Re: [O] Trouble evaluating R source code blocks with C-c C-c

[Vikas Rawal]

Thanks.

The code still seems to freeze.

The backtrace now is.

Debugger entered--Lisp error: (quit)
  process-send-string(#<process R> 
".ess.eval(\"lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg.1\nlibrary(car)\nlibrary(lmtest)\nlibrary(sandwich)\ncov1
         <- vcovHC(reg, type = \\\"HC1\\\")\nrobust_se    <- 
sqrt(diag(cov1))\n\ncov2         <- vcovHC(reg.1, type = 
\\\"HC1\\\")\nrobust_se2    <- sqrt(diag(cov2))\n                               
         # Adjust F statistic\nwald_results <- waldtest(reg, vcov = 
cov1)\nwald_results2 <- waldtest(reg.1, vcov = cov2)\n\n                        
                #coeftest(reg, vcov = hccm)->reg2\noptions(scipen = 
999)\nlibrary(stargazer)\nstargazer(reg.1,reg,\n          align=TRUE,\n         
 title=\\\"Regression of per capita calorie intake with monthly per capita 
consumer expenditure, and demographic and other socio-economic variables\\\",\n 
         dep.var.labels = c(\\\"Per capita calorie intake\\\",\\\"Log of per 
capita calorie intake\\\"),\n          se=list(NULL,robust_se,robust_se2),\n    
      omit=\\\"state\\\",\n          model.numbers=FALSE,\n          report = 
\\\"vct*\\\",\n          single.row=TRUE,\n          omit.labels = \\\"State 
and region dummies\\\")\", visibly = FALSE, output = TRUE, file = 
'/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/unknown!53134yFm')\n")
  ess-send-string--fallback(#<process R> 
".ess.eval(\"lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg.1\nlibrary(car)\nlibrary(lmtest)\nlibrary(sandwich)\ncov1
         <- vcovHC(reg, type = \\\"HC1\\\")\nrobust_se    <- 
sqrt(diag(cov1))\n\ncov2         <- vcovHC(reg.1, type = 
\\\"HC1\\\")\nrobust_se2    <- sqrt(diag(cov2))\n                               
         # Adjust F statistic\nwald_results <- waldtest(reg, vcov = 
cov1)\nwald_results2 <- waldtest(reg.1, vcov = cov2)\n\n                        
                #coeftest(reg, vcov = hccm)->reg2\noptions(scipen = 
999)\nlibrary(stargazer)\nstargazer(reg.1,reg,\n          align=TRUE,\n         
 title=\\\"Regression of per capita calorie intake with monthly per capita 
consumer expenditure, and demographic and other socio-economic variables\\\",\n 
         dep.var.labels = c(\\\"Per capita calorie intake\\\",\\\"Log of per 
capita calorie intake\\\"),\n          se=list(NULL,robust_se,robust_se2),\n    
      omit=\\\"state\\\",\n          model.numbers=FALSE,\n          report = 
\\\"vct*\\\",\n          single.row=TRUE,\n          omit.labels = \\\"State 
and region dummies\\\")\", visibly = FALSE, output = TRUE, file = 
'/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/unknown!53134yFm')\n" nil 
"Eval buffer")
  ess-send-string(#<process R> 
".ess.eval(\"lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg.1\nlibrary(car)\nlibrary(lmtest)\nlibrary(sandwich)\ncov1
         <- vcovHC(reg, type = \\\"HC1\\\")\nrobust_se    <- 
sqrt(diag(cov1))\n\ncov2         <- vcovHC(reg.1, type = 
\\\"HC1\\\")\nrobust_se2    <- sqrt(diag(cov2))\n                               
         # Adjust F statistic\nwald_results <- waldtest(reg, vcov = 
cov1)\nwald_results2 <- waldtest(reg.1, vcov = cov2)\n\n                        
                #coeftest(reg, vcov = hccm)->reg2\noptions(scipen = 
999)\nlibrary(stargazer)\nstargazer(reg.1,reg,\n          align=TRUE,\n         
 title=\\\"Regression of per capita calorie intake with monthly per capita 
consumer expenditure, and demographic and other socio-economic variables\\\",\n 
         dep.var.labels = c(\\\"Per capita calorie intake\\\",\\\"Log of per 
capita calorie intake\\\"),\n          se=list(NULL,robust_se,robust_se2),\n    
      omit=\\\"state\\\",\n          model.numbers=FALSE,\n          report = 
\\\"vct*\\\",\n          single.row=TRUE,\n          omit.labels = \\\"State 
and region dummies\\\")\", visibly = FALSE, output = TRUE, file = 
'/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/unknown!53134yFm')\n" nil 
"Eval buffer")
  ess-tracebug-send-region(#<process R> 1 1183 nil "Eval buffer" buffer)
  ess-send-region(#<process R> 1 1183 nil "Eval buffer" buffer)
  ess-eval-region(1 1183 nil "Eval buffer" buffer)
  ess-eval-buffer(nil)
  org-babel-R-evaluate-session("type2" 
"lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg.1\nlibrary(car)\nlibrary(lmtest)\nlibrary(sandwich)\ncov1
         <- vcovHC(reg, type = \"HC1\")\nrobust_se    <- 
sqrt(diag(cov1))\n\ncov2         <- vcovHC(reg.1, type = \"HC1\")\nrobust_se2   
 <- sqrt(diag(cov2))\n                                        # Adjust F 
statistic\nwald_results <- waldtest(reg, vcov = cov1)\nwald_results2 <- 
waldtest(reg.1, vcov = cov2)\n\n                                        
#coeftest(reg, vcov = hccm)->reg2\noptions(scipen = 
999)\nlibrary(stargazer)\nstargazer(reg.1,reg,\n          align=TRUE,\n         
 title=\"Regression of per capita calorie intake with monthly per capita 
consumer expenditure, and demographic and other socio-economic variables\",\n   
       dep.var.labels = c(\"Per capita calorie intake\",\"Log of per capita 
calorie intake\"),\n          se=list(NULL,robust_se,robust_se2),\n          
omit=\"state\",\n          model.numbers=FALSE,\n          report = \"vct*\",\n 
         single.row=TRUE,\n          omit.labels = \"State and region 
dummies\")" value ("replace" "scalar" "latex") nil nil)
  org-babel-R-evaluate("type2" 
"lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg.1\nlibrary(car)\nlibrary(lmtest)\nlibrary(sandwich)\ncov1
         <- vcovHC(reg, type = \"HC1\")\nrobust_se    <- 
sqrt(diag(cov1))\n\ncov2         <- vcovHC(reg.1, type = \"HC1\")\nrobust_se2   
 <- sqrt(diag(cov2))\n                                        # Adjust F 
statistic\nwald_results <- waldtest(reg, vcov = cov1)\nwald_results2 <- 
waldtest(reg.1, vcov = cov2)\n\n                                        
#coeftest(reg, vcov = hccm)->reg2\noptions(scipen = 
999)\nlibrary(stargazer)\nstargazer(reg.1,reg,\n          align=TRUE,\n         
 title=\"Regression of per capita calorie intake with monthly per capita 
consumer expenditure, and demographic and other socio-economic variables\",\n   
       dep.var.labels = c(\"Per capita calorie intake\",\"Log of per capita 
calorie intake\"),\n          se=list(NULL,robust_se,robust_se2),\n          
omit=\"state\",\n          model.numbers=FALSE,\n          report = \"vct*\",\n 
         single.row=TRUE,\n          omit.labels = \"State and region 
dummies\")" value ("replace" "scalar" "latex") nil nil)
  
org-babel-execute:R("lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg.1\nlibrary(car)\nlibrary(lmtest)\nlibrary(sandwich)\ncov1
         <- vcovHC(reg, type = \"HC1\")\nrobust_se    <- 
sqrt(diag(cov1))\n\ncov2         <- vcovHC(reg.1, type = \"HC1\")\nrobust_se2   
 <- sqrt(diag(cov2))\n                                        # Adjust F 
statistic\nwald_results <- waldtest(reg, vcov = cov1)\nwald_results2 <- 
waldtest(reg.1, vcov = cov2)\n\n                                        
#coeftest(reg, vcov = hccm)->reg2\noptions(scipen = 
999)\nlibrary(stargazer)\nstargazer(reg.1,reg,\n          align=TRUE,\n         
 title=\"Regression of per capita calorie intake with monthly per capita 
consumer expenditure, and demographic and other socio-economic variables\",\n   
       dep.var.labels = c(\"Per capita calorie intake\",\"Log of per capita 
calorie intake\"),\n          se=list(NULL,robust_se,robust_se2),\n          
omit=\"state\",\n          model.numbers=FALSE,\n          report = \"vct*\",\n 
         single.row=TRUE,\n          omit.labels = \"State and region 
dummies\")" ((:colname-names) (:rowname-names) (:result-params "replace" 
"scalar" "latex") (:result-type . value) (:comments . "") (:shebang . "") 
(:cache . "no") (:padline . "") (:noweb . "no") (:tangle . "no") (:exports . 
"results") (:results . "replace scalar latex") (:hlines . "no") (:session . 
"type2")))
  org-babel-execute-src-block(nil)
  org-babel-execute-src-block-maybe()
  org-babel-execute-maybe()
  org-babel-execute-safely-maybe()
  run-hook-with-args-until-success(org-babel-execute-safely-maybe)
  org-ctrl-c-ctrl-c(nil)
  call-interactively(org-ctrl-c-ctrl-c nil nil)
  command-execute(org-ctrl-c-ctrl-c)



> On 30-May-2016, at 6:48 am, Charles C. Berry <address@hidden> wrote:
> 
> On Sun, 29 May 2016, Vikas Rawal wrote:
> 
>> 
>>> 
>>> Vikas, can you edit the `sit-for' to `sleep-for' in
>>> 
>>> `org-babel-comint-eval-invisibly-and-wait-for-file'
>>> 
>>> and `eval-defun' the result and see if that has any effect?
>>> 
>> 
> 
>> Sorry, given my limited ability with lisp, I do not really
>> understand. Could you please spell out what do I have to do.
> 
> Vikas,
> 
> Copy the src-block at bottom to a *.org file or org-mode buffer. Then
> execute it with `C-c C-c y'.
> 
> You should see
> 
> #+RESULTS:
> : org-babel-comint-eval-invisibly-and-wait-for-file
> 
> appear afterwards.
> 
> Then try running your R code to see if it works reliably.
> 
> Does that seem to fix it?
> 
> If not, please check the session buffer to see if there were any
> warnings or errors.
> 
> Chuck
> 
> 
> #+BEGIN_SRC emacs-lisp
> (defun org-babel-comint-eval-invisibly-and-wait-for-file
>  (buffer file string &optional period)
>    "Evaluate STRING in BUFFER invisibly.
> Don't return until FILE exists.  Code in STRING must ensure that
> FILE exists at end of evaluation."
>  (unless (org-babel-comint-buffer-livep buffer)
>      (error "Buffer %s does not exist or has no process" buffer))
>        (if (file-exists-p file) (delete-file file))
>   (process-send-string
>      (get-buffer-process buffer)
>         (if (= (aref string (1- (length string))) ?\n) string (concat string 
> "\n")))
>    ;; From Tramp 2.1.19 the following cache flush is not necessary
>      (if (file-remote-p default-directory)
>              (with-parsed-tramp-file-name default-directory nil
>                 (tramp-flush-directory-property v "")))
>            (while (not (file-exists-p file)) (sleep-for (or period 0.25))))
> 
> #+END_SRC