[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
I'm having the same issue and trying to do the same, but I'm inexperienced with linux. How do you add -fpermissive to CXXFLAGS? -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
Seth, You can add it right into the 'make' command after configuration: make CXXFLAGS=-fpermissive -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
That did it, thank you very much Heidi! -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
Helpful suggestions from another forum led me to this solution: Add -fpermissive to your CXXFLAGS -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
Julian - thanks for the info, and sorry for the delayed response. I barely know enough to get around linux, and know nothing about using a patch. Is this part of the 'make' file command? Or do I add it into the Makefile somewhere? -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
this might work: make LDFLAGS=-Wl,--no-as-needed -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
Thanks so much for the fast response, but unfortunately I am still getting the same error message. Combing back through the output, I noticed another error further up: In file included from /home/hjtp/Downloads/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include/dbapi/driver/impl/dbapi_impl_result.hpp:35:0, from /home/hjtp/Downloads/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/dbapi/driver/public.cpp:34: /home/hjtp/Downloads/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp:234:32: error: reference ‘m_Conn’ cannot be declared ‘mutable’ [-fpermissive] make[8]: *** [public.o] Error 1 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
I am having this error while trying to install the rmblast package 2.2.23 in ubuntu (modified version of NCBI Blast to use with RepeatMasker: http://www.repeatmasker.org/RMBlast.html). Is there a fix for this? Here is the error I get after executing 'make': make[8]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver' make[7]: *** [all.nonusr] Error 2 make[7]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver' make[6]: *** [all.real] Error 2 make[6]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver' make[5]: *** [all_r.needs-reqs] Error 2 make[5]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver' make[4]: *** [all_r.real] Error 5 make[4]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi' make[3]: *** [all_r.needs-reqs] Error 2 make[3]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi' make[2]: *** [all_r.real] Error 5 make[2]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build' make[1]: *** [all_r.needs-reqs] Error 2 make[1]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build' make: *** [all] Error 2 Thanks for any suggestions! -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
have you tried applying a similar patch to the one used to fix this bug? (=setting LDFLAGS=-Wl,--no-as-needed) -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
** Changed in: ncbi-blast+ (Debian) Status: New = Fix Released -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
** Changed in: ncbi-blast+ (Debian) Status: Unknown = New -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
This bug was fixed in the package ncbi-blast+ - 2.2.25-3ubuntu1 --- ncbi-blast+ (2.2.25-3ubuntu1) oneiric; urgency=low * debian/rules: disable --as-needed build (LP: #803185) almost all private libs are underlinked, fixing them is not worth the effort -- Julian Taylor jtaylor.deb...@googlemail.com Mon, 18 Jul 2011 16:02:34 +0200 ** Branch linked: lp:ubuntu/ncbi-blast+ ** Changed in: ncbi-blast+ (Ubuntu) Status: New = Fix Released -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
** Branch linked: lp:~jtaylor/ubuntu/oneiric/ncbi-blast+/fix-803185 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 803185] Re: ncbi-blast+ version 2.2.25-3 failed to build on i386
most of the private libs of this package are underlinked: $ ldd -r /usr/lib/ncbi-blast+/*so 21 | grep -c undefined 8291 fixing this package seems like a lot of work and looking at the dependencies it does not seem like one gains much. I recommend building this one without --as-needed ** Bug watch added: Debian Bug tracker #633567 http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=633567 ** Also affects: ncbi-blast+ (Debian) via http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=633567 Importance: Unknown Status: Unknown -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/803185 Title: ncbi-blast+ version 2.2.25-3 failed to build on i386 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/803185/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
