[ESS-bugs] ess-mode 5.1.24; beginning of function regexp confused

Stephen Eglen stephen at inf.ed.ac.uk
Fri Oct 3 13:53:31 CEST 2003 

Hi,

Just found this small problem, but didn't think it major enough to
work on right now, so would file it is a bug for "some day later".

Put the R function below in an R buffer; then go to the closing brace
at the end of the function and do M-x ess-beginning-of-function
Instead of going to the top of the function, it goes back to the line:
  #     score.k <- function(k) {

contained within the function.

Stephen
----------------------------------------------------------------------
Kenv.tor1 <- function (pts1, pts2, poly, nsim, s, quiet = FALSE, soma=NULL) 
{

  ## This function adapted from Kenv.tor in splancs library.
  ## This allows us to compute u for each simulation.
  
    rect <- bbox(poly)
    kmax <- rep(0, length = length(s))
    kmin <- rep(1e+34, length = length(s))

    theor <- pi * (s^2)

    ## Equation for u from Diggle (1986)
    score.k <- function(k) { sum( ( sqrt(k) - sqrt(theor))^2) }

    ## Equation for u from Diggle (2002)
    ##score.k <- function(k) { sum( (1/(s^2))* ( k - theor)^2) }

#     score.k <- function(k) {
#       e <- 1:length(k)
#       sum( (1/(s[e]^2))* ( k[e] - theor[e])^2)
#     }
    u <- rep(0, length=nsim+1)
    ## Calculate u for real K12 function.
    k12.real <-  k12hat(pts1, pts2, poly, s)
    u[1] <- score.k(k12.real)

    ## Keep a copy of all the K functions; first row is the K function of
    ## the real data set, then subsequent rows are the simulations.
    ksim <- matrix(0, nrow=nsim+1, ncol=length(k12.real))
    ksim[1,] <- k12.real

    if (!is.null(soma)) {
      ## Find first index of s corresponding to element bigger than soma.
      bigger.soma <- which(s > soma)
      browser()
      stopifnot(length(bigger.soma) >= 1)
      soma.id <- bigger.soma[1]
    }

    soma.rejs <- 0
    for (isim in 1:nsim) {
        if (!quiet) 
            cat("Doing shift ", isim, "/", nsim, "\n")
        pts2 <- rtor.shift(pts2, rect)
        repeat {
          k12sim <- k12hat(pts1, pts2, poly, s);
          if (is.null(soma) || k12sim[soma.id] == 0)
            break
          else
            soma.rejs <- soma.rejs + 1
        }
        kmax <- pmax(kmax, k12sim)
        kmin <- pmin(kmin, k12sim)
        ksim[isim+1,] <- k12sim
        u[isim+1] <- score.k(k12sim)
    }
    list(lower = kmin, upper = kmax,
         real=k12.real, u=u,
         ksim=ksim,
         rank=rank(u)[1],
         soma.rejs=soma.rejs)
}


Emacs  : GNU Emacs 21.3.2 (i686-pc-linux-gnu, X toolkit, Xaw3d scroll bars)
 of 2003-05-02 on bushmills.inf.ed.ac.uk
Package: ess-mode 5.1.24

current state:
==============
(setq
 ess-language "S"
 ess-dialect "R"
 ess-ask-for-ess-directory nil
 ess-ask-about-transfile nil
 ess-directory nil
 ess-keep-dump-files "always"
 ess-source-directory "/tmp/"
 )
(ess-setq-vars-LOCAL): language=SAS, dialect=SAS, buf=unlikely-name.sas, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=SAS, ess-dialect=SAS buf=unlikely-name.sas 
(ess-mode-1.5): alist=((ess-local-customize-alist quote SAS-customize-alist) (ess-language . SAS) (ess-dialect . SAS) (ess-mode-editing-alist . SAS-editing-alist) (ess-mode-syntax-table . SAS-syntax-table) (inferior-ess-program . inferior-SAS-program-name) (ess-help-sec-regex . ^[A-Z. ---]+:$) (ess-help-sec-keys-alist .  ) (ess-object-name-db-file . ess-sas-namedb.el) (inferior-ess-objects-command . objects(%d)) (inferior-ess-help-command . help("%s",pager="cat",window=F)
) (inferior-ess-exit-command . endsas;
) (ess-loop-timeout . 500000) (inferior-ess-primary-prompt . ^) (inferior-ess-secondary-prompt . ^) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . inferior-SAS-args-temp) (ess-local-process-name)) 
(ess-mode-1.6): editing-alist=((sentence-end . ;[	
 */]*) (paragraph-start . ^[ 	]*$) (paragraph-separate . ^[ 	]*$) (paragraph-ignore-fill-prefix . t) (adaptive-fill-mode) (indent-line-function quote sas-indent-line) (require-final-newline . t) (comment-start . \*\|/\*) (comment-start-skip . \*+) (comment-end . ;\|\*/) (comment-column . 40) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (tab-stop-list . ess-sas-tab-stop-alist) (ess-mode-syntax-table . SAS-syntax-table) (font-lock-keywords-case-fold-search . t) (font-lock-defaults quote (SAS-mode-font-lock-keywords))) 
(ess-setq-vars-LOCAL): language=SAS, dialect=SAS, buf=unlikely-name.sas, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.
[ess-site.el]: ess-customize-alist=((ess-local-customize-alist quote SAS-customize-alist) (ess-language . SAS) (ess-dialect . SAS) (ess-mode-editing-alist . SAS-editing-alist) (ess-mode-syntax-table . SAS-syntax-table) (inferior-ess-program . inferior-SAS-program-name) (ess-help-sec-regex . ^[A-Z. ---]+:$) (ess-help-sec-keys-alist .  ) (ess-object-name-db-file . ess-sas-namedb.el) (inferior-ess-objects-command . objects(%d)) (inferior-ess-help-command . help("%s",pager="cat",window=F)
) (inferior-ess-exit-command . endsas;
) (ess-loop-timeout . 500000) (inferior-ess-primary-prompt . ^) (inferior-ess-secondary-prompt . ^) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . inferior-SAS-args-temp) (ess-local-process-name)) 
[ess-site.el _2_]: ess-customize-alist=((ess-local-customize-alist quote SAS-customize-alist) (ess-language . SAS) (ess-dialect . SAS) (ess-mode-editing-alist . SAS-editing-alist) (ess-mode-syntax-table . SAS-syntax-table) (inferior-ess-program . inferior-SAS-program-name) (ess-help-sec-regex . ^[A-Z. ---]+:$) (ess-help-sec-keys-alist .  ) (ess-object-name-db-file . ess-sas-namedb.el) (inferior-ess-objects-command . objects(%d)) (inferior-ess-help-command . help("%s",pager="cat",window=F)
) (inferior-ess-exit-command . endsas;
) (ess-loop-timeout . 500000) (inferior-ess-primary-prompt . ^) (inferior-ess-secondary-prompt . ^) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . inferior-SAS-args-temp) (ess-local-process-name)) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=independence.r 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.

(R): ess-dialect=R, buf=independence.r, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=Initial, -dialect=nil, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=independence.r
(inf-ess 1.1): procname=R temp-dialect=R, buf-name=*R* 
(inferior-ess) Method #3 start=/home/stephen/mosaics/beta_rgc/diggle_independence/ buf=*R*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(nil,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R*, Proc R, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')

(R): ess-dialect=R, buf=independence.r, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=independence.r
(inf-ess 1.1): procname=R:2 temp-dialect=R, buf-name=*R:2* 
(inferior-ess) Method #3 start=/home/stephen/mosaics/beta_rgc/diggle_independence/ buf=*R:2*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:2*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R:2* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(R,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R:2*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R:2*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:2*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R:2*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R:2*, Proc R:2, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=w78.R, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=w78.R 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=w78.R, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r.Rout, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r.Rout, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r.Rout, comint..echoes=nil, comint..sender=comint-simple-send

(R): ess-dialect=R, buf=*shell*, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=*shell*
(inf-ess 1.1): procname=R:3 temp-dialect=R, buf-name=*R:3* 
(inferior-ess) Method #3 start=~/ buf=*R:3*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:3*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R:3* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(R,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R:3*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R:3*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:3*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R:3*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R:3*, Proc R:3, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalizeQuantiles)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](4.Normalization)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalizeWithinArrays)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalize)*, comint..echoes=nil, comint..sender=comint-simple-send

(R): ess-dialect=R, buf=*shell*, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=*shell*
(inf-ess 1.1): procname=R:3 temp-dialect=R, buf-name=*R:3* 
(inferior-ess) Method #3 start=~/ buf=*R:3*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:3*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R:3* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(R:3,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R:3*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R:3*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:3*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R:3*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R:3*, Proc R:3, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalizeQuantiles)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-help-bogus-buffer-p *help[R:3](normalizeQuantiles)*) |--> nil [searching t]
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=onoff.R, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=onoff.R 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=onoff.R, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.

(R): ess-dialect=R, buf=onoff.R, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=onoff.R
(inf-ess 1.1): procname=R:3 temp-dialect=R, buf-name=*R:3* 
(inferior-ess) Method #3 start=/home/stephen/proj/rgc-genechip/sep26.2003/ buf=*R:3*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:3*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R:3* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(R:3,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R:3*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R:3*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R:3*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R:3*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R:3*, Proc R:3, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](count.fields)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](read.table)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalizeQuantiles)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-help-bogus-buffer-p *help[R:3](normalizeQuantiles)*) |--> nil [searching t]
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalizeBetweenArrays)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalize)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-help-bogus-buffer-p *help[R:3](normalize)*) |--> 14 [searching t]
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](normalize.AffyBatch)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=limma.R, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=limma.R 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=limma.R, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R:3](mean)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=onoff.R, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=onoff.R 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=onoff.R, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.

(R): ess-dialect=R, buf=*shell*, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=*shell*
(inf-ess 1.1): procname=R temp-dialect=R, buf-name=*R* 
(inferior-ess) Method #3 start=~/datastore/compiles/emacs/ buf=*R*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(R:3,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R*, Proc R, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R](shapiro.test)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R](truehist)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R](truehist)*, comint..echoes=nil, comint..sender=comint-simple-send
(ess-help-bogus-buffer-p *help[R](truehist)*) |--> 14 [searching t]
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=onoff.R, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=onoff.R 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=onoff.R, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r, comint..echoes=nil, comint..sender=comint-simple-send
(ess-mode-1): ess-language=S, ess-dialect=R buf=independence.r 
(ess-mode-1.5): alist=((ess-local-customize-alist quote R-customize-alist) (ess-language . S) (ess-dialect . R) (ess-suffix . R) (ess-loop-timeout . 500000) (ess-dump-filename-template concat (user-login-name) .%s. ess-suffix) (ess-mode-editing-alist . S-editing-alist) (ess-mode-syntax-table . S-syntax-table) (ess-help-sec-regex . ess-help-R-sec-regex) (ess-help-sec-keys-alist . R-help-sec-keys-alist) (ess-object-name-db-file . ess-r-namedb.el) (ess-retr-lastvalue-command . assign(".Last.value", .ess.lvsave, envir=NULL)
) (ess-save-lastvalue-command . assign(".ess.lvsave",.Last.value,inherits=TRUE)
) (ess-imenu-mode-function quote ess-imenu-R) (inferior-ess-program . inferior-R-program-name) (inferior-ess-objects-command . objects(pos = %d)
) (inferior-ess-search-list-command . search()
) (inferior-ess-help-command . help("%s", htmlhelp=FALSE)
) (inferior-ess-exit-command . q()) (inferior-ess-exit-prompt . Save workspace image? [y/n/c]: ) (inferior-ess-primary-prompt . \([A-Z][][A-Za-z0-9.]*\)*> ) (inferior-ess-secondary-prompt . + ?) (comint-use-prompt-regexp-instead-of-fields . t) (inferior-ess-start-file) (inferior-ess-start-args . ) (ess-STERM . iESS) (ess-editor . R-editor) (ess-pager . R-pager) (inferior-ess-language-start eval inferior-S-language-start)) 
(ess-mode-1.6): editing-alist=((paragraph-start concat ^$\| page-delimiter) (paragraph-separate concat ^$\| page-delimiter) (paragraph-ignore-fill-prefix . t) (require-final-newline . t) (comment-start . #) (comment-start-skip . #+ *) (comment-column . 40) (indent-line-function quote S-indent-line) (parse-sexp-ignore-comments . t) (ess-set-style . ess-default-style) (ess-local-process-name) (ess-mode-syntax-table . S-syntax-table) (add-log-current-defun-header-regexp . ^\(.+\)\s-+<-[ 	
]*function) (font-lock-defaults quote (ess-mode-font-lock-keywords nil nil ((46 . w))))) 
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=independence.r, comint..echoes=nil, comint..sender=comint-simple-send

Finished setting up ESS-mode.

(R): ess-dialect=R, buf=independence.r, start-arg=nil
 current-prefix-arg=nil
(inferior-ess 0): ess-start-args=--no-readline  
ess-setq-vars-default 0: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
ess-setq-vars-default 1: ess-language=S, -dialect=R, buf=*ESS*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 1): lang=S, dialect=R, tmp-dialect=R, buf=independence.r
(inf-ess 1.1): procname=R temp-dialect=R, buf-name=*R* 
(inferior-ess) Method #3 start=/home/stephen/mosaics/beta_rgc/diggle_independence/ buf=*R*
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R*, comint..echoes=nil, comint..sender=comint-simple-send
(inf-ess 2.1): ess-language=S, ess-dialect=R buf=*R* 
(inf-ess 2.2): start args = --no-readline , inf-ess-start-args=--no-readline  
(inf-ess finish [S(R), R(R,nil)]
(ess-multi 0):  inf-ess-start-args=--no-readline , comint-..echoes=nil
(i-ess 1): buf=*R*, lang=S, comint..echo=nil, comint..sender=comint-simple-send,
(i-ess 2): buf=*R*, lang=S, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*R*, comint..echoes=t, comint..sender=inferior-R-input-sender
(i-ess 3): curr-buf=*R*, comint..echo=t, comint..sender=inferior-R-input-sender,
(ess-multi post inf-ess: start-args=--no-readline , comint-echoes=t
(ess-multi 1):  start-args=--no-readline  
Making Process...Buf *R*, Proc R, Prog R
 Start File=nil, Args= --no-readline .
(R): inferior-ess-language-start=options(STERM='iESS', editor='emacsclient')
(ess-setq-vars-LOCAL): language=S, dialect=R, buf=*help[R](while)*, comint..echoes=nil, comint..sender=comint-simple-send

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