[Bug 775418] New: SuiteSparse does not ship library which contains the symbol SuiteSparse_time
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c0 Summary: SuiteSparse does not ship library which contains the symbol SuiteSparse_time Classification: openSUSE Product: openSUSE 12.2 Version: RC 2 Platform: x86-64 OS/Version: openSUSE 12.2 Status: NEW Severity: Normal Priority: P5 - None Component: Development AssignedTo: bnc-team-screening@forge.provo.novell.com ReportedBy: martin_helm@arcor.de QAContact: qa-bugs@suse.de Found By: --- Blocker: --- User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 A small library libuitesparseconfig which contains several symbols is not shipped in any of the packages related to SuiteSparse. Reproducible: Always Steps to Reproduce: 1. Use the following simple test program #include "suitesparse/umfpack.h" int main () { double stats [2]; umfpack_tic (stats); umfpack_toc (stats); return 0; } and compile it with gcc -o test_umfpack test_umfpack.c -lumfpack -llapack -lamd -lcholmod -lcolamd /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../lib64/libumfpack.so: undefined reference to `SuiteSparse_time' collect2: error: ld returned 1 exit status 2. fetch the source rpm for suitesparse and check in the subdirectory in SuiteSparse/SuiteSparse_config/ which contains the Makefile for libsuitesparseconfig.a and compile that and put it to a valid place 3. Now the test program compiles and works with out error using gcc -o test_umfpack test_umfpack.c -lumfpack -llapack -lamd -lcholmod -lcolamd -lsuitesparseconfig -lrt Actual Results: That also leads to a broken GNU Octave i that it misses all functionality from umfpack and cholmod since the configure checks for it fail during the rpm build (this affects also the octave builds from science for 12.1 and I guess for 11.4 since that does not differ). Expected Results: The small lib with the missing symbols should have been shipped out of the box -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c kk zhang <kkzhang@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |kkzhang@suse.com AssignedTo|bnc-team-screening@forge.pr |dmueller@suse.com |ovo.novell.com | -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c Dirk Mueller <dmueller@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|dmueller@suse.com |i@marguerite.su -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c1 Marguerite Su <i@marguerite.su> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |NEEDINFO InfoProvider| |martin_helm@arcor.de --- Comment #1 from Marguerite Su <i@marguerite.su> 2012-08-13 17:48:42 UTC --- Hi, Martin ------------------------------ check in the subdirectory in SuiteSparse/SuiteSparse_config/ which contains the Makefile for libsuitesparseconfig.a ------------------------------ Do you mean the static lib has it while shared lib not? Can you provide a patch for that? I know it sounds ridiculous, but I'm not a professional coder, I own the package because I'm the first packager and submiter. If it compiles but misses some inner functions, I don't have the ability to tweak that. Or we can drag devel:libraries:c_and_c++ repository maintainers in to see if anything they can do. Thanks for reporting. Marguerite -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c2 Martin Helm <martin_helm@arcor.de> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |martin_helm@arcor.de --- Comment #2 from Martin Helm <martin_helm@arcor.de> 2012-08-14 17:22:13 UTC --- Hi, I can look into it, it should not be difficult to make a patch which creates a small shared lib from the static one. Yes, it is somehow ridiculous that the symbols are only there. Give me two or three days before I submit a patch here since I want to be sure it is a clean solution and I am not available tomorrow. I leave the bug status at needinfo until I submitted the patch. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c3 --- Comment #3 from Marguerite Su <i@marguerite.su> 2012-08-14 20:05:48 UTC --- After some investigation, I think I know how to fix it. SuiteSparse_time symbol is in #ifdef SUITESPARSE_TIMER_ENABLED in SuiteSparse_config/SuiteSparse_config.c line 105. but it's only enabled in such cases: /* determine which timer to use, if any */ #ifndef NTIMER #ifdef _POSIX_C_SOURCE #if _POSIX_C_SOURCE >= 199309L #define SUITESPARSE_TIMER_ENABLED #endif #endif #endif in SuiteSparse_config/SuiteSparse_config.h line 123. So the solution might be: comment off #ifndef NTIMER ( I'm not a developer, I don't know which package or which part of the code provides NTIMER, or if it's a i586 or x86_64 only symbol. And I don't know if _POSIX_C_SOURCE can be cleaned either. Can you help examine that?) and add libSuiteSparse_config_1.so as a new package into suitesparse package. seems some packager (not me) didn't include it at all. basically this lib hasn't been used by Gegl, the only package needs suitesparse in openSUSE(not the science & education derivative) while but only needs libamd and umfpack), so this is not found by packagers. You can review my work at home:MargueriteSu:branches:devel:libraries:c_c++/suitesparse Hope it helps Marguerite -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c4 --- Comment #4 from Marguerite Su <i@marguerite.su> 2012-08-14 20:10:40 UTC --- ------------------------ seems some packager (not me) didn't include it at all. ------------------------ I mean in the spec file, packager use a loop to build shared libraries in child directories. but they didn't include directory SuiteSparse_config. which causes a completely missing of every function in SuiteSparse_config.c so even if you change the code inside, you'll still get the error, because the function never got built. Marguerite -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c5 --- Comment #5 from Martin Helm <martin_helm@arcor.de> 2012-08-14 21:09:12 UTC --- Created an attachment (id=502332) --> (http://bugzilla.novell.com/attachment.cgi?id=502332) Diff to ship libsuitesparse.a as part of suitesparse-devel -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c6 --- Comment #6 from Martin Helm <martin_helm@arcor.de> 2012-08-14 21:11:18 UTC --- I will check your change and report back. Btw GNU Octave is now in the oss repository and is affected by that missing symbols. I will use building it as test case. I hope I can do today before I leave. There is of course another solution (which I do not really like) to ship the libsuitesparseconfig.a simply together with suitsparse-devel and not to introduce a runtime dependency on a microscopic .so which also introduces a runtime dependency on a new package which is otherwise never needed. Diff for the spec file attached just to show what I mean. Your solution on the other hand sounds cleaner from a packaging point of view and I think a packager should decide what the right way is, I am just a developer with not to much knowledge about rpm design. So if your change works as expected as a developer I'ld say go for what you proposed. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c7 --- Comment #7 from Martin Helm <martin_helm@arcor.de> 2012-08-14 21:28:11 UTC --- I did now a osc co home:MargueriteSu:branches:devel:libraries:c_c++ suitesparse to get your changes and started a local build, but get an error here [ 74s] ~/rpmbuild/BUILD/SuiteSparse [ 74s] + for dir in AMD BTF CAMD CCOLAMD CHOLMOD COLAMD CSparse CXSparse KLU LDL RBio SPQR SuiteSparse_config UMFPACK [ 74s] + pushd SuiteSparse_config [ 74s] ~/rpmbuild/BUILD/SuiteSparse/SuiteSparse_config ~/rpmbuild/BUILD/SuiteSparse [ 74s] ++ grep -E '^VERSION =' Makefile [ 74s] ++ sed 's:VERSION = ::' [ 74s] + ver=4.0.2 [ 74s] + pushd Lib [ 74s] /var/tmp/rpm-tmp.u7cFPg: line 33: pushd: Lib: No such file or directory [ 74s] error: Bad exit status from /var/tmp/rpm-tmp.u7cFPg (%build) [ 74s] [ 74s] [ 74s] RPM build errors: [ 74s] Bad exit status from /var/tmp/rpm-tmp.u7cFPg (%build) The buildroot was: /var/tmp/build-root -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c8 --- Comment #8 from Marguerite Su <i@marguerite.su> 2012-08-15 16:21:20 UTC --- Oh, yes of course it fails. Because last night I just make a patch without modifying specfiles in details. I saw your patch and know what you want, I'd say I'm trying to implement it better In packaging, we'd say static libs are prohibited because of many reasons. even if we have to use it, we create a sub-package named "*-devel-static" to explicitly declares it's a static lib package. If not the guess, we have 4000 packages and numerous libraries, can you know which one needs to be replaced by shared libraries later? and introduce libsuitesparseconfig.a in suitesparse-devel will result a problem that your Octave will "Requires" a -devel package as runtime library. So I introduce a new package named libsuitesparseconfig which has a .so to do that work, actually this package was formerly known as UFConfig. And I also include libsuitesparseconfig.a into -devel-static as a fallback. They're not finished yet. Marguerite -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c9 Marguerite Su <i@marguerite.su> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEEDINFO |RESOLVED InfoProvider|martin_helm@arcor.de | Resolution| |FIXED --- Comment #9 from Marguerite Su <i@marguerite.su> 2012-08-15 17:42:20 UTC --- The problem is fixed in SR130934. install suitesparse-devel and your test file compiles without any problem using: gcc -o test_umfpack test_umfpack.c -lumfpack -llapack -lamd -lcholmod -lcolamd -lsuitesparseconfig -lrt mark bug as fixed. Marguerite -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c10 Marguerite Su <i@marguerite.su> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |REOPENED Resolution|FIXED | --- Comment #10 from Marguerite Su <i@marguerite.su> 2012-08-15 17:45:41 UTC --- We may need to push a maintenance update to 12.2 repository. set NEEDINFO from maintenance@opensuse.org -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c Marguerite Su <i@marguerite.su> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|REOPENED |NEEDINFO InfoProvider| |maintenance@opensuse.org -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c11 --- Comment #11 from Martin Helm <martin_helm@arcor.de> 2012-08-15 18:34:57 UTC --- Thanks, that looks exactly like what is needed and looks clean with the new .so file and rpm. I changed meanwhile the corresponding configure flags needed for an osc build of octave based on your suitesparse changes and post them after validating their correctness to #775567, they are a bit more complicated than the linker flags for the simple example I gave in the beginning and also affect the cholmod linker switches in octave. But that's now a nobrainer. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c12 --- Comment #12 from Marguerite Su <i@marguerite.su> 2012-08-15 18:56:03 UTC --- I'm happy to see you got what you want, XD. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c13 --- Comment #13 from Bernhard Wiedemann <bwiedemann@suse.com> 2012-08-16 07:00:09 CEST --- This is an autogenerated message for OBS integration: This bug (775418) was mentioned in https://build.opensuse.org/request/show/130995 Factory / suitesparse https://build.opensuse.org/request/show/130996 Factory / suitesparse -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c14 --- Comment #14 from Bernhard Wiedemann <bwiedemann@suse.com> 2012-08-16 14:00:15 CEST --- This is an autogenerated message for OBS integration: This bug (775418) was mentioned in https://build.opensuse.org/request/show/131025 Factory / suitesparse -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c15 Benjamin Brunner <bbrunner@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEEDINFO |REOPENED InfoProvider|maintenance@opensuse.org | --- Comment #15 from Benjamin Brunner <bbrunner@suse.com> 2012-08-20 13:55:27 CEST --- Could you do a maintenancerequest with the updated package for 12.2, please. Unfortunately we can't release maintenance-updates atm, but we will prepare the update now and release it as soon as 12.2 is released. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c16 Marguerite Su <i@marguerite.su> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|REOPENED |NEEDINFO InfoProvider| |bbrunner@suse.com --- Comment #16 from Marguerite Su <i@marguerite.su> 2012-08-20 12:28:52 UTC --- Hi, Benjamin, I read our policy on the Portal:Maintenance and found: * an update should not introduce new package dependencies * an update should not introduce new (sub-)packages Actually suitesparse introduces a new sub package and Octave introduce a new package dependency. By the way, the suitesparse and octave didn't fail in 12.2 repo: https://build.opensuse.org/package/show?package=suitesparse&project=openSUSE%3A12.2 https://build.opensuse.org/package/show?package=octave&project=openSUSE%3A12.2 Actually this problem is triggered by a version update of Octave in science repo which also can't be pushed into 12.2 right now due to maintenance policy. Are you sure we still need my fix and Octave maintainers' fix into 12.2? Greetings, Marguerite -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c17 Benjamin Brunner <bbrunner@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- InfoProvider|bbrunner@suse.com |meissner@suse.com --- Comment #17 from Benjamin Brunner <bbrunner@suse.com> 2012-08-20 15:42:50 CEST --- Oh I overlooked the new subpackage in the submission, sorry. Added Marcus Meissner to needinfo for doublecheck the update candidate. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
https://bugzilla.novell.com/show_bug.cgi?id=775418 https://bugzilla.novell.com/show_bug.cgi?id=775418#c18 Marguerite Su <i@marguerite.su> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEEDINFO |RESOLVED InfoProvider|meissner@suse.com | Resolution| |FIXED --- Comment #18 from Marguerite Su <i@marguerite.su> 2013-04-08 12:28:15 UTC --- It's an old time report, no answer from maintenance team. As 12.3 is released, I think we can just have it fixed. -- Configure bugmail: https://bugzilla.novell.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.
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