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