManager.o ../objects/vhdlparser/VhdlParserIF.o

gmake[2]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/vhdlparser'

gmake[1]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/vhdlparser'

/usr/bin/gmake -C src

gmake[1]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/src'

echo 'HEADERS += ' `ls -1 translator_??.h` >>Makefile.libdoxygen

/usr/bin/gmake -f Makefile.libdoxycfg all

gmake[2]: Entering directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/src'

/usr/bin/flex -PconfigYY -t config.l >../generated_src/doxygen/config.cpp

g++ -c -pipe -fsigned-char -D_LARGEFILE_SOURCE -Wall -W -O3 -I../generated_src/doxygen -I. -I../qtools -o ../objects/doxygen/config.o ../generated_src/doxygen/config.cpp

config.l: In member function ‘bool Config::parse(const char*, bool)’:

config.l:1764: error: ‘configYY_flex_debug’ was not declared in this scope

gmake[2]: *** [../objects/doxygen/config.o] Error 1

gmake[2]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/src'

gmake[1]: *** [all] Error 2

gmake[1]: Leaving directory `/nas02/home/r/m/rmendez/Work/Software/doxygen/src'

make: *** [all] Error 2

It seems a bug into the doxygen code I do not want to deal with. Do you know If I am doing something wrong building fete?

Thank you so much in advance,

Raul

Raul Mendez Giraldez, PhD

Dokholyan Lab

Dept. Biophysics & Biochemistry

Genetic Medicine

University of North Carolina

120 Mason Farm Road

Chapel Hill, NC 27599

From: Star, Keith [ke...@pnnl.gov]
Sent: Tuesday, November 11, 2014 11:12 AM
To: Baker, Nathan; Mendez Giraldez, Raul; apbs-...@lists.sourceforge.net
Cc: Jurrus, Elizabeth R
Subject: Re: [apbs-users] cannot use pre-builtl apbs 1.4.1 nor build it from source

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