Re: [Rd] invalid regular expression '[a-Z]'
On Wed, Mar 5, 2008 at 11:09 PM, Prof Brian Ripley
<[EMAIL PROTECTED]> wrote:
> On Wed, 5 Mar 2008, Henrik Bengtsson wrote:
>
> > On Wed, Mar 5, 2008 at 6:18 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> >> On 05/03/2008 8:56 PM, Henrik Bengtsson wrote:
> >> > Hi,
> >> >
> >> > just curious, but does anyone know the source/reason of observing the
> >> > following error on OSX but not on WinXP and Linux?
> >>
> >> Presumably in the locale you're using on OSX, "a" < "Z" is false. This
> >> is the ascii sort order used in the C locale. On my Windows box, "a" <
> >> "Z" is true, because it uses the English_Canada.1252 collation order.
> >
> > That's it indeed. The person who first reported the error had
> > sessionInfo() locale
> > 'en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8' and I
> > missed that 'C' in the middle, which I guess his system falls back to
> > if none of the previous ones exist?!?
>
> No. Those are settings for various categories, just as you showed for
> Window. The first setting appears to be LC_COLLATE, but what they mean is
> not documented on the system man page for setlocale.
>
> It's just that MacOS uses C collation order in English locales, even
> though almost everyone else uses aAbB or AaBb (the latter being what the
> English actually use, as do almost all book indices in dialects of
> English). But then there is no surprise that MacOS has to be different
> ... its implementaton of locales is idiosyncratic (to be generous).
>
> Note that even [A-Za-z] is unsafe -- as I recall Z is in the middle of the
> alphabet in Estonian locales. If you want alphabetic characters, use
> [[:alpha:]]. If you want ASCII alphabetic characters, write out the
> ranges as [AB...Zab...z]
>
> E.g. (F8 Linux)
>
> > Sys.setlocale("LC_COLLATE", "et_EE.utf8")
> [1] "et_EE.utf8"
> > paste(sort(c(letters,LETTERS)), collapse="")
> [1] "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsZzTtUuVvWwXxYy"
Alpha and Omega - you said it all.
Thanks for the clarifications.
/Henrik
>
>
> [...]
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Argument "nomatch" matched by multiple actual arguments ... %in% -> match?!?
When I run R CMD check R.oo on R v2.7.0 devel (2008-03-04 r44677) on
WinXP I get the following error while testing examples:
Error in match(x, table, nomatch = 0) :
formal argument "nomatch" matched by multiple actual arguments
Calls: setMethodS3 -> setMethodS3.default -> %in% -> match
Execution halted
How is that even possible with:
> get("%in%")
function (x, table)
match(x, table, nomatch = 0) > 0
All '%in' statements in setMethodS3.default are of kind (foo %in%
bar). The error does not happen if I run the example(Object)
explicitly.
/Henrik
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[Rd] Press delete key three times in R-2.6.1 to get segmentation fault (PR#10892)
Full_Name: Poor Yorick
Version: R-2.6.1
OS: 2.4.21-50.ELhugemem #1 SMP Tue May 8 17:10:31 EDT 2007 i686 i686 i386
GNU/Linux
Submission from: (NULL) (148.168.40.4)
After compiling R-2.6.1 with gcc-4.2.1 pressing the 'delete' key three times in
an interactive session causes R to malfunction, spitting out an infinite stream
of errors. I have also replicated the issue in R-2.5.1:
R version 2.6.1 (2007-11-26)
Copyright (C) 2007 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.
> (HERE I PRESS DELETE KEY 3 TIMES)
*** caught segfault ***
address (nil), cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
*** caught segfault ***
address (nil), cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
*** caught segfault ***
address (nil), cause 'memory not mapped'
( SAME MESSAGE 32 more times )
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Error in structure(list(name = name, exit = NULL, handler = handler,
"tûë" =
`tûë`, :
Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character'
In addition: There were 24 warnings (use warnings() to see them)
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
Error: value of 'SET_CXTAIL' must be a char or NULL, not a 'char'
(REPEATS INFINITELY)
Here is the xev record of a 'delete' key press in my terminal
KeyPress event, serial 20, synthetic NO, window 0xe1,
root 0x3e, subw 0x0, time 443263949, (167,-11), root:(213,54),
state 0x0, keycode 107 (keysym 0x, Delete), same_screen YES,
XLookupString gives 1 bytes: ""
KeyRelease event, serial 20, synthetic NO, window 0xe1,
root 0x3e, subw 0x0, time 443264060, (167,-11), root:(213,54),
state 0x0, keycode 107 (keysym 0x, Delete), same_screen YES,
XLookupString gives 1 bytes: ""
Here are the specs for the gcc that compiled R:
$ gcc -dumpspecs
*asm:
%{v:-V} %{Qy:} %{!Qn:-Qy} %{n} %{T} %{Ym,*} %{Yd,*} %{Wa,*:%*}
*asm_debug:
%{gstabs*:--gstabs}%{!gstabs*:%{g*:--gdwarf2}}
*asm_final:
*asm_options:
%a %Y %{c:%W{o*}%{!o*:-o %w%b%O}}%{!c:-o %d%w%u%O}
*invoke_as:
%{!S:-o %|.s |
as %(asm_options) %|.s %A }
*cpp:
%{posix:-D_POSIX_SOURCE} %{pthread:-D_REENTRANT}
*cpp_options:
%(cpp_unique_options) %1 %{m*} %{std*&ansi&trigraphs} %{W*&pedantic*}
%{w}
%{f*} %{g*:%{!g0:%{!fno-working-directory:-fworking-directory}}} %{O*} %{undef}
%{save-temps:-fpch-preprocess}
*cpp_debug_options:
%{d*}
*cpp_unique_options:
%{C|CC:%{!E:%eGCC does not support -C or -CC without -E}} %{!Q:-quiet}
%{nostdinc*} %{C} %{CC} %{v} %{I*&F*} %{P} %I %{MD:-MD %{!o:%b.d}%{o*:%.d%*}}
%{MMD:-MMD %{!o:%b.d}%{o*:%.d%*}} %{M} %{MM} %{MF*} %{MG} %{MP} %{MQ*} %{MT*}
%{!E:%{!M:%{!MM:%{MD|MMD:%{o*:-MQ %*} %{remap} %{g3:-dD} %{H} %C %{D*&U*&A*}
%{i*} %Z %i %{fmudflap:-D_MUDFLAP -include mf-runtime.h} %{fmudflapth:-D_MUDFLAP
-D_MUDFLAPTH -include mf-runtime.h} %{E|M|MM:%W{o*}}
*trad_capable_cpp:
cc1 -E %{traditional|ftraditional|traditional-cpp:-traditional-cpp}
*cc1:
%(cc1_cpu) %{profile:-p}
*cc1_options:
%{pg:%{fomit-frame-pointer:%e-pg and -fomit-frame-pointer are
incompatible}
Re: [Rd] Press delete key three times in R-2.6.1 to get segmentation (PR#10898)
[EMAIL PROTECTED] wrote: > Full_Name: Poor Yorick > Version: R-2.6.1 > OS: 2.4.21-50.ELhugemem #1 SMP Tue May 8 17:10:31 EDT 2007 i686 i686 i386 > GNU/Linux > Submission from: (NULL) (148.168.40.4) > > > After compiling R-2.6.1 with gcc-4.2.1 pressing the 'delete' key three times > in > an interactive session causes R to malfunction, spitting out an infinite > stream > of errors. I have also replicated the issue in R-2.5.1: You are specifically asked to not report bugs on obsolete versions of R and to check for prior similar reports. R 2.6.2 is the current version. This has been reported previously (over 2 years ago on R version 2.2.1) and was associated with a bug in readline, which is the underlying functionality that handles getting input from the user in the console. Since you are running a 2.4 series kernel, it suggests that you may also be running an older Linux distribution. Be sure that your system is updated, including the readline libraries, the current version of which is 5.2. HTH, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Press delete key three times in R-2.6.1 to get segmentation (PR#10899)
Marc Schwartz wrote: > [EMAIL PROTECTED] wrote: [SNIP] > > This has been reported previously (over 2 years ago on R version 2.2.1) > and was associated with a bug in readline, which is the underlying > functionality that handles getting input from the user in the console. > Sorry about the redundant submission. FWIW, I attempted to do a search on the R Bug Tracking System, but a user interface issue led me to believe that the search had turned up no results. It seems to me that pressing the 'Enter' key when the focus is on the 'Regular Expression' field should activate the 'Select Messages' submit button. However, I believe it activates the 'New Bug Report' button, which led me to believe that no results had been returned. -- Yorick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] parser failed on correct formula (PR#10901)
Full_Name: Vitaly Reshetyuk
Version: 2.6.2
OS: Windows XP SP2
Submission from: (NULL) (92.112.140.118)
> as.formula ("Something~
Ps_1+GIs_1+Es_1+RPs_1+Cs_1+IGs_1+Vs_1+Rs_1+MCs_1+TRs_1+VBs_1+Fs_1+Pd_1+GId_1+Ed_1+RPd_1+Cd_1+IGd_1+Vd_1+Rd_1+MCd_1+TRd_1+VBd_1+Fd_1+Ps_2+GIs_2+Es_2+RPs_2+Cs_2+IGs_2+Vs_2+Rs_2+MCs_2+TRs_2+VBs_2+Fs_2+Pd_2+GId_2+Ed_2+RPd_2+Cd_2+IGd_2+Vd_2+Rd_2+MCd_2+TRd_2+VBd_2+Fd_2+COM1_median+H1_median+H1E_median+H1I_median+H1D_median+H1DI_median+H1DE_median+H1S_median+H1SI_median+H1SE_median+F1_median+F1I_median+F1E_median+F1D_median+F1DI_median+F1DE_median+F1S_median+F1SI_median+F1SE_median+COM2_median+H2_median+H2E_median+H2I_median+H2D_median+H2DI_median+H2DE_median+H2S_median+H2SI_median+H2SE_median+F2_median+F2I_median+F2E_median+F2D_median+F2DI_median+F2DE_median+F2S_median+F2SI_median+F2SE_median+1I_median+D1I_median+S1I_median+2I_median+D2I_median+S2I_median+D1_median+S1_median+D2_median+S2_median+1E_median+D1E_median+S1E_median+2E_median+D2E_median+S2E_median+MCOM1_mean+MH1_mean+MH1D_mean+MH1DI_mean+MH1DE_mean+MH1S_mean+MH1SI_mean+MH1SE_mean+MF1_mean+MF1D_mean+MF1DI_mean+MF1DE_mean+M
F1S_mean
+
+MF1SI_mean+MF1SE_mean+MCOM2_mean+MH2_mean+MH2D_mean+MH2DI_mean+MH2DE_mean+MH2S_mean+MH2SI_mean+MH2SE_mean+MF2_mean+MF2D_mean+MF2DI_mean+MF2DE_mean+MF2S_mean+MF2SI_mean+MF2SE_mean+M1I_mean+MD1I_mean+MS1I_mean+M2I_mean+MD2I_mean+MS2I_mean+MD1_mean+MS1_mean+MD2_mean+MS2_mean+M1E_mean+MD1E_mean+MS1E_mean+M2E_mean+MD2E_mean+MS2E_mean+Pd_1diff+Ps_1diff+Pd_2diff+Ps_2diff+Pd_1Hdiff+Ps_1Hdiff+Pd_2Hdiff+Ps_2Hdiff+MCd_1diff+MCs_1diff+MCd_2diff+MCs_2diff+MCd_1Hdiff+MCs_1Hdiff+MCd_2Hdiff+MCs_2Hdiff+Cd_1diff+Cs_1diff+Cd_2diff+Cs_2diff+Cd_1Hdiff+Cs_1Hdiff+Cd_2Hdiff+Cs_2Hdiff+IGd_1diff+IGs_1diff+IGd_2diff+IGs_2diff+IGd_1Hdiff+IGs_1Hdiff+IGd_2Hdiff+IGs_2Hdiff+TRd_1diff+TRs_1diff+TRd_2diff+TRs_2diff+TRd_1Hdiff+TRs_1Hdiff+TRd_2Hdiff+TRs_2Hdiff+GId_1diff+GIs_1diff+GId_2diff+GIs_2diff+GId_1Hdiff+GIs_1Hdiff+GId_2Hdiff+GIs_2Hdiff+RPd_1diff+RPs_1diff+RPd_2diff+RPs_2diff+RPd_1Fdiff+RPs_1Fdiff+RPd_2Fdiff+RPs_2Fdiff+Fd_1diff+Fs_1diff+Fd_2diff+Fs_2diff+Fd_1Fdiff+Fs_1Fdiff+Fd_2Fdiff+Fs_2Fdiff+Rd_1diff
+Rs_1diff+Rd_2diff+Rs_2diff+Rd_1Fd
+
iff+Rs_1Fdiff+Rd_2Fdiff+Rs_2Fdiff+Vd_1diff+Vs_1diff+Vd_2diff+Vs_2diff+Vd_1Fdiff+Vs_1Fdiff+Vd_2Fdiff+Vs_2Fdiff+VBd_1diff+VBs_1diff+VBd_2diff+VBs_2diff+VBd_1Fdiff+VBs_1Fdiff+VBd_2Fdiff+VBs_2Fdiff+Ed_1diff+Es_1diff+Ed_2diff+Es_2diff+Ed_1Fdiff+Es_1Fdiff+Ed_2Fdiff+Es_2Fdiff+COM_diff+HF_1diff+HFD_1diff+HFS_1diff+HFDI_1diff+HFSI_1diff+HFDE_1diff+HFSE_1diff+HFDS_1diff+HFSD_1diff+HFI_1diff+HFE_1diff+HFDSI_1diff+HFSDI_1diff+HFDSE_1diff+HFSDE_1diff+HF_2diff+HFD_2diff+HFS_2diff+HFDI_2diff+HFSI_2diff+HFDE_2diff+HFSE_2diff+HFDS_2diff+HFSD_2diff+HFI_2diff+HFE_2diff+HFDSI_2diff+HFSDI_2diff+HFDSE_2diff+HFSDE_2diff+HH_diff+HHE_diff+HHI_diff+HHD_diff+HHS_diff+HHDI_diff+HHSI_diff+HHDE_diff+HHSE_diff+FF_diff+FFE_diff+FFI_diff+FFD_diff+FFS_diff+FFDI_diff+FFSI_diff+FFDE_diff+FFSE_diff+HF+HFD+HFS+HFDI+HFSI+HFDE+HFSE+HFDS+HFSD+HFI_1+HFE_1+HFDSI+HFSDI+HFDSE+HFSDE+HH1IE_diff+HH1DIE_diff+HH1SIE_diff+FF1IE_diff+FF1DIE_diff+FF1SIE_diff+1IE_diff+DD1IE_diff+SS1IE_diff+HH2IE_diff+HH2DIE_diff+HH2SIE_diff+FF
2IE_diff+FF2DIE_diff+FF2SIE_diff+2
+
IE_diff+DD2IE_diff+SS2IE_diff+DS_1diff+DS_2diff+DD_diff+DDE_diff+DDI_diff+SS_diff+SSE_diff+SSI_diff+EE_diff+II_diff+HHIE_diff+HHDIE_diff+HHSIE_diff+FFIE_diff+FFDIE_diff+FFSIE_diff+IE_diff+DDIE_diff+SSIE_diff+Pd_1rate+Ps_1rate+Pd_2rate+Ps_2rate+Pd_1Hrate+Ps_1Hrate+Pd_2Hrate+Ps_2Hrate+MCd_1rate+MCs_1rate+MCd_2rate+MCs_2rate+MCd_1Hrate+MCs_1Hrate+MCd_2Hrate+MCs_2Hrate+Cd_1rate+Cs_1rate+Cd_2rate+Cs_2rate+Cd_1Hrate+Cs_1Hrate+Cd_2Hrate+Cs_2Hrate+IGd_1rate+IGs_1rate+IGd_2rate+IGs_2rate+IGd_1Hrate+IGs_1Hrate+IGd_2Hrate+IGs_2Hrate+TRd_1rate+TRs_1rate+TRd_2rate+TRs_2rate+TRd_1Hrate+TRs_1Hrate+TRd_2Hrate+TRs_2Hrate+GId_1rate+GIs_1rate+GId_2rate+GIs_2rate+GId_1Hrate+GIs_1Hrate+GId_2Hrate+GIs_2Hrate+RPd_1rate+RPs_1rate+RPd_2rate+RPs_2rate+RPd_1Frate+RPs_1Frate+RPd_2Frate+RPs_2Frate+Fd_1rate+Fs_1rate+Fd_2rate+Fs_2rate+Fd_1Frate+Fs_1Frate+Fd_2Frate+Fs_2Frate+Rd_1rate+Rs_1rate+Rd_2rate+Rs_2rate+Rd_1Frate+Rs_1Frate+Rd_2Frate+Rs_2Frate+Vd_1rate+Vs_1rate+Vd_2rate+Vs_2rate+Vd_1Frate+Vs_1Frate+
Vd_2Frate+Vs_2Frate+VBd_1rate+VBs_
+
1rate+VBd_2rate+VBs_2rate+VBd_1Frate+VBs_1Frate+VBd_2Frate+VBs_2Frate+Ed_1rate+Es_1rate+Ed_2rate+Es_2rate+Ed_1Frate+Es_1Frate+Ed_2Frate+Es_2Frate+COM_rate+HF_1rate+HFD_1rate+HFS_1rate+HFDI_1rate+HFSI_1rate+HFDE_1rate+HFSE_1rate+HFDS_1rate+HFSD_1rate+HFI_1rate+HFE_1rate+HFDSI_1rate+HFSDI_1rate+HFDSE_1rate+HFSDE_1rate+HF_2rate+HFD_2rate+HFS_2rate+HFDI_2rate+HFSI_2rate+HFDE_2rate+HFSE_2rate+HFDS_2rate+HFSD_2rate+HFI_2rate+HFE_2rate+HFDSI_2rate+HFSDI_2rate+HFDSE_2rate+HFSDE_2rate+HH_rate+HHE_rate+HHI_rate+HHD_rate+HHS_rate+HHDI_rate+HHSI_rate+HHDE_rate+HHSE_rate+FF_rate+FFE_rate+FFI_rate+FFD_rate+FFS_rate+FFDI_rate+FFSI_rate+FFDE_rate+FFSE_rate+HF+HFD+HFS+HFDI+HFSI+HFDE+HFSE+HFDS+HFSD+HFI_1+HFE_1+HFDSI+HFSDI+HFDSE+HFSDE+HH1IE_rate+HH1DIE_rate+HH1SIE_rate+FF1IE_rate+FF1DIE_r
[Rd] apply(x, 2, mean) fails if x is a data frame containing a matrix (PR#10902)
> data <- data.frame(a=1:5, b=I(matrix(6:15,5))) > apply(data, 2, mean) Error in dim(newX) <- c(prod(d.call), d2) : dims [product 10] do not match the length of object [15] --please do not edit the information below-- Version: platform = i386-pc-mingw32 arch = i386 os = mingw32 system = i386, mingw32 status = major = 2 minor = 6.2 year = 2008 month = 02 day = 08 svn rev = 44383 language = R version.string = R version 2.6.2 (2008-02-08) Windows XP (build 2600) Service Pack 2 Locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 Search Path: .GlobalEnv, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, package:methods, Autoloads, package:base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] parser failed on correct formula (PR#10901)
On 3/6/2008 12:25 PM, [EMAIL PROTECTED] wrote:
> Full_Name: Vitaly Reshetyuk
> Version: 2.6.2
> OS: Windows XP SP2
> Submission from: (NULL) (92.112.140.118)
I don't know if your message got messed up on posting, but that
certainly isn't a legal formula. It contains a line break in the middle
of the name "Rd_1Fdiff" at the end of the second line.
If you post it again, could you please insert enough line breaks by hand
so the lines aren't so wide? Or if the wide lines are necessary to
trigger the "bug", code to generate the text (e.g. using paste( ,
collapse="+") would be a lot easier to work with.
Duncan Murdoch
>
>> as.formula ("Something~
> Ps_1+GIs_1+Es_1+RPs_1+Cs_1+IGs_1+Vs_1+Rs_1+MCs_1+TRs_1+VBs_1+Fs_1+Pd_1+GId_1+Ed_1+RPd_1+Cd_1+IGd_1+Vd_1+Rd_1+MCd_1+TRd_1+VBd_1+Fd_1+Ps_2+GIs_2+Es_2+RPs_2+Cs_2+IGs_2+Vs_2+Rs_2+MCs_2+TRs_2+VBs_2+Fs_2+Pd_2+GId_2+Ed_2+RPd_2+Cd_2+IGd_2+Vd_2+Rd_2+MCd_2+TRd_2+VBd_2+Fd_2+COM1_median+H1_median+H1E_median+H1I_median+H1D_median+H1DI_median+H1DE_median+H1S_median+H1SI_median+H1SE_median+F1_median+F1I_median+F1E_median+F1D_median+F1DI_median+F1DE_median+F1S_median+F1SI_median+F1SE_median+COM2_median+H2_median+H2E_median+H2I_median+H2D_median+H2DI_median+H2DE_median+H2S_median+H2SI_median+H2SE_median+F2_median+F2I_median+F2E_median+F2D_median+F2DI_median+F2DE_median+F2S_median+F2SI_median+F2SE_median+1I_median+D1I_median+S1I_median+2I_median+D2I_median+S2I_median+D1_median+S1_median+D2_median+S2_median+1E_median+D1E_median+S1E_median+2E_median+D2E_median+S2E_median+MCOM1_mean+MH1_mean+MH1D_mean+MH1DI_mean+MH1DE_mean+MH1S_mean+MH1SI_mean+MH1SE_mean+MF1_mean+MF1D_mean+MF1DI_mean+MF1DE_mea
n+M
> F1S_mean
> +
> +MF1SI_mean+MF1SE_mean+MCOM2_mean+MH2_mean+MH2D_mean+MH2DI_mean+MH2DE_mean+MH2S_mean+MH2SI_mean+MH2SE_mean+MF2_mean+MF2D_mean+MF2DI_mean+MF2DE_mean+MF2S_mean+MF2SI_mean+MF2SE_mean+M1I_mean+MD1I_mean+MS1I_mean+M2I_mean+MD2I_mean+MS2I_mean+MD1_mean+MS1_mean+MD2_mean+MS2_mean+M1E_mean+MD1E_mean+MS1E_mean+M2E_mean+MD2E_mean+MS2E_mean+Pd_1diff+Ps_1diff+Pd_2diff+Ps_2diff+Pd_1Hdiff+Ps_1Hdiff+Pd_2Hdiff+Ps_2Hdiff+MCd_1diff+MCs_1diff+MCd_2diff+MCs_2diff+MCd_1Hdiff+MCs_1Hdiff+MCd_2Hdiff+MCs_2Hdiff+Cd_1diff+Cs_1diff+Cd_2diff+Cs_2diff+Cd_1Hdiff+Cs_1Hdiff+Cd_2Hdiff+Cs_2Hdiff+IGd_1diff+IGs_1diff+IGd_2diff+IGs_2diff+IGd_1Hdiff+IGs_1Hdiff+IGd_2Hdiff+IGs_2Hdiff+TRd_1diff+TRs_1diff+TRd_2diff+TRs_2diff+TRd_1Hdiff+TRs_1Hdiff+TRd_2Hdiff+TRs_2Hdiff+GId_1diff+GIs_1diff+GId_2diff+GIs_2diff+GId_1Hdiff+GIs_1Hdiff+GId_2Hdiff+GIs_2Hdiff+RPd_1diff+RPs_1diff+RPd_2diff+RPs_2diff+RPd_1Fdiff+RPs_1Fdiff+RPd_2Fdiff+RPs_2Fdiff+Fd_1diff+Fs_1diff+Fd_2diff+Fs_2diff+Fd_1Fdiff+Fs_1Fdiff+Fd_2Fdiff+Fs_2Fdiff+Rd_1d
iff
> +Rs_1diff+Rd_2diff+Rs_2diff+Rd_1Fd
> +
> iff+Rs_1Fdiff+Rd_2Fdiff+Rs_2Fdiff+Vd_1diff+Vs_1diff+Vd_2diff+Vs_2diff+Vd_1Fdiff+Vs_1Fdiff+Vd_2Fdiff+Vs_2Fdiff+VBd_1diff+VBs_1diff+VBd_2diff+VBs_2diff+VBd_1Fdiff+VBs_1Fdiff+VBd_2Fdiff+VBs_2Fdiff+Ed_1diff+Es_1diff+Ed_2diff+Es_2diff+Ed_1Fdiff+Es_1Fdiff+Ed_2Fdiff+Es_2Fdiff+COM_diff+HF_1diff+HFD_1diff+HFS_1diff+HFDI_1diff+HFSI_1diff+HFDE_1diff+HFSE_1diff+HFDS_1diff+HFSD_1diff+HFI_1diff+HFE_1diff+HFDSI_1diff+HFSDI_1diff+HFDSE_1diff+HFSDE_1diff+HF_2diff+HFD_2diff+HFS_2diff+HFDI_2diff+HFSI_2diff+HFDE_2diff+HFSE_2diff+HFDS_2diff+HFSD_2diff+HFI_2diff+HFE_2diff+HFDSI_2diff+HFSDI_2diff+HFDSE_2diff+HFSDE_2diff+HH_diff+HHE_diff+HHI_diff+HHD_diff+HHS_diff+HHDI_diff+HHSI_diff+HHDE_diff+HHSE_diff+FF_diff+FFE_diff+FFI_diff+FFD_diff+FFS_diff+FFDI_diff+FFSI_diff+FFDE_diff+FFSE_diff+HF+HFD+HFS+HFDI+HFSI+HFDE+HFSE+HFDS+HFSD+HFI_1+HFE_1+HFDSI+HFSDI+HFDSE+HFSDE+HH1IE_diff+HH1DIE_diff+HH1SIE_diff+FF1IE_diff+FF1DIE_diff+FF1SIE_diff+1IE_diff+DD1IE_diff+SS1IE_diff+HH2IE_diff+HH2DIE_diff+HH2SIE_diff
+FF
> 2IE_diff+FF2DIE_diff+FF2SIE_diff+2
> +
> IE_diff+DD2IE_diff+SS2IE_diff+DS_1diff+DS_2diff+DD_diff+DDE_diff+DDI_diff+SS_diff+SSE_diff+SSI_diff+EE_diff+II_diff+HHIE_diff+HHDIE_diff+HHSIE_diff+FFIE_diff+FFDIE_diff+FFSIE_diff+IE_diff+DDIE_diff+SSIE_diff+Pd_1rate+Ps_1rate+Pd_2rate+Ps_2rate+Pd_1Hrate+Ps_1Hrate+Pd_2Hrate+Ps_2Hrate+MCd_1rate+MCs_1rate+MCd_2rate+MCs_2rate+MCd_1Hrate+MCs_1Hrate+MCd_2Hrate+MCs_2Hrate+Cd_1rate+Cs_1rate+Cd_2rate+Cs_2rate+Cd_1Hrate+Cs_1Hrate+Cd_2Hrate+Cs_2Hrate+IGd_1rate+IGs_1rate+IGd_2rate+IGs_2rate+IGd_1Hrate+IGs_1Hrate+IGd_2Hrate+IGs_2Hrate+TRd_1rate+TRs_1rate+TRd_2rate+TRs_2rate+TRd_1Hrate+TRs_1Hrate+TRd_2Hrate+TRs_2Hrate+GId_1rate+GIs_1rate+GId_2rate+GIs_2rate+GId_1Hrate+GIs_1Hrate+GId_2Hrate+GIs_2Hrate+RPd_1rate+RPs_1rate+RPd_2rate+RPs_2rate+RPd_1Frate+RPs_1Frate+RPd_2Frate+RPs_2Frate+Fd_1rate+Fs_1rate+Fd_2rate+Fs_2rate+Fd_1Frate+Fs_1Frate+Fd_2Frate+Fs_2Frate+Rd_1rate+Rs_1rate+Rd_2rate+Rs_2rate+Rd_1Frate+Rs_1Frate+Rd_2Frate+Rs_2Frate+Vd_1rate+Vs_1rate+Vd_2rate+Vs_2rate+Vd_1Frate+Vs_1Fra
te+
> Vd_2Frate+Vs_2Frate+VBd_1rate+VBs_
> +
> 1rate+VBd_2rate+VBs_2rate+VBd_1Frate+VBs_1Frate+VBd_2Frate+VBs_2Frate+Ed_1rate+Es_1rate+Ed_2rate+Es_2rate+Ed_1Frate+Es_1Frate+Ed_2Frate+Es_2Frate+COM_rate+HF_1rate+HFD_1rate+HFS_1rate+HFDI_1rate+HFSI_1rate+HFDE_1rate+HFS
[Rd] Memory allocation error in 2.6.2 (PR#10903)
Full_Name: Peter Bosa Version: 2.6.2 OS: RHES 4.2 - 4.5 Submission from: (NULL) (67.138.101.226) I am experiencing a memory allocation error with R 2.6.2 which was not present in previous versions of R (2.4 and 2.2). I have several Linux machines with various Redhat OS versions loaded on them, ranging from 4.2 through 4.5. Each machine has 6 GB of RAM and 2 to 4 GB of virtual memory. The processes I am running include calculations on large matrices (1,015 x 2,029). While the programs are large users of memory, they were stable (i.e. no memory crashes with the earlier versions of R) on all machines. However, running the same programs using R 2.6.2, I consistently get the error message "Cannot allocate vector of size 15.7kb". I am calling the programs with the --max-vsize=3G command...no difference. Using a garbage collection command, I can see that the programs never use more heap than 2.5 GB. And, as stated before, this was not an issue when the same machines were loaded with R 2.4 or 2.2. I have verified that the OS settings are exactly the same as before (unlimited allocation of memory to programs). Also, when I re-install R 2.4, the programs run correctly. I have not been able to test R 2.5 or R 2.6.0, since I cannot find binary packages of these versions, and I have yet to compile the source code. Any thoughts? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Memory allocation error in 2.6.2 (PR#10903)
Before submitting a bug report, it is probably wise to bring it up on r-devel first. Remember, someone has to clean out all those false bug reports manually. There are so many potential reasons for your problem, which indicates fragmented memory allocations. One obvious one is that one of the packages you are using have been updated. In order for anyone to say anything about your problem, the minimum you can do is post your sessionInfo():s. Then maybe one of the authors of those packages reads this and know exactly what is going on. Also, some kind of script is also useful, because maybe it is obvious from your code. You might simply have "been lucky" in previously. My $0.02 /Henrik On Thu, Mar 6, 2008 at 10:10 AM, <[EMAIL PROTECTED]> wrote: > Full_Name: Peter Bosa > Version: 2.6.2 > OS: RHES 4.2 - 4.5 > Submission from: (NULL) (67.138.101.226) > > > I am experiencing a memory allocation error with R 2.6.2 which was not > present > in previous versions of R (2.4 and 2.2). I have several Linux machines with > various Redhat OS versions loaded on them, ranging from 4.2 through 4.5. Each > machine has 6 GB of RAM and 2 to 4 GB of virtual memory. > > The processes I am running include calculations on large matrices (1,015 x > 2,029). While the programs are large users of memory, they were stable (i.e. > no > memory crashes with the earlier versions of R) on all machines. However, > running > the same programs using R 2.6.2, I consistently get the error message "Cannot > allocate vector of size 15.7kb". I am calling the programs with the > --max-vsize=3G command...no difference. Using a garbage collection command, I > can see that the programs never use more heap than 2.5 GB. And, as stated > before, this was not an issue when the same machines were loaded with R 2.4 > or > 2.2. > > I have verified that the OS settings are exactly the same as before > (unlimited > allocation of memory to programs). Also, when I re-install R 2.4, the > programs > run correctly. I have not been able to test R 2.5 or R 2.6.0, since I cannot > find binary packages of these versions, and I have yet to compile the source > code. > > Any thoughts? > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Argument "nomatch" matched by multiple actual arguments ... %in% -> match?!?
Hi,
a follow up. If I replace all 'foo %in% bar' in setMethodS3.default()
with is.element(foo, bar) the error goes away. Here is is.element():
> is.element
function (el, set)
match(el, set, 0) > 0
Not much of a difference compared to "%in%"(),
> get("%in%")
function (x, table)
match(x, table, nomatch = 0) > 0
except that the 'nomatch' argument is not named in is.element().
Also, none of calls used variable names 'x', 'table', 'el', 'set', or
'nomatch'.
/Henrik
On Thu, Mar 6, 2008 at 2:27 AM, Henrik Bengtsson <[EMAIL PROTECTED]> wrote:
> When I run R CMD check R.oo on R v2.7.0 devel (2008-03-04 r44677) on
> WinXP I get the following error while testing examples:
>
> Error in match(x, table, nomatch = 0) :
> formal argument "nomatch" matched by multiple actual arguments
> Calls: setMethodS3 -> setMethodS3.default -> %in% -> match
> Execution halted
>
> How is that even possible with:
>
> > get("%in%")
> function (x, table)
> match(x, table, nomatch = 0) > 0
>
>
> All '%in' statements in setMethodS3.default are of kind (foo %in%
> bar). The error does not happen if I run the example(Object)
> explicitly.
>
> /Henrik
>
__
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[Rd] javareconf (PR#10905)
Full_Name: Vic.Bancroft
Version: 2.6.2
OS: Red Hat Enterprise Linux ES release 4 (Nahant Update 6)
Submission from: (NULL) (66.241.32.158)
Running the script, javareconf, output intended for /dev/null is generating an
error . . .
Here is a patch for the java reconfiguration shell script,
Index: src/scripts/javareconf
===
--- src/scripts/javareconf (revision 44691)
+++ src/scripts/javareconf (working copy)
@@ -230,7 +230,7 @@
done
if test -z "${jmdinc}"; then
# ultima-ratio: use find and pray that it works
- jmdinc=`find "${jinc}/" -name jni_md.h 2>dev/null |head -n 1
2>/dev/null`
+ jmdinc=`find "${jinc}/" -name jni_md.h 2>/dev/null |head -n 1
2>/dev/null`
if test -n "${jmdinc}"; then jmdinc=`dirname "${jmdinc}"`; fi
fi
if test -n "${jmdinc}"; then
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Re: [Rd] Great tool
I believe that codetools is "incredibly usefull", but it is very difficult to learn how to use it... Anythink else thant reading the code available ? For exemple, how to track down free varaible ? I try findGlobals(get(functionNames),FALSE)$variables but it does not work... Christophe Gabor Grothendieck wrote: > > Tracking down the free variables in a function when > reworking old code. > > On Jan 21, 2008 12:41 PM, Charles C. Berry <[EMAIL PROTECTED]> wrote: >> On Sun, 20 Jan 2008, Gabor Grothendieck wrote: >> >> > I agree. Its incredibly useful. >> >> OK gentlemen, you have piqued my curiosity. >> >> Can you give an example or two of situations you encountered in which a >> codetools function was so helpful? >> >> Chuck >> >> >> >> > >> > On Jan 20, 2008 11:02 PM, Henrik Bengtsson <[EMAIL PROTECTED]> >> wrote: >> >> Hi, >> >> >> >> I just have drop a note to say that the 'codetools' (and the part of R >> >> CMD check that use it) is a pleasure to use and saves me from hours of >> >> troubleshooting. Each time it finds something I am amazed how >> >> accurate it is. Thanks to Luke T. and everyone else involved in >> >> creating it. >> >> >> >> Cheers, >> >> >> >> Henrik >> >> >> >> __ >> >> R-devel@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >> > >> > __ >> > R-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > >> >> Charles C. Berry(858) 534-2098 >> Dept of Family/Preventive >> Medicine >> E mailto:[EMAIL PROTECTED] UC San Diego >> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego >> 92093-0901 >> >> >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- View this message in context: http://www.nabble.com/Great-tool-tp14990920p15885369.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
