Menu
▾
▴
#138 NEEDINFO: Rkward crashes when calculating NMDS
---Problem description---
I encountered the error message quoted below. Additionally, I saw the following symptoms:
Please fill in (if applicable)
What - in detail - did you do directly before you encountered this problem?
library(vegan)
metab.pos.root1.concat.mrbayes.nmds <- metaMDS(comm=metab.pos.root1.concat.mrbayes, distance="manhattan", k=2, trymax=10000, engine="monoMDS", autotransform=FALSE, noshare=FALSE, stepacross=FALSE, wascores=FALSE, expand=FALSE, plot=TRUE)
metab.pos.root1.concat.mrbayes has over 14000 columns and 18 rows
When you try to repeat the above, does the problem occur again (no, sometimes, always)?
Always.
If applicable: When doing the same thing in an R session outside of RKWard, do you see the same problem?
RStudio and R console do not produce any output, they just hang.
Do you have any further information that might help us to track this problem down? In particular, if applicable, can you provide sample data and sample R code to reproduce this problem?
No
RKWard is available in many different packagings, and sometimes problems are specific to one method of installation. How did you install RKWard (which file(s) did you download)?
https://build.opensuse.org/package/show?project=devel%3Alanguages%3AR%3Areleased&package=rkward
---Error Message---
Message code: r_engine_has_died
Connection closed unexpectedly. Last error was: QLocalSocket: Remote closed
The R backend will be shut down immediately. This means, you can not use any more functions that rely on it. I.e. you can do hardly anything at all, not even save the workspace (but if you're lucky, R already did that). What you can do, however, is save any open command-files, the output, or copy data out of open data editors. Quit RKWard after that. Sorry!
---Session Info---
RKWard version: 0.6.3
KDE version (runtime): 4.14.6
KDE version (compile time): 4.14.2
Qt build key: x86_64 linux g++-4 full-config
Local KDE directory: /home/vojta/.kde4/
RKWard storage directory: /home/vojta/.rkward/
Backend version (as known to the frontend): 3.2.0
Debug message file (this may contain relevant diagnostic output in case of trouble):
/tmp/rkward.frontend.vrA671
- backend not available or rk.sessionInfo() canceled -
$ cat /tmp/rkward.frontend.vrA671
Object::connect: No such signal KateBuffer::respellCheckBlock(KateDocument,int,int)
Assert 'false' failed at /home/abuild/rpmbuild/BUILD/rkward-0.6.3/rkward/misc/rkstandardicons.cpp - function iconForWindow line 171
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.sheet.binary.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.sheet.binary.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.addin.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.slideshow.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.slideshow.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.sheet.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.sheet.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.presentation.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.presentation.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-word.template.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-word.template.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.template.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-excel.template.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.template.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.template.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-word.document.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-word.document.macroEnabled.12"
rkward(671) KMimeTypeRepository::parents: "/usr/share/mime/subclasses" refers to unknown mimetype "application/vnd.ms-powerpoint.slide.macroEnabled.12"
rkward(671)/kparts KParts::StatusBarExtension::removeStatusBarItem: StatusBarExtension::removeStatusBarItem. Widget not found : QObject(0x0)
rkward(671) KDirWatch::removeFile: doesn't know ""
Object::connect: No such signal KateBuffer::respellCheckBlock(KateDocument,int,int)
Calling appendChild() on a null node does nothing.
Calling appendChild() on a null node does nothing.
Object::connect: No such signal KateBuffer::respellCheckBlock(KateDocument,int,int)
Calling appendChild() on a null node does nothing.
Calling appendChild() on a null node does nothing.
Object::connect: No such signal KateBuffer::respellCheckBlock(KateDocument,int,int)
Calling appendChild() on a null node does nothing.
Calling appendChild() on a null node does nothing.
QPainter::begin: Widget painting can only begin as a result of a paintEvent
QPainter::translate: Painter not active
QPainter::setClipRect: Painter not active
QPainter::font: Painter not active
QPainter::setFont: Painter not active
QPainter::setPen: Painter not active
Assert 'devices.contains (devnum)' failed at /home/abuild/rpmbuild/BUILD/rkward-0.6.3/rkward/rbackend/rkwarddevice/rkgraphicsdevice.cpp - function closeDevice line 119
QCoreApplication::postEvent: Unexpected null receiver
rkward(671)/kparts KParts::StatusBarExtension::removeStatusBarItem: StatusBarExtension::removeStatusBarItem. Widget not found : QObject(0x0)
QProcess: Destroyed while process is still running.
Hi!
Thanks for reporting (and sorry about the long silence).
This does look like an issue in R or package "vegan", then. You may want to report it to the vegan mainainters. Bug tracker appears to be at https://github.com/vegandevs/vegan/issues . While the symptoms are a bit different in RKWard vs. R console (crash vs. hang), this does not indicate a problem in RKWard to me.
If I got you wrong on this, or you have any other particular reason to believe that this should be addressed in RKWard, rather than the package, please just reply. Otherwise, I'll close this report in a few weeks.
Regards
Thomas
It can be problem with vegan, but I wonder why it should crash Rkward... I reported the problem to vegan's developers, I'll see what they think about it.
OK, it was confirmed as vegan bug https://github.com/vegandevs/vegan/issues/152 but still it shouldn't crash whole Rkward, I think...
True. But as far as I understood your report, so far, you are not technically seeing a crash, but rather "only" the message that the R backend has become unavailable.
We can't really do anything about the latter: If package code crashes in the R backend, that means the backend is crahed. (This is more than just a regular error, it's an undefined execution state). What we could do better, is to allow the R backend to be restarted, without having to close the entire session. That's on our TODO list, but it's not something entirely trivial to implement.
Please let me know, if you are actually seeing a crash of the RKWard frontend.
Technically You are right, "just" backend crashes, but practically, You loose Your session and have to restore from backup. So that I vote for that restart feature and I hope to see it soon.
Ok, thanks for the clarification. I'm closing this (specific) issue ticket, then.
Thanks for reporting!