Note: This is a public test instance of Red Hat Bugzilla. The data contained within is a snapshot of the live data so any changes you make will not be reflected in the production Bugzilla. Email is disabled so feel free to test any aspect of the site that you want. File any problems you find or give feedback at bugzilla.redhat.com.
Bug 1136388
Summary: | Segmentation fault during build: ../bin/R --vanilla < ok-errors.R > ok-errors.Rout.fail | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
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: |
|
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. |