Opened 11 years ago

Closed 10 years ago

#12201 closed defect (worksforme)

The new R spkg breaks building from source on at least one OS X system.

Reported by: mderickx Owned by: tbd
Priority: major Milestone: sage-duplicate/invalid/wontfix
Component: packages: standard Keywords: r-project
Cc: vbraun, kcrisman, leif Merged in:
Authors: Reviewers: Maarten Derickx
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: Stopgaps:

Status badges

Description (last modified by kcrisman)

On OS X 10.6.8 I cannot install this spkg in sage-4.8.alpha3 (I build the alpha3 from source so the old spkg does install).

Doing

md:sage-4.8.alpha3 maarten$ ./sage -f ../sage-4.8.alpha4/spkg/standard/r-2.14.0.p0.spkg

Hangs as described on: http://pastebin.com/7K7qLMJh

The guilty command is: /Users/maarten/Downloadssage-4.8.alpha3/spkg/build/r-2.14.0.p0/src/bin/exec/R --no-restore --slave --args nextArg--pkglocknextArg--data-compress=xznextArg--byte-compilenextArg-lnextArg../../../librarynextArgMASS.tgz

This was introduced by #12057 since alpha3 builds ok on this setup.


For reference, on other OS X 10.6.8 systems thus far this has not happened. If anyone hears of another, we'd definitely like to know.

Change History (11)

comment:1 Changed 11 years ago by mderickx

@kcrisman: I don't use R myself so the only other R's on my system are R's in other sage installations, but those are not on my path so it should not have an unwanted effect. Since I don't use it, I also don't have any R specific environment variables set of wich I am aware.

@Volker: I tried using dtrace yesterday evening (never used it before), but since it is so extremely flexible I did not find out yet the way to get usefull information about the hanging processes. Any help on wich commands to feed to dtrace is appreciated.

comment:2 Changed 11 years ago by kcrisman

  • Component changed from statistics to packages
  • Dependencies #12057 deleted
  • Description modified (diff)
  • Keywords r-project added
  • Owner changed from amhou to tbd

Thanks, Maarten. No, in this case you definitely shouldn't have one of those problems. It remains possible that there are some other env variables set strangely, but I wouldn't have a clue.

comment:3 Changed 10 years ago by kcrisman

comment:4 Changed 10 years ago by leif

  • Cc leif added

comment:5 Changed 10 years ago by kcrisman

Maarten, is this still an issue? I.e., does Sage build okay? Otherwise we may want to close this.

comment:6 Changed 10 years ago by mderickx

  • Status changed from new to needs_review

I didn't build sage on my laptop for a while (moved most of my sage related stuff to mderickx.nl) so this was a good reminder. Indeed the R spkg doesn't hang anymore. I don't know what changed. Maybe it's the new gcc?

comment:7 Changed 10 years ago by mderickx

  • Status changed from needs_review to positive_review

comment:8 Changed 10 years ago by jdemeyer

  • Milestone changed from sage-5.1 to sage-duplicate/invalid/wontfix
  • Reviewers set to Maarten Derickx

comment:9 follow-up: Changed 10 years ago by leif

Replying to mderickx:

I didn't build sage on my laptop for a while (moved most of my sage related stuff to mderickx.nl) so this was a good reminder. Indeed the R spkg doesn't hang anymore. I don't know what changed. Maybe it's the new gcc?

So this ticket should be changed to "WorksForMe" or whatever?

FWIW, this R spkg keeps segfaulting for me (when byte-compiling the base package) with GCC 4.7.x (FSF 4.7.0 local install or the new optional GCC 4.7.1 spkg) on Ubuntu 10.04.4 x86_64. I don't recall when or which R spkg did install, but presumably some previous definitely did a while ago.

comment:10 in reply to: ↑ 9 Changed 10 years ago by leif

Replying to leif:

Replying to mderickx:

I didn't build sage on my laptop for a while (moved most of my sage related stuff to mderickx.nl) so this was a good reminder. Indeed the R spkg doesn't hang anymore. I don't know what changed. Maybe it's the new gcc?

So this ticket should be changed to "WorksForMe" or whatever?

Ok, I see you just did so.

comment:11 Changed 10 years ago by jdemeyer

  • Resolution set to worksforme
  • Status changed from positive_review to closed
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