Compilation error of develop-version due to problem with shell?
Dear all,
I have problems compiling the develop-version of IMP, while the master is fine. Running: "cmake ../imp -DCMAKE_BUILD_TYPE=Debug -DIMP_DISABLED_MODULES=cgal:membrane -DIMP_PER_CPP_COMPILATION=core" works, but "make -j 8" crashes after about 20% with the following message: " Scanning dependencies of target imp_benchmark /bin/sh: 1: Syntax error: Bad fd number make[2]: *** [doxygen/base/tags] Error 2 make[1]: *** [modules/base/CMakeFiles/IMP.base-doc.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... "
A similar error occurs when calling "git imp update": Fetching changes from origin tools/git/gitflow/git-imp: 125: tools/git/gitflow/git-imp: Syntax error: Bad fd number
I found, that "Bad fd number" is often related to the shell used in the makefiles. For our system sh points to dash, not bash. Might that be the reason why I run into problems? Which shell are you using? When I change in tools/git/gitflow/git-imp "#!/bin/sh" to "#!/bin/bash" git imp update works again. Is there a way, that I don't have to search and replace every single "#! bin/sh"? Or do you have any other ideas or hints, what I could try? Could doxygen cause part of the problem?
Thank you very much in advance!
Pia
Pia Unverdorben (Dipl. Math.) Max-Planck Institut für Biochemie Am Klopferspitz 18 D-82152 Martinsried
unverdor@biochem.mpg.de
Thanks for the more info (specifically the dash vs bash bit). It looks like it might be some of our custom commands that are at issue: http://www.itk.org/Bug/print_bug_page.php?bug_id=3306. I'll look through to see if I can find anything.
On Jul 8, 2013, at 9:25 AM, Pia Unverdorben unverdor@biochem.mpg.de wrote:
> Dear all, > > I have problems compiling the develop-version of IMP, while the master is fine. > Running: > "cmake ../imp -DCMAKE_BUILD_TYPE=Debug -DIMP_DISABLED_MODULES=cgal:membrane -DIMP_PER_CPP_COMPILATION=core" > works, but > "make -j 8" > crashes after about 20% with the following message: > " > Scanning dependencies of target imp_benchmark > /bin/sh: 1: Syntax error: Bad fd number > make[2]: *** [doxygen/base/tags] Error 2 > make[1]: *** [modules/base/CMakeFiles/IMP.base-doc.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > " > > A similar error occurs when calling "git imp update": > Fetching changes from origin > tools/git/gitflow/git-imp: 125: tools/git/gitflow/git-imp: Syntax error: Bad fd number > > I found, that "Bad fd number" is often related to the shell used in the makefiles. For our system sh points to dash, not bash. > Might that be the reason why I run into problems? > Which shell are you using? > When I change in tools/git/gitflow/git-imp "#!/bin/sh" to "#!/bin/bash" git imp update works again. Is there a way, that I don't have to search and replace every single "#! bin/sh"? > Or do you have any other ideas or hints, what I could try? Could doxygen cause part of the problem? > > > Thank you very much in advance! > > Pia > > > > Pia Unverdorben (Dipl. Math.) > Max-Planck Institut für Biochemie > Am Klopferspitz 18 > D-82152 Martinsried > > unverdor@biochem.mpg.de > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
I just submitted a patch to develop that hopefully fixes it. If there are further problems, can you run "make VERBOSE=1" that way it will print out the problematic commands. Thanks, and sorry it was slow.
On Jul 8, 2013, at 9:25 AM, Pia Unverdorben unverdor@biochem.mpg.de wrote:
> Dear all, > > I have problems compiling the develop-version of IMP, while the master is fine. > Running: > "cmake ../imp -DCMAKE_BUILD_TYPE=Debug -DIMP_DISABLED_MODULES=cgal:membrane -DIMP_PER_CPP_COMPILATION=core" > works, but > "make -j 8" > crashes after about 20% with the following message: > " > Scanning dependencies of target imp_benchmark > /bin/sh: 1: Syntax error: Bad fd number > make[2]: *** [doxygen/base/tags] Error 2 > make[1]: *** [modules/base/CMakeFiles/IMP.base-doc.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > " > > A similar error occurs when calling "git imp update": > Fetching changes from origin > tools/git/gitflow/git-imp: 125: tools/git/gitflow/git-imp: Syntax error: Bad fd number > > I found, that "Bad fd number" is often related to the shell used in the makefiles. For our system sh points to dash, not bash. > Might that be the reason why I run into problems? > Which shell are you using? > When I change in tools/git/gitflow/git-imp "#!/bin/sh" to "#!/bin/bash" git imp update works again. Is there a way, that I don't have to search and replace every single "#! bin/sh"? > Or do you have any other ideas or hints, what I could try? Could doxygen cause part of the problem? > > > Thank you very much in advance! > > Pia > > > > Pia Unverdorben (Dipl. Math.) > Max-Planck Institut für Biochemie > Am Klopferspitz 18 > D-82152 Martinsried > > unverdor@biochem.mpg.de > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Thank you very much! Now everything compiles again just fine!
On 08.07.2013, at 18:41, Daniel Russel wrote:
> I just submitted a patch to develop that hopefully fixes it. If there are further problems, can you run "make VERBOSE=1" that way it will print out the problematic commands. Thanks, and sorry it was slow. > > > On Jul 8, 2013, at 9:25 AM, Pia Unverdorben unverdor@biochem.mpg.de wrote: > >> Dear all, >> >> I have problems compiling the develop-version of IMP, while the master is fine. >> Running: >> "cmake ../imp -DCMAKE_BUILD_TYPE=Debug -DIMP_DISABLED_MODULES=cgal:membrane -DIMP_PER_CPP_COMPILATION=core" >> works, but >> "make -j 8" >> crashes after about 20% with the following message: >> " >> Scanning dependencies of target imp_benchmark >> /bin/sh: 1: Syntax error: Bad fd number >> make[2]: *** [doxygen/base/tags] Error 2 >> make[1]: *** [modules/base/CMakeFiles/IMP.base-doc.dir/all] Error 2 >> make[1]: *** Waiting for unfinished jobs.... >> " >> >> A similar error occurs when calling "git imp update": >> Fetching changes from origin >> tools/git/gitflow/git-imp: 125: tools/git/gitflow/git-imp: Syntax error: Bad fd number >> >> I found, that "Bad fd number" is often related to the shell used in the makefiles. For our system sh points to dash, not bash. >> Might that be the reason why I run into problems? >> Which shell are you using? >> When I change in tools/git/gitflow/git-imp "#!/bin/sh" to "#!/bin/bash" git imp update works again. Is there a way, that I don't have to search and replace every single "#! bin/sh"? >> Or do you have any other ideas or hints, what I could try? Could doxygen cause part of the problem? >> >> >> Thank you very much in advance! >> >> Pia >> >> >> >> Pia Unverdorben (Dipl. Math.) >> Max-Planck Institut für Biochemie >> Am Klopferspitz 18 >> D-82152 Martinsried >> >> unverdor@biochem.mpg.de >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
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Pia Unverdorben