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


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