Bug 1136388
| Summary: | Segmentation fault during build: ../bin/R --vanilla < ok-errors.R > ok-errors.Rout.fail | ||||||||||
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| Product: | [Fedora] Fedora | Reporter: | Karsten Hopp <karsten> | ||||||||
| Component: | R | Assignee: | David Sommerseth <davids> | ||||||||
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||||||
| Severity: | high | Docs Contact: | |||||||||
| Priority: | medium | ||||||||||
| Version: | 21 | CC: | davids, gustavold, michel, normand, ovasik, tcallawa | ||||||||
| Target Milestone: | --- | ||||||||||
| Target Release: | --- | ||||||||||
| Hardware: | ppc64le | ||||||||||
| OS: | Linux | ||||||||||
| Whiteboard: | |||||||||||
| Fixed In Version: | R-3.1.1-6.fc21 | Doc Type: | Bug Fix | ||||||||
| Doc Text: | Story Points: | --- | |||||||||
| Clone Of: | Environment: | ||||||||||
| Last Closed: | 2014-09-23 05:07:21 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: | |||||||||
| Embargoed: | |||||||||||
| Bug Depends On: | |||||||||||
| Bug Blocks: | 1071880 | ||||||||||
| Attachments: |
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Description
Karsten Hopp
2014-09-02 13:22:39 UTC
I don't have any PPC machines, so this bug is probably going to sit here doing nothing. That said, you might try: * Running the core through gdb and seeing if anything obvious happens there. * Filing a bug with the R upstream (including the core and/or backtrace) Created attachment 934322 [details]
ok-errors.Rout.fail
I did a mock build on a ppc64 guest and failed the same way as above.
I found the following "ok-errors.Rout.fail" file in the tests/ subdir.
as per its comment seems the tests voluntarily tried the limits.
next attachment with gdb
Created attachment 934326 [details]
R_gdb_core_backtrace.log
the attached R_gdb_core_backtrace.log show that core is a concequence of the infinit loop in eval.c that is detected but seems not handled properly.
===
...
#9101 0x00003fff797cf47c in do_begin (call=0x1003732faa8, op=0x100362a4120, args=0x1003732f840, rho=0x1003730c7a8) at eval.c:1633
#9102 0x00003fff797cbfa4 in Rf_eval (e=0x1003732faa8, rho=0x1003730c7a8) at eval.c:629
#9103 0x00003fff797cdadc in Rf_applyClosure (call=<optimized out>, op=<optimized out>, arglist=0x10036298888, rho=<optimized out>, suppliedenv=0x100362cb548) at eval.c:1044
#9104 0x00003fff797cbd44 in Rf_eval (e=0x1003732f878, rho=0x1003732f450) at eval.c:676
#9105 0x00003fff797cf47c in do_begin (call=0x1003732faa8, op=0x100362a4120, args=0x1003732f840, rho=0x1003732f450) at eval.c:1633
#9106 0x00003fff797cbfa4 in Rf_eval (e=0x1003732faa8, rho=0x1003732f450) at eval.c:629
#9107 0x00003fff797cdadc in Rf_applyClosure (call=<optimized out>, op=<optimized out>, arglist=0x10036298888, rho=<optimized out>, suppliedenv=0x100362cb548) at eval.c:1044
#9108 0x00003fff797cbd44 in Rf_eval (e=0x1003732f4f8, rho=0x100362cb510) at eval.c:676
#9109 0x00003fff798034d4 in Rf_ReplIteration (rho=0x100362cb510, savestack=<optimized out>, browselevel=<optimized out>, state=0x3fffd16afb50) at main.c:260
===
tracked upstream by https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15963 (In reply to Tom "spot" Callaway from comment #1) > I don't have any PPC machines, so this bug is probably going to sit here > doing nothing. That said, you might try: Tom, we do have ppc64 systems for that. Please ask on #fedora-ppc or send me your public ssh key. []'s Gustavo The issue is related to the stack being too small when running the ok-errors.R test case. This test will cause an infinite recursion loop, which should be interrupted by R. On x86_64, this works as expected. On ppc64, the stack size needs to be doubled to 16384 (ulimit -s 16384) to be able to run successfully, otherwise the segfault will happen. I'm currently testing ppc64 builds with modifying the ulimit before running 'make check' in the .spec file. Created attachment 938242 [details]
Patch to R.spec file with a fix
R-3.1.1-6.fc21 has been submitted as an update for Fedora 21. https://admin.fedoraproject.org/updates/R-3.1.1-6.fc21 Package R-3.1.1-6.fc21: * should fix your issue, * was pushed to the Fedora 21 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing R-3.1.1-6.fc21' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2014-10948/R-3.1.1-6.fc21 then log in and leave karma (feedback). R-3.1.1-6.fc21 has been pushed to the Fedora 21 stable repository. If problems still persist, please make note of it in this bug report. |