Bug 1402549

Summary:	libsbml: FTBFS in Fedora Rawhide
Product:	[Fedora] Fedora	Reporter:	Orion Poplawski <orion>
Component:	libsbml	Assignee:	Zbigniew Jędrzejewski-Szmek <zbyszek>
Status:	CLOSED RAWHIDE	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	unspecified	Docs Contact:
Priority:	unspecified
Version:	rawhide	CC:	anto.trande, zbyszek
Target Milestone:	---
Target Release:	---
Hardware:	Unspecified
OS:	Unspecified
URL:	http://apps.fedoraproject.org/koschei/package/libsbml
Whiteboard:
Fixed In Version:	libsbml-5.14.0-1.fc26	Doc Type:	If docs needed, set a value
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2016-12-09 02:55:20 UTC	Type:	Bug
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:

Description Orion Poplawski 2016-12-07 19:28:22 UTC

Description of problem:
Package libsbml fails to build from source in Fedora Rawhide.

Version-Release number of selected component (if applicable):
5.13.0-5.fc26

Steps to Reproduce:
koji build --scratch f26 libsbml-5.13.0-5.fc26.src.rpm

Additional info:
This package is tracked by Koschei. See:
http://apps.fedoraproject.org/koschei/package/libsbml

https://kojipkgs.fedoraproject.org//work/tasks/159/16780159/build.log

23: Test command: /usr/bin/mono "/builddir/build/BUILD/libSBML-5.13.0-Source/build/src/bindings/csharp/TestRunner.exe" "-d" "/builddir/build/BUILD/libSBML-5.13.0-Source/src/sbml/test/test-data" "-l" "/builddir/build/BUILD/libSBML-5.13.0-Source/build/src/bindings/csharp/libsbmlcsP.dll" "-w" "/builddir/build/BUILD/libSBML-5.13.0-Source/src/bindings/csharp" "-p" "/builddir/build/BUILD/libSBML-5.13.0-Source/build/src/bindings/csharp"
23: Environment variables: 
23:  LD_LIBRARY_PATH=/builddir/build/BUILD/libSBML-5.13.0-Source/build/src/bindings/csharp:/builddir/build/BUILD/libSBML-5.13.0-Source/build/src/bindings/csharp:
23: Test timeout computed to be: 3000
23: LibSBML C# Testrunner
23: =====================
23: Running the tests with: 
23: 	Data Directory:   /builddir/build/BUILD/libSBML-5.13.0-Source/src/sbml/test/test-data
23: 
23: .............................................................................................................................................E..................E.E...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................<!-- Created by foo version bar on 2016-12-07 03:55 with libSBML version 5.13.0. -->
23: .....................................
23: 
23: Total Number of Tests 1854, failures 3
23: 
23: 
23: Error in 'test_ASTNode_create': 
23: ====================
23: Exception of type 'LibSBMLCSTest.math.TestASTNode+AssertionError' was thrown.
23:   at LibSBMLCSTest.math.TestASTNode.assertTrue (System.Boolean condition) [0x0000c] in <a807feec6b9e440b8942aeaf7daad177>:0 
23:   at LibSBMLCSTest.math.TestASTNode.test_ASTNode_create () [0x00028] in <a807feec6b9e440b8942aeaf7daad177>:0 
23:   at (wrapper managed-to-native) System.Reflection.MonoMethod:InternalInvoke (System.Reflection.MonoMethod,object,object[],System.Exception&)
23:   at System.Reflection.MonoMethod.Invoke (System.Object obj, System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00038] in <1fd744d936be4a229b315d57c3b96c68>:0 
23: 
23: 
23: Error in 'test_ASTNode_setCharacter': 
23: ====================
23: Exception of type 'LibSBMLCSTest.math.TestASTNode+AssertionError' was thrown.
23:   at LibSBMLCSTest.math.TestASTNode.assertTrue (System.Boolean condition) [0x0000c] in <a807feec6b9e440b8942aeaf7daad177>:0 
23:   at LibSBMLCSTest.math.TestASTNode.test_ASTNode_setCharacter () [0x002f1] in <a807feec6b9e440b8942aeaf7daad177>:0 
23:   at (wrapper managed-to-native) System.Reflection.MonoMethod:InternalInvoke (System.Reflection.MonoMethod,object,object[],System.Exception&)
23:   at System.Reflection.MonoMethod.Invoke (System.Object obj, System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00038] in <1fd744d936be4a229b315d57c3b96c68>:0 
23: 
23: 
23: Error in 'test_ASTNode_setName': 
23: ====================
23: Exception of type 'LibSBMLCSTest.math.TestASTNode+AssertionError' was thrown.
23:   at LibSBMLCSTest.math.TestASTNode.assertTrue (System.Boolean condition) [0x0000c] in <a807feec6b9e440b8942aeaf7daad177>:0 
23:   at LibSBMLCSTest.math.TestASTNode.test_ASTNode_setName () [0x00106] in <a807feec6b9e440b8942aeaf7daad177>:0 
23:   at (wrapper managed-to-native) System.Reflection.MonoMethod:InternalInvoke (System.Reflection.MonoMethod,object,object[],System.Exception&)
23:   at System.Reflection.MonoMethod.Invoke (System.Object obj, System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00038] in <1fd744d936be4a229b315d57c3b96c68>:0 
23: 
23: 
23/28 Test #23: test_csharp_bindings_full .........***Failed  Required regular expression not found.Regex=[failures 0
]  1.72 sec

The following tests FAILED:
	 23 - test_csharp_bindings_full (Failed)

Comment 1 Antonio T. (sagitter) 2016-12-07 19:30:23 UTC

Reported to upstream: https://sourceforge.net/p/sbml/libsbml/429/

Comment 2 Zbigniew Jędrzejewski-Szmek 2016-12-08 15:26:17 UTC

I now tested with 5.14.0. The result is identical:
http://koji.fedoraproject.org/koji/taskinfo?taskID=16798806

In koji, the tests always fail on i686. So this might be arch-specific.
I'm now building on amd64, and if this succeeds, I'll push the update to git master. If only this one test is failing and only on i686, I think it makes sense to disable it until we figure out a proper fix.

Comment 3 Zbigniew Jędrzejewski-Szmek 2016-12-09 02:55:20 UTC

It builds with that test disabled on i686. It would be nice to fix it properly of course.