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.
Cheers
Derek
===============================
Derek McPhee
Information Services
Queen's University Belfast
e-mail da.mcphee at qub.ac.uk
Tel 028 90973840
Fax 028 90975066
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. >
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