Compiling error?

Seung Joong Kim

23 Apr 2009 23 Apr '09

1:21 p.m.

Hi all,

I keep getting a compiling error on my Mac and linux, since yesterday. Is there anyone who has the same problem? Did I miss some essential configurations?

g++ -pthread -o modules/search/pyext/search_wrap.os -c -O3 -fPIC -fno-strict-aliasing -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -DNDEBUG -DIMP_LITTLE_ENDIAN -DIMP_SWIG_WRAPPER -Ibuild/include -I. -I/usr/include/python2.5 modules/search/pyext/search_wrap.cc benchmarks/random_collisions.cpp: In function 'int main()': benchmarks/random_collisions.cpp:62: error: 'BoxSweepClosePairsFinder' was not declared in this scope benchmarks/random_collisions.cpp:62: error: 'cpf' was not declared in this scope benchmarks/random_collisions.cpp:62: error: expected type-specifier before 'BoxSweepClosePairsFinder' benchmarks/random_collisions.cpp:62: error: expected `;' before 'BoxSweepClosePairsFinder' g++ -o benchmarks/connectivity benchmarks/connectivity.o -Lbuild/lib -limp -limp_misc -limp_domino -limp_core -limp_atom -limp_algebra -limp scons: *** [benchmarks/random_collisions.o] Error 1 scons: building terminated because of errors.

Thanks a lot!

-- Seung Joong Kim, Ph.D. Postdoctoral Scholar, Andrej Sali group Department of Biopharmaceutical Sciences, School of Pharmacy University of California at San Francisco (UCSF)

Show replies by date

Daniel Russel

23 Apr 23 Apr

1:22 p.m.

My bad. BoxSweep depends on CGAL and I forgot to turn off the usage in benchmarks. I'll fix it.

On Thu, Apr 23, 2009 at 1:21 PM, Seung Joong Kim sjkim@salilab.org wrote:

> Hi all, > > I keep getting a compiling error on my Mac and linux, since yesterday. Is > there anyone who has the same problem? Did I miss some essential > configurations? > > > g++ -pthread -o modules/search/pyext/search_wrap.os -c -O3 -fPIC > -fno-strict-aliasing -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -DNDEBUG > -DIMP_LITTLE_ENDIAN -DIMP_SWIG_WRAPPER -Ibuild/include -I. > -I/usr/include/python2.5 modules/search/pyext/search_wrap.cc > benchmarks/random_collisions.cpp: In function 'int main()': > benchmarks/random_collisions.cpp:62: error: 'BoxSweepClosePairsFinder' was > not declared in this scope > benchmarks/random_collisions.cpp:62: error: 'cpf' was not declared in this > scope > benchmarks/random_collisions.cpp:62: error: expected type-specifier before > 'BoxSweepClosePairsFinder' > benchmarks/random_collisions.cpp:62: error: expected `;' before > 'BoxSweepClosePairsFinder' > g++ -o benchmarks/connectivity benchmarks/connectivity.o -Lbuild/lib -limp > -limp_misc -limp_domino -limp_core -limp_atom -limp_algebra -limp > scons: *** [benchmarks/random_collisions.o] Error 1 > scons: building terminated because of errors. > > Thanks a lot! > > -- > Seung Joong Kim, Ph.D. > > Postdoctoral Scholar, Andrej Sali group > Department of Biopharmaceutical Sciences, School of Pharmacy > University of California at San Francisco (UCSF) > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >

Seung Joong Kim

26 Apr 26 Apr

2:37 p.m.

Hi Daniel,

Thanks for fixing it. It is certainly fixed for trunk version, but I'm still having the same error for branches/stable version. Could you fix it also?

Daniel Russel wrote: > My bad. BoxSweep depends on CGAL and I forgot to turn off the usage in > benchmarks. I'll fix it. > > On Thu, Apr 23, 2009 at 1:21 PM, Seung Joong Kim <sjkim@salilab.org > mailto:sjkim@salilab.org> wrote: > > Hi all, > > I keep getting a compiling error on my Mac and linux, since > yesterday. Is there anyone who has the same problem? Did I miss > some essential configurations? > > > g++ -pthread -o modules/search/pyext/search_wrap.os -c -O3 -fPIC > -fno-strict-aliasing -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -DNDEBUG -DIMP_LITTLE_ENDIAN -DIMP_SWIG_WRAPPER -Ibuild/include > -I. -I/usr/include/python2.5 modules/search/pyext/search_wrap.cc > benchmarks/random_collisions.cpp: In function 'int main()': > benchmarks/random_collisions.cpp:62: error: > 'BoxSweepClosePairsFinder' was not declared in this scope > benchmarks/random_collisions.cpp:62: error: 'cpf' was not declared > in this scope > benchmarks/random_collisions.cpp:62: error: expected > type-specifier before 'BoxSweepClosePairsFinder' > benchmarks/random_collisions.cpp:62: error: expected `;' before > 'BoxSweepClosePairsFinder' > g++ -o benchmarks/connectivity benchmarks/connectivity.o > -Lbuild/lib -limp -limp_misc -limp_domino -limp_core -limp_atom > -limp_algebra -limp > scons: *** [benchmarks/random_collisions.o] Error 1 > scons: building terminated because of errors. > > Thanks a lot! > > -- > Seung Joong Kim, Ph.D. > > Postdoctoral Scholar, Andrej Sali group > Department of Biopharmaceutical Sciences, School of Pharmacy > University of California at San Francisco (UCSF) > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org mailto:IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > ------------------------------------------------------------------------ > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >

-- Seung Joong Kim, Ph.D. Postdoctoral Scholar, Andrej Sali group Department of Biopharmaceutical Sciences, School of Pharmacy University of California at San Francisco (UCSF)

Daniel Russel

9:48 p.m.

It will get fixed once a nightly test passes. Or just delete the cpp file from benchmarks.

On Apr 26, 2009, at 2:37 PM, Seung Joong Kim sjkim@salilab.org wrote:

> Hi Daniel, > > Thanks for fixing it. It is certainly fixed for trunk version, but > I'm still having the same error for branches/stable version. Could > you fix it also? > > > Daniel Russel wrote: >> My bad. BoxSweep depends on CGAL and I forgot to turn off the usage >> in benchmarks. I'll fix it. >> >> On Thu, Apr 23, 2009 at 1:21 PM, Seung Joong Kim <sjkim@salilab.org >> mailto:sjkim@salilab.org> wrote: >> >> Hi all, >> >> I keep getting a compiling error on my Mac and linux, since >> yesterday. Is there anyone who has the same problem? Did I miss >> some essential configurations? >> >> >> g++ -pthread -o modules/search/pyext/search_wrap.os -c -O3 -fPIC >> -fno-strict-aliasing -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC >> -DNDEBUG -DIMP_LITTLE_ENDIAN -DIMP_SWIG_WRAPPER -Ibuild/include >> -I. -I/usr/include/python2.5 modules/search/pyext/search_wrap.cc >> benchmarks/random_collisions.cpp: In function 'int main()': >> benchmarks/random_collisions.cpp:62: error: >> 'BoxSweepClosePairsFinder' was not declared in this scope >> benchmarks/random_collisions.cpp:62: error: 'cpf' was not declared >> in this scope >> benchmarks/random_collisions.cpp:62: error: expected >> type-specifier before 'BoxSweepClosePairsFinder' >> benchmarks/random_collisions.cpp:62: error: expected `;' before >> 'BoxSweepClosePairsFinder' >> g++ -o benchmarks/connectivity benchmarks/connectivity.o >> -Lbuild/lib -limp -limp_misc -limp_domino -limp_core -limp_atom >> -limp_algebra -limp >> scons: *** [benchmarks/random_collisions.o] Error 1 >> scons: building terminated because of errors. >> >> Thanks a lot! >> >> -- Seung Joong Kim, Ph.D. >> >> Postdoctoral Scholar, Andrej Sali group >> Department of Biopharmaceutical Sciences, School of Pharmacy >> University of California at San Francisco (UCSF) >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org mailto:IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> --- >> --------------------------------------------------------------------- >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > > > -- > Seung Joong Kim, Ph.D. > > Postdoctoral Scholar, Andrej Sali group > Department of Biopharmaceutical Sciences, School of Pharmacy > University of California at San Francisco (UCSF) > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Ben Webb

27 Apr 27 Apr

4:44 p.m.

Seung Joong Kim wrote: > Thanks for fixing it. It is certainly fixed for trunk version, but I'm > still having the same error for branches/stable version. Could you fix > it also?

I have just updated the stable branch, since the builds are working again. So it should be fixed in the stable branch as well now.

The nightly builds also now make sure the benchmarks are built, so will fail in future if the benchmarks break again (and thus, the stable branch should remain, er, stable).

Ben

-- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

Daniel Russel

23 Apr 23 Apr

1:24 p.m.

fixed.

On Thu, Apr 23, 2009 at 1:21 PM, Seung Joong Kim sjkim@salilab.org wrote:

5722

Age (days ago)

5726

Last active (days ago)

List overview

Download

5 comments

3 participants

tags (0)

participants (3)

Ben Webb
Daniel Russel
Seung Joong Kim