* Trouble evaluating R source code blocks with C-c C-c @ 2016-05-26 14:33 Vikas Rawal 2016-05-26 18:52 ` John Hendy 0 siblings, 1 reply; 14+ messages in thread From: Vikas Rawal @ 2016-05-26 14:33 UTC (permalink / raw) To: org-mode mailing list I face a strange problem with evaluating R source code blocks. Occasionally, they take much longer to produce the results when I try to evaluate them with C-c C-c. On the other hand, if I do C-c ‘, go to a temporary R buffer, and evaluate the code, everything works fine. In face, when I use C-c C-c, the session would sometimes get stuck. Then I have to stop the process using C-g, I find that the code had run in R, but the result was not being inserted in Org buffer. Has anyone else faced this problem? I am on OS-X, Emacs 24, Org-mode version 8.3.4 (release_8.3.4-748-g7e320e, and ess-version: 15.09-devel [elpa: 20150913.638] Vikas ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-26 14:33 Trouble evaluating R source code blocks with C-c C-c Vikas Rawal @ 2016-05-26 18:52 ` John Hendy 2016-05-28 7:58 ` Vikas Rawal 0 siblings, 1 reply; 14+ messages in thread From: John Hendy @ 2016-05-26 18:52 UTC (permalink / raw) To: Vikas Rawal; +Cc: org-mode mailing list Could you give a minimal example? The behavior does ring a bell, but I can't recall what the solution might have been. I'd be happy to try and reproduce if you'd like. I think my typical go-to is to wipe ESS and re-download/make... That's all I'm good for without more info. Sorry! John On Thu, May 26, 2016 at 9:33 AM, Vikas Rawal <vikaslists@agrarianresearch.org> wrote: > I face a strange problem with evaluating R source code blocks. Occasionally, they take much longer to produce the results when I try to evaluate them with C-c C-c. On the other hand, if I do C-c ‘, go to a temporary R buffer, and evaluate the code, everything works fine. In face, when I use C-c C-c, the session would sometimes get stuck. Then I have to stop the process using C-g, I find that the code had run in R, but the result was not being inserted in Org buffer. > > Has anyone else faced this problem? > > I am on OS-X, Emacs 24, Org-mode version 8.3.4 (release_8.3.4-748-g7e320e, and ess-version: 15.09-devel [elpa: 20150913.638] > > Vikas > > > > ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-26 18:52 ` John Hendy @ 2016-05-28 7:58 ` Vikas Rawal 2016-05-28 14:27 ` William Denton 0 siblings, 1 reply; 14+ messages in thread From: Vikas Rawal @ 2016-05-28 7:58 UTC (permalink / raw) To: John Hendy; +Cc: org-mode mailing list Thanks John. Appreciate that you cared to respond to such a vague query. I am at a loss with this one. It does not happen all the time. I think it happens when I am processing large datasets, and CPUs and RAM of my system are struggling to keep up. But I could be wrong. Let me take your advice and upgrade ESS. Hope that would help. Vikas > On 27-May-2016, at 12:22 am, John Hendy <jw.hendy@gmail.com> wrote: > > Could you give a minimal example? The behavior does ring a bell, but I > can't recall what the solution might have been. I'd be happy to try > and reproduce if you'd like. > > I think my typical go-to is to wipe ESS and re-download/make... That's > all I'm good for without more info. > > > Sorry! > John > > On Thu, May 26, 2016 at 9:33 AM, Vikas Rawal > <vikaslists@agrarianresearch.org> wrote: >> I face a strange problem with evaluating R source code blocks. Occasionally, they take much longer to produce the results when I try to evaluate them with C-c C-c. On the other hand, if I do C-c ‘, go to a temporary R buffer, and evaluate the code, everything works fine. In face, when I use C-c C-c, the session would sometimes get stuck. Then I have to stop the process using C-g, I find that the code had run in R, but the result was not being inserted in Org buffer. >> >> Has anyone else faced this problem? >> >> I am on OS-X, Emacs 24, Org-mode version 8.3.4 (release_8.3.4-748-g7e320e, and ess-version: 15.09-devel [elpa: 20150913.638] >> >> Vikas >> >> >> >> ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-28 7:58 ` Vikas Rawal @ 2016-05-28 14:27 ` William Denton 2016-05-28 16:57 ` Charles C. Berry 2016-05-29 2:02 ` Vikas Rawal 0 siblings, 2 replies; 14+ messages in thread From: William Denton @ 2016-05-28 14:27 UTC (permalink / raw) To: Vikas Rawal; +Cc: org-mode mailing list On 28 May 2016, Vikas Rawal wrote: > Thanks John. Appreciate that you cared to respond to such a vague query. I am > at a loss with this one. It does not happen all the time. I think it happens > when I am processing large datasets, and CPUs and RAM of my system are > struggling to keep up. But I could be wrong. I've had the same kind of thing happen---but C-g (sometimes many) to kill the command, then rerunning, usually works without any trouble. Some strange combination of CPU and RAM and all that, the kind of thing that's not easily reproducible. Relatedly, sometimes if I have ":results output" for one block and then ":results values" for the next one, the second block picks up the output from the first one. But then other times not! Seems to depend on how intensive the R work is. Bill -- William Denton :: Toronto, Canada :: https://www.miskatonic.org/ Caveat lector. ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-28 14:27 ` William Denton @ 2016-05-28 16:57 ` Charles C. Berry 2016-05-28 17:01 ` Charles C. Berry 2016-05-29 2:02 ` Vikas Rawal 1 sibling, 1 reply; 14+ messages in thread From: Charles C. Berry @ 2016-05-28 16:57 UTC (permalink / raw) To: William Denton; +Cc: org-mode mailing list, Vikas Rawal On Sat, 28 May 2016, William Denton wrote: > On 28 May 2016, Vikas Rawal wrote: > >> Thanks John. Appreciate that you cared to respond to such a vague query. I >> am at a loss with this one. It does not happen all the time. I think it >> happens when I am processing large datasets, and CPUs and RAM of my system >> are struggling to keep up. But I could be wrong. > > I've had the same kind of thing happen---but C-g (sometimes many) to kill the > command, then rerunning, usually works without any trouble. Some strange > combination of CPU and RAM and all that, the kind of thing that's not easily > reproducible. > Try this: customize `debug-on-quit' to `t' (and set for current session). Then when you have to quit via C-g, you will get a backtrace showing where the process was hanging and how it got there. This might be helpful in figuring out what is going on. Run your code and when you finally have to C-g out copy the *Backtrace* buffer and report it back here (or on the ESS list if appropriate). Chuck ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-28 16:57 ` Charles C. Berry @ 2016-05-28 17:01 ` Charles C. Berry 2016-05-29 12:31 ` Vikas Rawal 2016-05-29 13:13 ` Vikas Rawal 0 siblings, 2 replies; 14+ messages in thread From: Charles C. Berry @ 2016-05-28 17:01 UTC (permalink / raw) To: William Denton; +Cc: org-mode mailing list, Vikas Rawal p.s. one more thing - below On Sat, 28 May 2016, Charles C. Berry wrote: > On Sat, 28 May 2016, William Denton wrote: > >> On 28 May 2016, Vikas Rawal wrote: >> >>> Thanks John. Appreciate that you cared to respond to such a vague query. I >>> am at a loss with this one. It does not happen all the time. I think it >>> happens when I am processing large datasets, and CPUs and RAM of my system >>> are struggling to keep up. But I could be wrong. >> >> I've had the same kind of thing happen---but C-g (sometimes many) to kill >> the command, then rerunning, usually works without any trouble. Some >> strange combination of CPU and RAM and all that, the kind of thing that's >> not easily reproducible. >> > > Try this: customize `debug-on-quit' to `t' (and set for current session). > > Then when you have to quit via C-g, you will get a backtrace showing where > the process was hanging and how it got there. This might be helpful in > figuring out what is going on. > > Run your code and when you finally have to C-g out copy the *Backtrace* > buffer and report it back here (or on the ESS list if appropriate). > After you copy the buffer, you should type 'q' in the *Backtrace* buffer to finish up or you may have some odd messages and hangups afterwards. Chuck ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-28 17:01 ` Charles C. Berry @ 2016-05-29 12:31 ` Vikas Rawal 2016-05-29 13:13 ` Vikas Rawal 1 sibling, 0 replies; 14+ messages in thread From: Vikas Rawal @ 2016-05-29 12:31 UTC (permalink / raw) To: Charles C. Berry; +Cc: William Denton, org-mode mailing list [-- Attachment #1: Type: text/plain, Size: 7014 bytes --] Does this back-trace say anything? sit-for(0.25) org-babel-comint-eval-invisibly-and-wait-for-file("type2" "/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/babel-53134TSq/R-53134IWW" "{\n function(object,transfer.file) {\n object\n invisible(\n if (\n inherits(\n try(\n {\n tfile<-tempfile()\n write.table(object, file=tfile, sep=\"\\t\",\n na=\"nil\",row.names=FALSE,col.names=FALSE,\n quote=FALSE)\n file.rename(tfile,transfer.file)\n },\n silent=TRUE),\n \"try-error\"))\n {\n if(!file.exists(transfer.file))\n file.create(transfer.file)\n }\n )\n }\n}(object=.Last.value,transfer.file=\"/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/babel-53134TSq/R-53134IWW\")") org-babel-R-evaluate-session("type2" "lm(log_cal~sector+SocialGroup+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+SocialGroup+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+SocialGroup+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+SocialGroup+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+SocialGroup+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region,data=regdata,weights=weight)->reg\nlm(adj_cal~sector+SocialGroup+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 28-May-2016, at 10:31 pm, Charles C. Berry <ccberry@ucsd.edu> wrote: > > > p.s. one more thing - below > > On Sat, 28 May 2016, Charles C. Berry wrote: > >> On Sat, 28 May 2016, William Denton wrote: >> >>> On 28 May 2016, Vikas Rawal wrote: >>>> Thanks John. Appreciate that you cared to respond to such a vague query. I am at a loss with this one. It does not happen all the time. I think it happens when I am processing large datasets, and CPUs and RAM of my system are struggling to keep up. But I could be wrong. >>> I've had the same kind of thing happen---but C-g (sometimes many) to kill the command, then rerunning, usually works without any trouble. Some strange combination of CPU and RAM and all that, the kind of thing that's not easily reproducible. >> >> Try this: customize `debug-on-quit' to `t' (and set for current session). >> >> Then when you have to quit via C-g, you will get a backtrace showing where the process was hanging and how it got there. This might be helpful in figuring out what is going on. >> >> Run your code and when you finally have to C-g out copy the *Backtrace* buffer and report it back here (or on the ESS list if appropriate). >> > > After you copy the buffer, you should type 'q' in the *Backtrace* buffer to finish up or you may have some odd messages and hangups afterwards. > > Chuck [-- Attachment #2: Type: text/html, Size: 15128 bytes --] ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-28 17:01 ` Charles C. Berry 2016-05-29 12:31 ` Vikas Rawal @ 2016-05-29 13:13 ` Vikas Rawal 2016-05-29 17:58 ` Charles C. Berry 1 sibling, 1 reply; 14+ messages in thread From: Vikas Rawal @ 2016-05-29 13:13 UTC (permalink / raw) To: Charles C. Berry; +Cc: William Denton, org-mode mailing list [-- Attachment #1: Type: text/plain, Size: 12763 bytes --] And this time it has this additional line: run-hook-with-args-until-success(org-babel-execute-safely-maybe) ------------------ sit-for(0.25) org-babel-comint-eval-invisibly-and-wait-for-file("type2" "/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/babel-53134TSq/R-53134vJF" "{\n function(object,transfer.file) {\n object\n invisible(\n if (\n inherits(\n try(\n {\n tfile<-tempfile()\n write.table(object, file=tfile, sep=\"\\t\",\n na=\"nil\",row.names=FALSE,col.names=TRUE,\n quote=FALSE)\n file.rename(tfile,transfer.file)\n },\n silent=TRUE),\n \"try-error\"))\n {\n if(!file.exists(transfer.file))\n file.create(transfer.file)\n }\n )\n }\n}(object=.Last.value,transfer.file=\"/var/folders/hj/hqfjch716qg5php160jbtfgh0000gn/T/babel-53134TSq/R-53134vJF\")") org-babel-R-evaluate-session("type2" "library(plyr)\nlibrary(Hmisc)\ng->tempg\n\n # CV_untreated\nas.integer(tempg$state_region/10)->tempg$State.code.68\nfactor(tempg$State.code.68)->tempg$State.code.68\ndata.frame(State=0,adjusted_cv=0)->e\n\nfor (i in c(1:35)) {\n subset(tempg,as.numeric(tempg$State.code.68)==i)->dd\n wtd.var(dd$adj_cal,weight=dd$weight)^0.5/wtd.mean(dd$adj_cal,weight=dd$weight)->cvs\n data.frame(State=i,adjusted_cv=cvs)->e1\n rbind(e,e1)->e\n}\n\nddply(tempg,.(State.code.68),summarise,value=wtd.mean(adj_cal,weight))->s1\n\ndata.frame(State=99,adjusted_cv=0)->f2\nwtd.var(tempg$adj_cal,weight=tempg$weight)^0.5/wtd.mean(tempg$adj_cal,weight=tempg$weight)->f2[1,2]\nrbind(e,f2)->cv1\n\n # CV_grouped data\nddply(tempg,.(sex,agegroup,fractile_adj),summarise,calories=wtd.mean(adj_cal,weight))->l1\nddply(tempg,.(sex,agegroup,fractile_adj),summarise,weight=sum(weight))->w\n\nmerge(w,l1,by=c(\"sex\",\"agegroup\",\"fractile_adj\"))->l1\n\nddply(tempg,.(fractile_adj_state,State.code.68,agegroup,sex),summarise,value=wtd.mean(adj_cal,weight))->s3\n\nddply(tempg,.(fractile_adj_state,State.code.68,agegroup,sex),summarise,sum_weight=sum(weight))->sw\n\nmerge(s3,sw,by=c(\"fractile_adj_state\",\"State.code.68\",\"agegroup\",\"sex\"))->s3\n\nfactor(s3$State.code.68)->s3$State.code.68\n\ndata.frame(State=99,grouped_cv=wtd.var(l1$calories,weight=l1$weight)^0.5/wtd.mean(l1$calories,weight=l1$weight))->cv3\n\nfor (i in c(1:35)) {\n subset(s3,as.numeric(s3$State.code.68)==i)->s3sub\n data.frame(State=i,grouped_cv=wtd.var(s3sub$value,s3sub$sum_weight)^0.5/wtd.mean(s3sub$value,s3sub$sum_weight))->t1\n rbind(cv3,t1)->cv3\n}\n\n# CV_from regression model\nregdata->p\nexp(predict.lm(reg))->p$predicted_cal\n\ndata.frame(State=99,predicted_cv=wtd.var(p$predicted_cal,weight=p$weight)^0.5/wtd.mean(p$predicted_cal,weight=p$weight),adjr2=summary(reg)$adj.r.squared)->cv2\n\n\n#data.frame(State=0,predicted_cv=0,adjr2=0)->e\n\nfor (i in c(1:35)) {\n subset(regdata,as.numeric(p$State.code.68)==i)->dd\n factor(dd$state_region)->dd$state_region\nfmla <- as.formula(\n ifelse(length(levels(dd$state_region))==1,\"log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)\",\"log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region\"))\n\n\n lm(fmla,data=dd,weights=weight)->regstate\n exp(predict.lm(regstate))->dd$predicted_cal\n wtd.var(dd$predicted_cal,weight=dd$weight)^0.5/wtd.mean(dd$predicted_cal,weight=dd$weight)->cvs\n data.frame(State=i,predicted_cv=cvs,adjr2=summary(regstate)$adj.r.squared)->e1\n rbind(cv2,e1)->cv2\n}\n\nsubset(cv2,select=-adjr2)->cv2\n\nmerge(cv1,cv3,by=\"State\")->t\nmerge(t,cv2,by=\"State\")->t\nmerge(t,statecode,by.x=\"State\",by.y=\"State.code.68\",all.x=TRUE)->t\nt$State.68[t$State==99]<-\"India\"\nround(t$grouped_cv,4)->t$grouped_cv\nround(t$adjusted_cv,4)->t$adjusted_cv\nround(t$predicted_cv,4)->t$predicted_cv\nnames(t)<-c(\"State.code.68\",\"CV (unit-level data)\",\"CV (grouped data)\",\"CV (based on regression model)\",\"State\")\nt->finvar\nt[order(t$State),c(5,2,3,4)]" value ("replace" "value") t nil) org-babel-R-evaluate("type2" "library(plyr)\nlibrary(Hmisc)\ng->tempg\n\n # CV_untreated\nas.integer(tempg$state_region/10)->tempg$State.code.68\nfactor(tempg$State.code.68)->tempg$State.code.68\ndata.frame(State=0,adjusted_cv=0)->e\n\nfor (i in c(1:35)) {\n subset(tempg,as.numeric(tempg$State.code.68)==i)->dd\n wtd.var(dd$adj_cal,weight=dd$weight)^0.5/wtd.mean(dd$adj_cal,weight=dd$weight)->cvs\n data.frame(State=i,adjusted_cv=cvs)->e1\n rbind(e,e1)->e\n}\n\nddply(tempg,.(State.code.68),summarise,value=wtd.mean(adj_cal,weight))->s1\n\ndata.frame(State=99,adjusted_cv=0)->f2\nwtd.var(tempg$adj_cal,weight=tempg$weight)^0.5/wtd.mean(tempg$adj_cal,weight=tempg$weight)->f2[1,2]\nrbind(e,f2)->cv1\n\n # CV_grouped data\nddply(tempg,.(sex,agegroup,fractile_adj),summarise,calories=wtd.mean(adj_cal,weight))->l1\nddply(tempg,.(sex,agegroup,fractile_adj),summarise,weight=sum(weight))->w\n\nmerge(w,l1,by=c(\"sex\",\"agegroup\",\"fractile_adj\"))->l1\n\nddply(tempg,.(fractile_adj_state,State.code.68,agegroup,sex),summarise,value=wtd.mean(adj_cal,weight))->s3\n\nddply(tempg,.(fractile_adj_state,State.code.68,agegroup,sex),summarise,sum_weight=sum(weight))->sw\n\nmerge(s3,sw,by=c(\"fractile_adj_state\",\"State.code.68\",\"agegroup\",\"sex\"))->s3\n\nfactor(s3$State.code.68)->s3$State.code.68\n\ndata.frame(State=99,grouped_cv=wtd.var(l1$calories,weight=l1$weight)^0.5/wtd.mean(l1$calories,weight=l1$weight))->cv3\n\nfor (i in c(1:35)) {\n subset(s3,as.numeric(s3$State.code.68)==i)->s3sub\n data.frame(State=i,grouped_cv=wtd.var(s3sub$value,s3sub$sum_weight)^0.5/wtd.mean(s3sub$value,s3sub$sum_weight))->t1\n rbind(cv3,t1)->cv3\n}\n\n# CV_from regression model\nregdata->p\nexp(predict.lm(reg))->p$predicted_cal\n\ndata.frame(State=99,predicted_cv=wtd.var(p$predicted_cal,weight=p$weight)^0.5/wtd.mean(p$predicted_cal,weight=p$weight),adjr2=summary(reg)$adj.r.squared)->cv2\n\n\n#data.frame(State=0,predicted_cv=0,adjr2=0)->e\n\nfor (i in c(1:35)) {\n subset(regdata,as.numeric(p$State.code.68)==i)->dd\n factor(dd$state_region)->dd$state_region\nfmla <- as.formula(\n ifelse(length(levels(dd$state_region))==1,\"log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)\",\"log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region\"))\n\n\n lm(fmla,data=dd,weights=weight)->regstate\n exp(predict.lm(regstate))->dd$predicted_cal\n wtd.var(dd$predicted_cal,weight=dd$weight)^0.5/wtd.mean(dd$predicted_cal,weight=dd$weight)->cvs\n data.frame(State=i,predicted_cv=cvs,adjr2=summary(regstate)$adj.r.squared)->e1\n rbind(cv2,e1)->cv2\n}\n\nsubset(cv2,select=-adjr2)->cv2\n\nmerge(cv1,cv3,by=\"State\")->t\nmerge(t,cv2,by=\"State\")->t\nmerge(t,statecode,by.x=\"State\",by.y=\"State.code.68\",all.x=TRUE)->t\nt$State.68[t$State==99]<-\"India\"\nround(t$grouped_cv,4)->t$grouped_cv\nround(t$adjusted_cv,4)->t$adjusted_cv\nround(t$predicted_cv,4)->t$predicted_cv\nnames(t)<-c(\"State.code.68\",\"CV (unit-level data)\",\"CV (grouped data)\",\"CV (based on regression model)\",\"State\")\nt->finvar\nt[order(t$State),c(5,2,3,4)]" value ("replace" "value") t nil) org-babel-execute:R("library(plyr)\nlibrary(Hmisc)\ng->tempg\n\n # CV_untreated\nas.integer(tempg$state_region/10)->tempg$State.code.68\nfactor(tempg$State.code.68)->tempg$State.code.68\ndata.frame(State=0,adjusted_cv=0)->e\n\nfor (i in c(1:35)) {\n subset(tempg,as.numeric(tempg$State.code.68)==i)->dd\n wtd.var(dd$adj_cal,weight=dd$weight)^0.5/wtd.mean(dd$adj_cal,weight=dd$weight)->cvs\n data.frame(State=i,adjusted_cv=cvs)->e1\n rbind(e,e1)->e\n}\n\nddply(tempg,.(State.code.68),summarise,value=wtd.mean(adj_cal,weight))->s1\n\ndata.frame(State=99,adjusted_cv=0)->f2\nwtd.var(tempg$adj_cal,weight=tempg$weight)^0.5/wtd.mean(tempg$adj_cal,weight=tempg$weight)->f2[1,2]\nrbind(e,f2)->cv1\n\n # CV_grouped data\nddply(tempg,.(sex,agegroup,fractile_adj),summarise,calories=wtd.mean(adj_cal,weight))->l1\nddply(tempg,.(sex,agegroup,fractile_adj),summarise,weight=sum(weight))->w\n\nmerge(w,l1,by=c(\"sex\",\"agegroup\",\"fractile_adj\"))->l1\n\nddply(tempg,.(fractile_adj_state,State.code.68,agegroup,sex),summarise,value=wtd.mean(adj_cal,weight))->s3\n\nddply(tempg,.(fractile_adj_state,State.code.68,agegroup,sex),summarise,sum_weight=sum(weight))->sw\n\nmerge(s3,sw,by=c(\"fractile_adj_state\",\"State.code.68\",\"agegroup\",\"sex\"))->s3\n\nfactor(s3$State.code.68)->s3$State.code.68\n\ndata.frame(State=99,grouped_cv=wtd.var(l1$calories,weight=l1$weight)^0.5/wtd.mean(l1$calories,weight=l1$weight))->cv3\n\nfor (i in c(1:35)) {\n subset(s3,as.numeric(s3$State.code.68)==i)->s3sub\n data.frame(State=i,grouped_cv=wtd.var(s3sub$value,s3sub$sum_weight)^0.5/wtd.mean(s3sub$value,s3sub$sum_weight))->t1\n rbind(cv3,t1)->cv3\n}\n\n# CV_from regression model\nregdata->p\nexp(predict.lm(reg))->p$predicted_cal\n\ndata.frame(State=99,predicted_cv=wtd.var(p$predicted_cal,weight=p$weight)^0.5/wtd.mean(p$predicted_cal,weight=p$weight),adjr2=summary(reg)$adj.r.squared)->cv2\n\n\n#data.frame(State=0,predicted_cv=0,adjr2=0)->e\n\nfor (i in c(1:35)) {\n subset(regdata,as.numeric(p$State.code.68)==i)->dd\n factor(dd$state_region)->dd$state_region\nfmla <- as.formula(\n ifelse(length(levels(dd$state_region))==1,\"log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)\",\"log_cal~sector+sex+AgeChild+AgeAdult+foodprice+log(MPCE)+state_region\"))\n\n\n lm(fmla,data=dd,weights=weight)->regstate\n exp(predict.lm(regstate))->dd$predicted_cal\n wtd.var(dd$predicted_cal,weight=dd$weight)^0.5/wtd.mean(dd$predicted_cal,weight=dd$weight)->cvs\n data.frame(State=i,predicted_cv=cvs,adjr2=summary(regstate)$adj.r.squared)->e1\n rbind(cv2,e1)->cv2\n}\n\nsubset(cv2,select=-adjr2)->cv2\n\nmerge(cv1,cv3,by=\"State\")->t\nmerge(t,cv2,by=\"State\")->t\nmerge(t,statecode,by.x=\"State\",by.y=\"State.code.68\",all.x=TRUE)->t\nt$State.68[t$State==99]<-\"India\"\nround(t$grouped_cv,4)->t$grouped_cv\nround(t$adjusted_cv,4)->t$adjusted_cv\nround(t$predicted_cv,4)->t$predicted_cv\nnames(t)<-c(\"State.code.68\",\"CV (unit-level data)\",\"CV (grouped data)\",\"CV (based on regression model)\",\"State\")\nt->finvar\nt[order(t$State),c(5,2,3,4)]" ((:colname-names) (:rowname-names) (:result-params "replace" "value") (:result-type . value) (:comments . "") (:shebang . "") (:cache . "no") (:padline . "") (:noweb . "no") (:tangle . "no") (:exports . "results") (:results . "replace value") (:hlines . "no") (:session . "type2") (:colnames . "yes") (:hline . "yes"))) 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 28-May-2016, at 10:31 pm, Charles C. Berry <ccberry@ucsd.edu> wrote: > > > p.s. one more thing - below > > On Sat, 28 May 2016, Charles C. Berry wrote: > >> On Sat, 28 May 2016, William Denton wrote: >> >>> On 28 May 2016, Vikas Rawal wrote: >>>> Thanks John. Appreciate that you cared to respond to such a vague query. I am at a loss with this one. It does not happen all the time. I think it happens when I am processing large datasets, and CPUs and RAM of my system are struggling to keep up. But I could be wrong. >>> I've had the same kind of thing happen---but C-g (sometimes many) to kill the command, then rerunning, usually works without any trouble. Some strange combination of CPU and RAM and all that, the kind of thing that's not easily reproducible. >> >> Try this: customize `debug-on-quit' to `t' (and set for current session). >> >> Then when you have to quit via C-g, you will get a backtrace showing where the process was hanging and how it got there. This might be helpful in figuring out what is going on. >> >> Run your code and when you finally have to C-g out copy the *Backtrace* buffer and report it back here (or on the ESS list if appropriate). >> > > After you copy the buffer, you should type 'q' in the *Backtrace* buffer to finish up or you may have some odd messages and hangups afterwards. > > Chuck [-- Attachment #2: Type: text/html, Size: 20831 bytes --] ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-29 13:13 ` Vikas Rawal @ 2016-05-29 17:58 ` Charles C. Berry 2016-05-30 0:37 ` Vikas Rawal 0 siblings, 1 reply; 14+ messages in thread From: Charles C. Berry @ 2016-05-29 17:58 UTC (permalink / raw) To: Vikas Rawal; +Cc: William Denton, org-mode mailing list On Sun, 29 May 2016, Vikas Rawal wrote: > And this time it has this additional line: run-hook-with-args-until-success(org-babel-execute-safely-maybe) Actually, I saw that line in your previous posting. But this may help: > > ------------------ > > sit-for(0.25) > org-babel-comint-eval-invisibly-and-wait-for-file("type2" [rest deleted] `sit-for' is in this loop: `(while (not (file-exists-p file)) (sit-for (or period 0.25)))' which suggests that the file to which the results should be written is not being created or there is an issue with `sit-for'. Does anyone know why `sit-for' is used here rather than `sleep-for'? I ask because I see that `sit-for' because it seems to me that `sleep-for' would be enough and `sit-for' has inline comments that suggest some unresolved issues. 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? Chuck ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-29 17:58 ` Charles C. Berry @ 2016-05-30 0:37 ` Vikas Rawal 2016-05-30 1:18 ` Charles C. Berry 0 siblings, 1 reply; 14+ messages in thread From: Vikas Rawal @ 2016-05-30 0:37 UTC (permalink / raw) To: Charles C. Berry; +Cc: William Denton, org-mode mailing list > > 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. Much appreciate your help. Vikas ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-30 0:37 ` Vikas Rawal @ 2016-05-30 1:18 ` Charles C. Berry 2016-05-30 10:24 ` Vikas Rawal 0 siblings, 1 reply; 14+ messages in thread From: Charles C. Berry @ 2016-05-30 1:18 UTC (permalink / raw) To: Vikas Rawal; +Cc: William Denton, org-mode mailing list 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 ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-30 1:18 ` Charles C. Berry @ 2016-05-30 10:24 ` Vikas Rawal 2016-05-30 16:22 ` Charles C. Berry 0 siblings, 1 reply; 14+ messages in thread From: Vikas Rawal @ 2016-05-30 10:24 UTC (permalink / raw) To: Charles C. Berry; +Cc: William Denton, org-mode mailing list 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 <ccberry@ucsd.edu> 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 ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-30 10:24 ` Vikas Rawal @ 2016-05-30 16:22 ` Charles C. Berry 0 siblings, 0 replies; 14+ messages in thread From: Charles C. Berry @ 2016-05-30 16:22 UTC (permalink / raw) To: Vikas Rawal; +Cc: William Denton, org-mode mailing list On Mon, 30 May 2016, Vikas Rawal wrote: > Thanks. > > The code still seems to freeze. > > The backtrace now is. > OK, let me abbreviate this by cutting off the ends of long lines: > Debugger entered--Lisp error: (quit) > process-send-string(#<process R> ".ess.eval(\"lm(log_cal~sector+ [...] > ess-send-string--fallback(#<process R> ".ess.eval(\"lm(log_cal~ [...] > ess-send-string(#<process R> ".ess.eval(\"lm(log_cal~sector+sex+ [...] > 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+ [...] > org-babel-R-evaluate("type2" "lm(log_cal~sector+sex+AgeChild+AgeAdult+ [...] > org-babel-execute:R("lm(log_cal~sector+sex+AgeChild+AgeAdult+foodprice+ [...] > 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) > And what you had previously was [using some abbreviations]: sit-for(0.25) org-babel-comint-eval-invisibly-and-wait-for-file("type2" [filename] [R command string] [...] org-babel-R-evaluate-session("type2" [R command string] ... org-babel-R-evaluate("type2" [R command string] ... org-babel-execute:R( [R command string] ... 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) What you can see is that everything is the same right up to this line `org-babel-R-evaluate-session(...' but in the top (most recent) version ess-* functions are shown right up to process-send-string, which means that ess is still trying to complete its work. In the older (bottom) version ess is done and babel is waiting for the resulting file. This makes me wonder what R is doing. Can you check the activity monitor (you are on OS X, right?) and see what is happening? If the R code takes a long time to run and the R process is chewing up CPU or reading from/writing to disk this would explain it. If that isn't it, you might try to put in some checkpoints to see how far the R code got. I'd put something like cat("Starting",file="progress.txt") at the top of your src code and cat(".",file="progress.txt",append=TRUE) after every line and cat("Done\n",file="progress.txt",append=TRUE) after the last command at the very bottom. Then if the R code hangs somewhere you can open `progress.txt', count up the dots, and see where it got to. If that does not appeal to you, then profiling the R code might do. see ?Rprof. Finally, you aren't doing something exotic - like trying to run src blocks from a local buffer in a remote session - are you? If so, that adds a layer of complexity that needs discussion. HTH, Chuck ^ permalink raw reply [flat|nested] 14+ messages in thread
* Re: Trouble evaluating R source code blocks with C-c C-c 2016-05-28 14:27 ` William Denton 2016-05-28 16:57 ` Charles C. Berry @ 2016-05-29 2:02 ` Vikas Rawal 1 sibling, 0 replies; 14+ messages in thread From: Vikas Rawal @ 2016-05-29 2:02 UTC (permalink / raw) To: William Denton; +Cc: org-mode mailing list > On 28-May-2016, at 7:57 pm, William Denton <wtd@pobox.com> wrote: > > On 28 May 2016, Vikas Rawal wrote: > >> Thanks John. Appreciate that you cared to respond to such a vague query. I am at a loss with this one. It does not happen all the time. I think it happens when I am processing large datasets, and CPUs and RAM of my system are struggling to keep up. But I could be wrong. > > I've had the same kind of thing happen---but C-g (sometimes many) to kill the command, then rerunning, usually works without any trouble. Some strange combination of CPU and RAM and all that, the kind of thing that's not easily reproducible. > This seems to be write. Upgrading ess did not help. The odd thing is that running the same code by doing C-‘ to open a temporary R buffer and running to code from there works fine. But then I come back to the org buffer, C-c C-c, and the whole thing just freezes. The R session shows that the code is running. I have to use C-g in the org-buffer, which releases the org buffer, and C-c several times in the R session, to stop the commands. If I have waited enough, doing C-c C-c at the end in the R session ends the command and actually shows the output of the last command in R buffer. Which means that the last command had been completed. But the output was not inserted in the org buffer, and R was going on doing something. Let me try ‘debug-on-quit' Vikas ^ permalink raw reply [flat|nested] 14+ messages in thread
end of thread, other threads:[~2016-05-30 16:22 UTC | newest] Thread overview: 14+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2016-05-26 14:33 Trouble evaluating R source code blocks with C-c C-c Vikas Rawal 2016-05-26 18:52 ` John Hendy 2016-05-28 7:58 ` Vikas Rawal 2016-05-28 14:27 ` William Denton 2016-05-28 16:57 ` Charles C. Berry 2016-05-28 17:01 ` Charles C. Berry 2016-05-29 12:31 ` Vikas Rawal 2016-05-29 13:13 ` Vikas Rawal 2016-05-29 17:58 ` Charles C. Berry 2016-05-30 0:37 ` Vikas Rawal 2016-05-30 1:18 ` Charles C. Berry 2016-05-30 10:24 ` Vikas Rawal 2016-05-30 16:22 ` Charles C. Berry 2016-05-29 2:02 ` Vikas Rawal
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