Package Details: ugene 1.24.0-1

Git Clone URL: https://aur.archlinux.org/ugene.git (read-only)
Package Base: ugene
Description: A free cross-platform genome analysis suite.
Upstream URL: http://ugene.net/
Licenses: GPL
Submitter: bmpvieira
Maintainer: WFCody
Last Packager: WFCody
Votes: 18
Popularity: 1.113334
First Submitted: 2010-02-25 18:22
Last Updated: 2016-08-15 10:15

Latest Comments

WFCody commented on 2016-06-06 19:09

The best strategy is probably to open an issue on the github site of the project. The developers seem very responsive and I follow those issues so I will integrate any fixes listed there

arbacle commented on 2016-06-06 14:39

Hello, that problem seems fixed, but now I get an error when the compiling process reaches one of the auxiliary programs, bundled with Ugene - MUSCLE.

----------------------------------------------------
src/MuscleWorkPool.cpp: In constructor ‘U2::MuscleWorkPool::MuscleWorkPool(MuscleContext*, const U2::MuscleTaskSettings&, U2::TaskStateInfo&, int, const U2::MAlignment&, U2::MAlignment&, bool)’:
src/MuscleWorkPool.cpp:32:103: error: cannot convert ‘bool’ to ‘bool*’ in initialization
bReversed(false), bRight(false), History(NULL), bLockLeft(NULL), bLockRight(false), msaIn(NULL)
^
Makefile.Release:2590: recipe for target '_tmp/obj/release/MuscleWorkPool.o' failed
make[2]: *** [_tmp/obj/release/MuscleWorkPool.o] Error 1
----------------------------------------------------------

I've tried to lookup the error, but couldn't find it (I've searched for the previous one also, but either I was looking too soon after it got posted before Google could cache it, or my Google-Fu was bad).

Also a question - is this place suitable for such "error reports", or there's a more official way to do this? If that's the case and I'm muddying the comment section, please excuse me.

WFCody commented on 2016-06-03 07:07

The same issue came up recently on the Github issue tracker

https://github.com/ugeneunipro/ugene/issues/13

GCC seems to break building quite a bit. Last GCC-issue got solved with the hmmer3.patch. We will see if the developers come up with a solution this time too. I will also try to build with clang, because if GCC is breaking stuff like this it is no fun...

EDIT: updated by using "QMAKE_CFLAGS_ISYSTEM="
as qmake argument and this seems to be working (package is compiling)

apson commented on 2016-06-02 21:25

Hi
I also have a problem compiling..
g++ -c -pipe -O2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -w -D_REENTRANT -fPIC -DU2_DISTRIBUTION_INFO=sources -DUGENE_VERSION=1.22.0 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=22 -DUGENE_VER_PATCH=0 -DUGENE_X86_64 -DUGENE_DATA_DIR=\"/usr/share/ugene/data\" -DHI_EXCLUDED -DNDEBUG -DQT_NO_DEBUG -DQT_CORE_LIB -I. -isystem /usr/include/qt5 -isystem /usr/include -Isrc -isystem /usr/include/qt -isystem /usr/include/qt/QtCore -Irelease -I/usr/lib/qt/mkspecs/linux-g++ -o _tmp/obj/release/string_conversion.o src/common/string_conversion.cc
In file included from /usr/include/c++/6.1.1/ext/string_conversions.h:41:0,
from /usr/include/c++/6.1.1/bits/basic_string.h:5402,
from /usr/include/c++/6.1.1/string:52,
from src/client/minidump_file_writer.h:37,
from src/client/minidump_file_writer-inl.h:39,
from src/client/minidump_file_writer.cc:40:
/usr/include/c++/6.1.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
#include_next <stdlib.h>
^
In file included from /usr/include/c++/6.1.1/ext/string_conversions.h:41:0,
from /usr/include/c++/6.1.1/bits/basic_string.h:5402,
from /usr/include/c++/6.1.1/string:52,
from src/common/string_conversion.h:35,
from src/common/string_conversion.cc:34:
/usr/include/c++/6.1.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
#include_next <stdlib.h>
^
compilation terminated.
compilation terminated.
Makefile.Release:390: recipe for target '_tmp/obj/release/string_conversion.o' failed
make[2]: *** [_tmp/obj/release/string_conversion.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Makefile.Release:377: recipe for target '_tmp/obj/release/minidump_file_writer.o' failed
make[2]: *** [_tmp/obj/release/minidump_file_writer.o] Error 1
make[2]: Leaving directory '/tmp/yaourt-tmp-spot/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad'
Makefile:38: recipe for target 'release' failed
make[1]: *** [release] Error 2
make[1]: Leaving directory '/tmp/yaourt-tmp-spot/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad'
Makefile:102: recipe for target 'sub-src-libs_3rdparty-breakpad-make_first-ordered' failed
make: *** [sub-src-libs_3rdparty-breakpad-make_first-ordered] Error 2
==> ERROR: A failure occurred in build().
Aborting...
==> ERROR: Makepkg was unable to build ugene.



find / -iname "stdlib.h"

/usr/include/stdlib.h
/usr/include/isc/stdlib.h
/usr/include/bits/stdlib.h
/usr/include/bsd/stdlib.h
/usr/include/c++/6.1.1/stdlib.h
/usr/include/c++/6.1.1/tr1/stdlib.h
/usr/include/wine/msvcrt/stdlib.h
/usr/include/lwres/stdlib.h


Many thanks!

arbacle commented on 2016-06-02 18:21

Hello!
I can't compile version 1.22.0, because it throws an error:

cd src/libs_3rdparty/breakpad/ && ( test -e Makefile || /usr/bin/qmake-qt5 /tmp/yaourt-tmp-misho/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad/breakpad.pro CONFIG+=x64 PREFIX=/usr -o Makefile ) && make -f Makefile
make[1]: Entering directory '/tmp/yaourt-tmp-misho/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad'
make -f Makefile.Release
make[2]: Entering directory '/tmp/yaourt-tmp-misho/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad'
g++ -c -pipe -O2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -w -D_REENTRANT -fPIC -DU2_DISTRIBUTION_INFO=sources -DUGENE_VERSION=1.22.0 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=22 -DUGENE_VER_PATCH=0 -DUGENE_X86_64 -DUGENE_DATA_DIR=\"/usr/share/ugene/data\" -DHI_EXCLUDED -DNDEBUG -DQT_NO_DEBUG -DQT_CORE_LIB -I. -isystem /usr/include/qt5 -isystem /usr/include -Isrc -isystem /usr/include/qt -isystem /usr/include/qt/QtCore -Irelease -I/usr/lib/qt/mkspecs/linux-g++ -o _tmp/obj/release/minidump_file_writer.o src/client/minidump_file_writer.cc
In file included from /usr/include/c++/6.1.1/ext/string_conversions.h:41:0,
from /usr/include/c++/6.1.1/bits/basic_string.h:5402,
from /usr/include/c++/6.1.1/string:52,
from src/client/minidump_file_writer.h:37,
from src/client/minidump_file_writer-inl.h:39,
from src/client/minidump_file_writer.cc:40:
/usr/include/c++/6.1.1/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
#include_next <stdlib.h>
^
compilation terminated.
Makefile.Release:509: recipe for target '_tmp/obj/release/minidump_file_writer.o' failed
make[2]: *** [_tmp/obj/release/minidump_file_writer.o] Error 1
make[2]: Leaving directory '/tmp/yaourt-tmp-misho/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad'
Makefile:38: recipe for target 'release' failed
make[1]: *** [release] Error 2
make[1]: Leaving directory '/tmp/yaourt-tmp-misho/aur-ugene/src/ugene-1.22.0/src/libs_3rdparty/breakpad'
Makefile:102: recipe for target 'sub-src-libs_3rdparty-breakpad-make_first-ordered' failed
make: *** [sub-src-libs_3rdparty-breakpad-make_first-ordered] Error 2

"locate stdlib.h", gives the following:

/usr/include/stdlib.h
/usr/include/bits/stdlib.h
/usr/include/boost/cstdlib.hpp
/usr/include/bsd/stdlib.h
/usr/include/c++/6.1.1/stdlib.h
/usr/include/c++/6.1.1/tr1/stdlib.h
/usr/include/calc/have_stdlib.h
/usr/include/freetype2/freetype/config/ftstdlib.h
/usr/include/wine/msvcrt/stdlib.h

If I can help with more information, tell me what you need. Thanks!

WFCody commented on 2016-04-14 11:48

Thanks to Ugene developer dkandrov, the issue has been patched. Most likely a bug introduced by the newest gcc.

WFCody commented on 2016-04-14 07:23

I opened an issue on Github
https://github.com/ugeneunipro/ugene/issues/12

I really don't know what is wrong at this moment. I will fix the package as soon as I do.

boina commented on 2016-04-13 21:02

So we can't use the PKGBUILD to install ugene? or is there a workaround that I don't see.

My Best,
thanks, jose.

WFCody commented on 2016-04-11 16:36

I do indeed get the same issue.

isnan and isinf should be defined by <cmath> which is not explicitly included in that file.

https://github.com/ugeneunipro/ugene/blob/master/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp

math.h should be included by this file

https://github.com/ugeneunipro/ugene/blob/master/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.h

so in fact isinf et al should be defined!

boina commented on 2016-04-11 12:01

Hello!! so I made some progress but I'm stuck again.
The problem was not with locales. Packages qt5-script and qt5-svg were missing. They should be included as dependencies.
Now it starts compiling and goes well for a long time before crashing with the following errors:

src/hmmer3/hmmer3_funcs.cpp:36:22: error: ‘isnan’ no se declaró en este ámbito
return !isnan( x ) && !isinf( x );

AND

src/hmmer3/hmmer3_funcs.cpp:36:37: error: ‘isinf’ no se declaró en este ámbito
return !isnan( x ) && !isinf( x );

I don't know if this could be for something related to my system or maybe another non-satisfied dependency??

Any ideas?
Thanks, Jose.

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