[EMBOSS] Packaging EMBOSS for Fedora

Julian Sikorski belegdol at gmail.com
Tue Sep 29 19:34:56 UTC 2009

W dniu 29.07.2009 13:54, Julian Sikorski pisze:
> W dniu 19.07.2009 18:18, uludag at ebi.ac.uk pisze:
>>> there seem to be some problems with make install:
>>> /usr/bin/make  install-exec-hook
>>> make[7]: Entering directory
>>> `/builddir/build/BUILD/EMBOSS-6.1.0/jemboss/org/emboss/jemboss/editor'
>>> mkdir -p --
>>> /builddir/build/BUILDROOT/EMBOSS-6.1.0-1.fc11.x86_64/usr/share/EMBOSS/jemboss/org/emboss/jemboss/editor
>>> /usr/bin/install: cannot stat `*.class': No such file or directory
>> Looks like we didn't test the --with-java and --with-javaos configure
>> options well, before this release. However, most users will not need these
>> two options any more as EMBOSS-6.1.0 includes precompiled jemboss class
>> files collected in a java archive file. You should hopefully not get the
>> above error if you omit these two options when you configure your emboss
>> installation.
>> Regards,
>> Mahmut
> Thank you, removing these two seems to have done the trick!
> Julian
Another problem arose. I was pointed out that another problem pointed
out by rpmlint should be fixed:

EMBOSS-libs.x86_64: W: shared-lib-calls-exit
/usr/lib64/libeplplot.so.3.2.7 exit@

According to the tool, it means the following:

This library package calls exit() or _exit(), probably in a non-fork()
context. Doing so from a library is strongly discouraged - when a
library function calls exit(), it prevents the calling program from
handling the error, reporting it to the user, closing files properly,
and cleaning up any state that the program has. It is preferred for the
library to return an actual error code and let the calling program
decide how to handle the situation.

Also, the guidelines [1] say that the .jar files should be compiled from
source, so fixing the problem with --with-java would definitely help here.



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