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Tasklist

FS#21569 - [avogadro] needs a rebuild for sip

Attached to Project: Arch Linux
Opened by zeld (zeld) - Tuesday, 02 November 2010, 12:06 GMT
Last edited by Andrea Scarpino (BaSh) - Saturday, 18 December 2010, 14:09 GMT
Task Type Bug Report
Category Upstream Bugs
Status Closed
Assigned To Andrea Scarpino (BaSh)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 6
Private No

Details

Description:
I tried to recompile avogadro from source because the binary do not run and give me this error:

$ avogadro
The _C_API object in the sip python module is invalid.
Could not initialize SIP API !
terminate called after throwing an instance of 'boost::python::error_already_set'
Aborted
$


Additional info:
extra/avogadro 1.0.1-1


zeld
This task depends upon

Closed by  Andrea Scarpino (BaSh)
Saturday, 18 December 2010, 14:09 GMT
Reason for closing:  Fixed
Additional comments about closing:  avogadro 1.0.1-5
Comment by Andrea Scarpino (BaSh) - Tuesday, 02 November 2010, 14:10 GMT
  • Field changed: Summary ([avogadro] 1.0.1-1 do not compile and the binary package do not run → [avogadro] needs a rebuild for sip)
we need a patch to make it build with sip 4.11.2

/build/src/avogadro-1.0.1/libavogadro/src/python/sip.cpp: In static member function 'static void* QClass_converters<T>::QClass_from_PyQt(PyObject*)':
/build/src/avogadro-1.0.1/libavogadro/src/python/sip.cpp:207:21: error: 'struct sipSimpleWrapper' has no member named 'u'
make[2]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/sip.cpp.o] Error 1
make[1]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/all] Error 2
Comment by K. Takacs (silent) - Tuesday, 09 November 2010, 07:15 GMT
  • Field changed: Percent Complete (100% → 0%)
avogadro-1.0.1-2-i686:
The _C_API object in the sip python module is invalid.
Could not initialize SIP API !
terminate called after throwing an instance of 'boost::python::error_already_set'
Aborted
Fedora 14 gives the same error as well
Comment by Hector Mtz-Seara Monne (hseara) - Monday, 15 November 2010, 16:39 GMT
There has been a change in the sip API and avogadro do not suport it in the currect release:
there are three options:
a) Downgrade sip to 4.10.5-1.
b) Wait till the next release.
c) Apply the following path to avogadro ( http://bugs.gentoo.org/attachment.cgi?id=254359):

--- libavogadro/src/python/sip.cpp.old 2010-11-14 14:55:44.928487067 -0800
+++ libavogadro/src/python/sip.cpp 2010-11-14 15:37:31.589487066 -0800
@@ -198,13 +198,19 @@
#endif

// reinterpret to sipWrapper
+#if SIP_API_MAJOR_NR >= 8
+ sipSimpleWrapper *wrapper = reinterpret_cast<sipSimpleWrapper*>(obj_ptr);
+ return wrapper->data;
+#else
+
#ifdef SIP_4_8
sipSimpleWrapper *wrapper = reinterpret_cast<sipSimpleWrapper*>(obj_ptr);
#else
sipWrapper *wrapper = reinterpret_cast<sipWrapper*>(obj_ptr);
+ // return the C++ pointer
#endif
- // return the C++ pointer
return wrapper->u.cppPtr;
+#endif
}

QClass_converters()
Comment by K. Takacs (silent) - Monday, 15 November 2010, 19:08 GMT
As a temporary solution I installed the 1.1 binary from http://avogadro.openmolecules.net/nightly/linux/unstable/. It works, but it is really unstable.
Comment by Andrea Scarpino (BaSh) - Wednesday, 17 November 2010, 09:18 GMT
@ hseara
we already include that patch into avogadro
Comment by Hector Mtz-Seara Monne (hseara) - Wednesday, 17 November 2010, 13:29 GMT
Sorry, I think I confused the patch. In the following link you can find the correct one:

http://gold.cryos.net:8080/#change,299

This patch has already been applied to the master. But until a new release appear no chance.
Comment by Andrea Scarpino (BaSh) - Wednesday, 17 November 2010, 14:26 GMT
that link does not work. The last patch applied in avogadro is https://github.com/cryos/avogadro/commit/c3e2e3cba551de8c512c3f38e3b495b031cb0f9b
and we already applied it in our package
Comment by K. Takacs (silent) - Wednesday, 17 November 2010, 15:16 GMT
The last link from hseara works now and that patch appears to be the solution. I have not built it yet.
Comment by Andrea Scarpino (BaSh) - Wednesday, 17 November 2010, 15:47 GMT
ok now it works and........we already have that patch in our package!
Comment by Eskil Andersen (eskil) - Saturday, 20 November 2010, 04:51 GMT
I still get this when trying to run, and I just did full update:

The _C_API object in the sip python module is invalid.
Could not initialize SIP API !
terminate called after throwing an instance of 'boost::python::error_already_set'
Comment by Hector Mtz-Seara Monne (hseara) - Tuesday, 23 November 2010, 14:01 GMT
The patch applied for correcting SIP version is different from the one in the upstream. The patch applied in the upstream can be found in:
http://gold.cryos.net:8080/#change,299

Only one file has to be changed: avogadro/src/python/sip.cpp. No patch is needed for cmake/modules/PythonDeps.cmake.
Comment by Xyne (Xyne) - Saturday, 18 December 2010, 04:23 GMT
What's going on with this? Are we waiting for an upstream fix?
I tried to look for a working patch on gold.cryos.net but the site takes several minutes to load a nearly empty page.

Considering that the package is completely unusable because of this, perhaps the severity should be higher than "low". ;)
Comment by Xyne (Xyne) - Saturday, 18 December 2010, 04:42 GMT
Here's the Fedora bug report and an apparently working patch:
https://bugzilla.redhat.com/show_bug.cgi?id=642248

I applied the patch but the build fails:

[ 95%] Building CXX object avogadro/src/CMakeFiles/avogadro-app.dir/qrc_avogadro.cxx.o
Linking CXX executable ../../bin/avogadro
[ 95%] Built target avogadro-app
make: *** [all] Error 2
Aborting...
Comment by Andrea Scarpino (BaSh) - Saturday, 18 December 2010, 11:52 GMT
  • Field changed: Category (Packages: Extra → Upstream Bugs)
  • Field changed: Severity (Low → High)
still no fix from upstream...
Comment by K. Takacs (silent) - Saturday, 18 December 2010, 12:35 GMT

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