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AstraZeneca add-ons to Orange.

License: GNU Lesser General Public License v3.0

Python 94.54% Shell 1.15% C++ 4.31%

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egonw pedroalmeida girschic johan-westin-work engpedrorafael jonnastalringhome jonnastalring amaziz chemphy jcheminform gaybro8777 vikasdubey0551 caixiong110 zahrapahlavanyali rnaimehaom

azorange's Issues

install error

Hi.
I tried to install AZOrange in ubuntu 12.04 (32bit) .
But setup.py was faild .
And I got following message.

"in details.log"
----------------------------------------------------------------------
test -z "/home/chemoinfo/AZOrange/orangeDependencies/opencv/lib/python2.7/site-packages/opencv" || /bin/mkdir -p "/home/chemoinfo/AZOrange/orangeDependencies/opencv/lib/python2.7/site-packages/opencv"
/usr/bin/install -c -m 644 init.py cv.py ml.py highgui.py adaptors.py matlab_syntax.py '/home/chemoinfo/AZOrange/orangeDependencies/opencv/lib/python2.7/site-packages/opencv'
/bin/bash: line 15: --destdir: command not foTraceback (most recent call last):
File "setup.py", line 1165, in main
self.__build()
File "setup.py", line 199, in __build
self.compileOpenCV()
File "setup.py", line 969, in compileOpenCV
checkStatus(stat, out,"Error installing opencv.")
File "setup.py", line 26, in checkStatus
sys.exit(1)
SystemExit: 1
und
make[4]: *** [install-pkgpyexecPYTHON] Error 127
make[4]: Leaving directory /tmp/AZOBuildDir/orangeDependencies/src/opencv/interfaces/swig/python' make[3]: *** [install-am] Error 2 make[3]: Leaving directory/tmp/AZOBuildDir/orangeDependencies/src/opencv/interfaces/swig/python'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory /tmp/AZOBuildDir/orangeDependencies/src/opencv/interfaces/swig' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory/tmp/AZOBuildDir/orangeDependencies/src/opencv/interfaces'
make: *** [install-recursive] Error 1

    ++++++++++++++++++


    Error installing opencv.
    AZOrange is not built.

Are there ideas to solve the problem ?
Please give me some advice.
Thanks.

FTM needs upgrade

It is needed a version that can be compiled in Ubuntu 64 bits.

Installation Aborted

@engpedrorafael @egonw @larscarlsson @JonnaStalring @johan-westin-work
ERROR: Detail Code: 2048_1653982697.87
#install - Output from command: URL transformed to HTTPS due to an HSTS policy
--2022-05-31 13:08:16-- https://infosys.informatik.uni-mainz.de/research/azorange/ftm-for-azorange/at_download/file
Resolving infosys.informatik.uni-mainz.de (infosys.informatik.uni-mainz.de)... 134.93.178.16
Connecting to infosys.informatik.uni-mainz.de (infosys.informatik.uni-mainz.de)|134.93.178.16|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2022-05-31 13:08:17 ERROR 404: Not Found.

ERROR: Detail Code: 256_1653982697.87
#install - Output from command: mv: cannot stat 'file': No such file or directory
ERROR: Detail Code: 512_1653982697.88
#install - Output from command: tar (child): ftm.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now

Incompatibility with Ubuntu 12.10 (Quantal Quetzal)

Ubuntu has updated gcc compiler to version 4.7.2 and therefore installation fails when compiling rdkit.
Other dependencies may also fail to compile.

Segmentation fault on exit

After import of module Orange, when exiting, it is reported Segmentation Fault.
Everything seems to be working though...

Use CDK 1.2.x or 1.3.x

Right now, AZOrange seems to be using CDK 1.0.2, while Cinfony 1.0 is using 1.2.5. Using a copy from the 1.2 series is really important as it is much more stable than CDK 1.0.x.

Install error

Hi, I followed the install instructions up to step 8 (python install.py), but get the error as shown in the install.log output below.

Log for AZOrange installation (Wed Oct 16 07:22:54 2013)
============================================================
Setup Configuration:
Detail Code: OK_1381929774.4
------------------------------------------------------------
Requirements and System Info (Wed Oct 16 07:22:54 2013)
------------------------------------------------------------
/usr/include/python2.7
Linux br-vb-ub 3.8.0-19-generic #30-Ubuntu SMP Wed May 1 16:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 13.04
Release:    13.04
Codename:   raring
------------------------------------------------------------
Preparing Directories (Wed Oct 16 07:22:54 2013)
------------------------------------------------------------
Removing existing buildDir
Detail Code: OK_1381929775.58
Detail Code: OK_1381929775.93
Creating buildDir
Detail Code: OK_1381929775.93
Removing existing installDir
Detail Code: OK_1381929776.03
Detail Code: OK_1381929776.14
Creating installDir
Detail Code: OK_1381929776.14
Detail Code: OK_1381929776.15
------------------------------------------------------------
Not downloading ftm (Wed Oct 16 07:22:56 2013)
------------------------------------------------------------
------------------------------------------------------------
http://infosys.informatik.uni-mainz.de/research/azorange/structuralclustering-for-azorange/at_download/file (Wed Oct 16 07:22:56 2013)
------------------------------------------------------------
Detail Code: OK_1381929776.15
------------------------------------------------------------
Downloading clustering to trunk (http://infosys.informatik.uni-mainz.de/research/azorange/structuralclustering-for-azorange/at_download/file:1.1) (Wed Oct 16 07:22:56 2013)
------------------------------------------------------------
Detail Code: OK_1381929776.16
Detail Code: OK_1381929776.16
Detail Code: OK_1381930264.7
Detail Code: OK_1381930264.72
Detail Code: OK_1381930265.16
Detail Code: OK_1381930265.18
------------------------------------------------------------
Downloading fminer to trunk (https://github.com/amaunz/fminer2.git:0.0) (Wed Oct 16 07:31:05 2013)
------------------------------------------------------------
Detail Code: OK_1381930296.47
------------------------------------------------------------
OpenAZOrange: Using current files. (Wed Oct 16 07:31:36 2013)
------------------------------------------------------------
trunk: /home/XXXXX/build-dirs/python-packages/AZOrange
Detail Code: OK_1381930296.47
------------------------------------------------------------
Downloading cinfony to trunk (http://cinfony.googlecode.com/files/cinfony-1.0.tar.gz:1.0) (Wed Oct 16 07:31:36 2013)
------------------------------------------------------------
Detail Code: OK_1381930296.47
Detail Code: OK_1381930297.17
Detail Code: OK_1381930297.21
Detail Code: OK_1381930297.21
Detail Code: OK_1381930297.22
Detail Code: OK_1381930297.4
------------------------------------------------------------
Downloading rdkit to trunk (http://rdkit.googlecode.com/files/RDKit_2011_06_1.tgz:2011.06) (Wed Oct 16 07:31:37 2013)
------------------------------------------------------------
Detail Code: OK_1381930297.4
Detail Code: OK_1381930308.92
Detail Code: OK_1381930309.43
Detail Code: OK_1381930309.43
Detail Code: OK_1381930309.43
Detail Code: OK_1381930309.43
------------------------------------------------------------
Downloading cdk to trunk (http://switch.dl.sourceforge.net/project/cdk/cdk/1.2.7/cdk-1.2.7.jar:1.2.7) (Wed Oct 16 07:31:49 2013)
------------------------------------------------------------
Detail Code: OK_1381930309.44
Detail Code: OK_1381930424.64
Detail Code: OK_1381930424.66
Detail Code: OK_1381930424.82
------------------------------------------------------------
Checking out from orange bitbucket to trunk (https://bitbucket.org/biolab/orange:2.5a2) (Wed Oct 16 07:33:44 2013)
------------------------------------------------------------
Detail Code: OK_1381932556.42
Detail Code: OK_1381932561.4
Detail Code: OK_1381932561.87
Applying Patch...
Detail Code: OK_1381932561.9
Detail Code: OK_1381932561.94
------------------------------------------------------------
Downloading AppsPack to trunk (http://software.sandia.gov/appspack/downloads/appspack-5.0.1.tar.gz:5.0.1) (Wed Oct 16 08:09:21 2013)
------------------------------------------------------------
Detail Code: OK_1381932561.94
Detail Code: OK_1381932575.09
Detail Code: OK_1381932575.19
Detail Code: OK_1381932575.19
Detail Code: OK_1381932575.31
------------------------------------------------------------
Downloading opencv to trunk (http://downloads.sourceforge.net/project/opencvlibrary/opencv-unix/2.0/OpenCV-2.0.0.tar.bz2:2.0.0) (Wed Oct 16 08:09:35 2013)
------------------------------------------------------------
Detail Code: OK_1381932575.31
Detail Code: OK_1381932740.4
Detail Code: OK_1381932747.81
Detail Code: OK_1381932747.81
Applying Patch...
Detail Code: OK_1381932748.01
Detail Code: OK_1381932748.37
------------------------------------------------------------
Downloading Boost to trunk (http://downloads.sourceforge.net/project/boost/boost/1.34.1/boost_1_34_1.tar.gz:1.34.1) (Wed Oct 16 08:12:28 2013)
------------------------------------------------------------
Detail Code: OK_1381932748.37
Detail Code: OK_1381933034.07
Detail Code: OK_1381933036.81
Detail Code: OK_1381933036.93
Detail Code: OK_1381933037.07
------------------------------------------------------------
Checking out from plearn SVN to trunk (svn://svn.berlios.de/plearn/trunk:8124) (Wed Oct 16 08:17:17 2013)
------------------------------------------------------------
Detail Code: OK_1381933037.08
Detail Code: OK_1381933128.85
Detail Code: OK_1381933128.9
------------------------------------------------------------
Applying Patch... (Wed Oct 16 08:18:48 2013)
------------------------------------------------------------
Detail Code: OK_1381933128.94
------------------------------------------------------------
Not downloading Oasa (Wed Oct 16 08:18:48 2013)
------------------------------------------------------------
------------------------------------------------------------
Compiling and Installing (Wed Oct 16 08:18:48 2013)
------------------------------------------------------------
Copying from Trunk to build dir
/home/XXXXX/build-dirs/python-packages/AZOrange -> /tmp/AZOBuildDir
Detail Code: OK_1381933148.84
Detail Code: OK_1381933149.09
Detail Code: OK_1381933149.19
Compiling by running setup.py
Installation will be to made to /home/XXXXX/local/AZOrange
ERROR: Detail Code: 256_1381935964.12
------------------------------------------------------------
ERROR: Installation aborted! (Wed Oct 16 09:06:04 2013)
------------------------------------------------------------
------------------------------------------------------------
Finished (Wed Oct 16 09:06:04 2013)
------------------------------------------------------------
The process spent 103 minutes
ERRORS during installation!!
------------------------------------------------------------
Support FeedBack (Wed Oct 16 09:06:04 2013)
------------------------------------------------------------
No emails specified for feedBack

ERROR: Installation aborted!

Ubuntu 11.10, x86

Same error on older version (10.x)

All system updates

Tried several releases (from 0.3 to the most recent one)

install.log

Compiling by running setup.py
Installation will be to made to /home/miha/AZOrange

ERROR: Detail Code: 256_1319962291.22

ERROR: Installation aborted! (Sun Oct 30 09:11:31 2011)

Finished (Sun Oct 30 09:11:31 2011)

The process spent 35 minutes

ERRORS during installation!!

Support FeedBack (Sun Oct 30 09:11:31 2011)

details.log

In file included from ../include/opencv/cxcore.h:2123:0,
from cxcore/_cxcore.h:60,
from cxcore/cxprecomp.cpp:43:
../include/opencv/cxcore.hpp:169:13: error: ‘ptrdiff_t’ does not name a type
In file included from ../include/opencv/cxcore.hpp:2243:0,
from ../include/opencv/cxcore.h:2123,
from cxcore/_cxcore.h:60,
from cxcore/cxprecomp.cpp:43:
../include/opencv/cxoperations.hpp:1916:15: error: ‘ptrdiff_t’ does not name a type
../include/opencv/cxoperations.hpp:2465:31: error: ‘ptrdiff_t’ does not name a type
In file included from ../include/opencv/cxcore.hpp:2244:0,
from ../include/opencv/cxcore.h:2123,
from cxcore/_cxcore.h:60,
from cxcore/cxprecomp.cpp:43:
../include/opencv/cxmat.hpp: In member function ‘void cv::Mat::locateROI(cv::Size&, cv::Point&) const’:
../include/opencv/cxmat.hpp:356:5: error: ‘ptrdiff_t’ was not declared in this scope
../include/opencv/cxmat.hpp:356:5: note: suggested alternatives:
/usr/include/c++/4.6/i686-linux-gnu/./bits/c++config.h:156:28: note: ‘std::ptrdiff_t’
/usr/include/c++/4.6/i686-linux-gnu/./bits/c++config.h:156:28: note: ‘std::ptrdiff_t’
../include/opencv/cxmat.hpp:356:15: error: expected ‘;’ before ‘delta1’
../include/opencv/cxmat.hpp:358:9: error: ‘delta1’ was not declared in this scope
../include/opencv/cxmat.hpp:367:31: error: ‘delta2’ was not declared in this scope
make[2]: *** [cxprecomp.lo] Error 1
make[2]: Leaving directory /tmp/AZOBuildDir/orangeDependencies/src/opencv/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/tmp/AZOBuildDir/orangeDependencies/src/opencv'
make: *** [all] Error 2

    ++++++++++++++++++


    Error compiling opencv.
    AZOrange is not built.

ERROR: Installation aborted! (Sun Oct 30 09:11:31 2011)

Finished (Sun Oct 30 09:11:31 2011)

The process spent 35 minutes

ERRORS during installation!!

Support FeedBack (Sun Oct 30 09:11:31 2011)

No emails specified for feedBack

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