Re: [R] FW: R

From: Ricky Rankin <r.rankin_at_qub.ac.uk>
Date: Mon, 21 May 2007 13:35:34 +0100

AJ,

Can you test and let us know if this is OK

Ricky



Principal Analyst
Information Services
Queen's University Belfast
 
tel: 02890 974824
fax: 02890 976586
email: r.rankin_at_qub.ac.uk

-----Original Message-----
From: Da.McPhee_at_Queens-Belfast.AC.UK [mailto:Da.McPhee_at_Queens-Belfast.AC.UK] Sent: 21 May 2007 12:41
To: Peter Dalgaard
Cc: Da.McPhee_at_Queens-Belfast.AC.UK; Dr. A. J. McKnight; r-help_at_stat.math.ethz.ch; Ricky Rankin Subject: Re: [R] FW: R

Hi All

I think I've now got this working on XC cluster. Latest version 2.5.0.

Just type R.

man R for man pages.

Cheers

Derek

On Dec 11 2006, Peter Dalgaard wrote:

> Da.McPhee_at_Queens-Belfast.AC.UK wrote:
> > Hi Ricky / AJ
> >
> > Progress of sorts. I got passed the last problem by looking at the
> > makefiles but run in to the next one, see below.
> >
> > It has created files in /contrib/R-2.4.0. there is an " R " under
> > /contrib/R-2.4.0/bin/R.
> >
> > Running it gives :-
> >
> >
> > /contrib/R-2.4.0/bin/R
> >
> > R version 2.4.0 (2006-10-03)
> > Copyright (C) 2006 The R Foundation for Statistical Computing
> > ISBN 3-900051-07-0
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> >
> > *** caught segfault ***
> > address 40b843f0, cause 'memory not mapped'
> >
> > Traceback:
> > 1: .Call("La_dgesv", a, b, tol, PACKAGE = "base")
> > 2: solve.default(rgb)
> > 3: solve(rgb)
> > 4: drop(whitexyz %*% solve(rgb))
> > 5: make.rgb(red = c(0.625, 0.34), green = c(0.28, 0.595), blue =
> > c(0.155, 0.07), gamma = 1.8, white = "D65", name = "Apple RGB")
> > 6: eval(expr, envir, enclos)
> > 7: eval(i, envir)
> > 8: sys.source(codeFile, env, keep.source = keep.source)
> > 9: try(sys.source(codeFile, env, keep.source = keep.source)) 10:
> > loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
> > keep.source) 11: try({ ns <- loadNamespace(package, c(which.lib.loc,
> > lib.loc), keep.source = keep.source) dataPath <-
> > file.path(which.lib.loc, package, "data") env <- attachNamespace(ns,
> > pos = pos, dataPath = dataPath)}) 12: library(package, lib.loc =
> > lib.loc, character.only = TRUE, logical = TRUE, warn.conflicts =
> > warn.conflicts, keep.source = keep.source, version = version) 13:
> > require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only =
> > TRUE, save = FALSE) 14: .First.sys()
> >
> > Possible actions:
> > 1: abort (with core dump)
> > 2: normal R exit
> > 3: exit R without saving workspace
> > 4: exit R saving workspace
> > Selection: 14
> > aborting ...
> > Segmentation fault (core dumped)
> >
> > The make command fails with :-
> >
> > make[4]: Leaving directory `/contrib/R-2.4.0/src/library/grDevices/src'
> >
> > *** caught segfault ***
> > address 4084b2f0, cause 'memory not mapped'
> >
> > Traceback:
> > 1: .Call("La_dgesv", a, b, tol, PACKAGE = "base")
> > 2: solve.default(rgb)
> > 3: solve(rgb)
> > 4: drop(whitexyz %*% solve(rgb))
> > 5: make.rgb(red = c(0.625, 0.34), green = c(0.28, 0.595), blue =
> > c(0.155, 0.07), gamma = 1.8, white = "D65", name = "Apple RGB")
> > 6: eval(expr, envir, enclos)
> > 7: eval(i, envir)
> > 8: sys.source(codeFile, env, keep.source = keep.source)
> > 9: try(sys.source(codeFile, env, keep.source = keep.source)) 10:
> > loadNamespace(package, lib.loc, keep.source, TRUE, TRUE) 11:
> > code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,
> > compress = compress) 12: tools:::makeLazyLoading("grDevices") aborting
> > ... /bin/sh: 18508 Memory fault(coredump) make[3]: *** [all] Error 139
> > make[3]: Leaving directory `/contrib/R-2.4.0/src/library/grDevices'
> > make[2]: *** [R] Error 1 make[2]: Leaving directory
> > `/contrib/R-2.4.0/src/library' make[1]: *** [R] Error 1 make[1]:
> > Leaving directory `/contrib/R-2.4.0/src' make: *** [R] Error 1
> >
> > Do not hold out much hope from mailing list, as they did not answer my
> > last email, but have included it anyway.
> >
> >
> "They" might not have had enough information to go on (and r-devel had
> been a better target). Things like OS and computer versions. (I can't
> seem to find the earlier report though).
>
> Looks like you have broken lapack libraries, so you may want to upgrade
> them or override the selection made during the configure phase.
>
> Make sure to read
> http://cran.r-project.org/doc/manuals/R-admin.html
> and in particular Appendix A3 which discusses some of these issues.
>
> > Cheers
> >
> > Derek
> >
> >
> > ================================
> >
> > Derek McPhee
> > Information Services
> > Queen's University Belfast
> > e-mail da.mcphee_at_qub.ac.uk
> > Tel 028 90973840
> > Fax 028 90975066
> >
> > ______________________________________________
> > R-help_at_stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting
> > guide http://www.R-project.org/posting-guide.html and provide
> > commented, minimal, self-contained, reproducible code.
> >
>
>

-- 
================================

Derek McPhee
Information Services
Queen's University Belfast
e-mail da.mcphee_at_qub.ac.uk
Tel 028 90973840
Fax 028 90975066

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Received on Mon 21 May 2007 - 12:58:01 GMT

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