Re: org-babel strange html print in R
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Jeremie Juste writes: > Hello, > > Thanks for the input. > I didn't see the full mail of stardiviner for some reason. About this, I found Gmail put my emails into Spams folder. I can't figure out what reasons. I also found similar situations in some people in Emacs-help guys. Anyway, If you can, please report my emails "Not Spam". Thanks :) > > :results value html in the following code generates an error for me. > (Org mode version 9.2.3,R version 3.6.2). > but :results value output the "html" in an org-table format > > #+begin_src R :results value html > library(xtable) > x <- rnorm(100) > y <- x + rnorm(100) > print(xtable(summary(lm(y ~ x))),type="html") > #+end_src > > Best regards, > Jeremie > > Jack Kamm writes: > >> Hi, >> >> stardiviner writes: >> >>> You should try ~:results value html~. Here is what I got correctly: >> >> Yes, this seems like the best solution for this case. >> >> On the other hand, it would be desirable if ":results output" didn't >> mangle the output, due to trying to clean up prompts. There is probably >> some corner case out there where this is a more serious issue -- but for >> this case, it seems best to just use ":results value html". >> >> I was planning to submit my implementation of ":session :results output" >> that avoids the prompt mangling [0], but now I'm leaning towards putting >> this off, until a more compelling case arises to justify it. >> >> [0] >> https://github.com/jackkamm/ob-session-async/blob/master/lisp/ob-session-async-R.el - -- [ stardiviner ] I try to make every word tell the meaning what I want to express. Blog: https://stardiviner.github.io/ IRC(freenode): stardiviner, Matrix: stardiviner GPG: F09F650D7D674819892591401B5DF1C95AE89AC3 -BEGIN PGP SIGNATURE- iQFIBAEBCAAyFiEE8J9lDX1nSBmJJZFAG13xyVromsMFAl5Do/gUHG51bWJjaGls ZEBnbWFpbC5jb20ACgkQG13xyVromsN8ewf/YkjUlLOAAAtpBRgOdIZg2N0JKxVt vwXxH5G+5VOJNgH0avDRrGnI+2r5Kooqs0lpfIjoy5yi9tkG9Z4GShKa2iYP2wLA hbsN0OJxZ3ChdCjbyW2ABNdzCVL6T3oremxy8DzdZGrM2sSmFFSKK+N8s/PI7IJP 2wE7jjUCoNFcB6XGodcZiRXE+Ms/k1gPfzyJxvbeOdX1GQriQE8ecofEpomkz3F0 VQZ/sgec9mAsKZMC9054H0br5DT1c3Wo/DnaKnVpw24wrwWyMJSj02XSau+GIFLq 3hAx01mrP4ud7aUs/TnwCfaVrvH0i/4iO+KhJr6KyZB2gPMTXTs4nuf5Zw== =dAR8 -END PGP SIGNATURE-
Re: org-babel strange html print in R
Hi, Jeremie Juste writes: > :results value html in the following code generates an error for me. > (Org mode version 9.2.3,R version 3.6.2). > but :results value output the "html" in an org-table format Hmm, I can confirm that ":session :results value html" is working for me, same as for stardiviner. Could you give more info about the error you're seeing? I'm using R 3.6.2 and Org 9.4. But I'd be surprised if it doesn't work for Org 9.2 -- git blame suggests that html output has been supported in ob-R since at least 2015. But it wouldn't hurt to upgrade to the latest released version of Org (9.3).
Re: org-babel strange html print in R
Hello, Thanks for the input. I didn't see the full mail of stardiviner for some reason. :results value html in the following code generates an error for me. (Org mode version 9.2.3,R version 3.6.2). but :results value output the "html" in an org-table format #+begin_src R :results value html library(xtable) x <- rnorm(100) y <- x + rnorm(100) print(xtable(summary(lm(y ~ x))),type="html") #+end_src Best regards, Jeremie Jack Kamm writes: > Hi, > > stardiviner writes: > >> You should try ~:results value html~. Here is what I got correctly: > > Yes, this seems like the best solution for this case. > > On the other hand, it would be desirable if ":results output" didn't > mangle the output, due to trying to clean up prompts. There is probably > some corner case out there where this is a more serious issue -- but for > this case, it seems best to just use ":results value html". > > I was planning to submit my implementation of ":session :results output" > that avoids the prompt mangling [0], but now I'm leaning towards putting > this off, until a more compelling case arises to justify it. > > [0] > https://github.com/jackkamm/ob-session-async/blob/master/lisp/ob-session-async-R.el
Re: org-babel strange html print in R
Hi, stardiviner writes: > You should try ~:results value html~. Here is what I got correctly: Yes, this seems like the best solution for this case. On the other hand, it would be desirable if ":results output" didn't mangle the output, due to trying to clean up prompts. There is probably some corner case out there where this is a more serious issue -- but for this case, it seems best to just use ":results value html". I was planning to submit my implementation of ":session :results output" that avoids the prompt mangling [0], but now I'm leaning towards putting this off, until a more compelling case arises to justify it. [0] https://github.com/jackkamm/ob-session-async/blob/master/lisp/ob-session-async-R.el
Re: org-babel strange html print in R
You should try ~:results value html~. Here is what I got correctly: #+begin_src R :results value html library(xtable) x <- rnorm(100) y <- x + rnorm(100) print(xtable(summary(lm(y ~ x))),type="html") #+end_src #+RESULTS[<2020-02-11 13:14:59> 91ff0df2529284897e3585e3ec2e640290ee8308]: #+begin_export html Estimate Std. Error t value Pr(>|t|) (Intercept) -0.0064 0.1069 -0.06 0.9520 x 1.1066 0.1022 10.83 0. #+end_export Jeremie Juste writes: > Hello, > > I've found that some strange results when outputing html from R. > Do you have some insights on a potential solution? > > Best regards, > Jeremie > > Org mode version 9.3.4 (9.3.4-elpa @ /home/djj/.emacs.d/elpa/org-20200206/) > > #+PROPERTY: header-args:R :eval yes :exports results :colnames yes :results > output :output-dir images/:cache yes :session *R* > > #+begin_src R :results output html > library(xtable) > x <- rnorm(100) > y <- x + rnorm(100) > print(xtable(summary(lm(y ~ x))),type="html") > #+end_src > > > #+RESULTS: > #+begin_export html > > > > > < > < > < > Estimate < > Std. Error < > t value < > Pr(>|t|) > < > (Intercept) -0.0130 0.1023 -0.13 0.8991 > < > x 1.0011 0.0987 10.14 0. > > #+end_export > > > ** Expected results > #+begin_export html > > Estimate Std. Error t value > Pr(>|t|) > (Intercept) -0.0130 > 0.1023 -0.13 align="right"> 0.8991 > x 1.0011 align="right"> 0.0987 10.14 > 0. > > #+end_export -- [ stardiviner ] I try to make every word tell the meaning what I want to express. Blog: https://stardiviner.github.io/ IRC(freenode): stardiviner, Matrix: stardiviner GPG: F09F650D7D674819892591401B5DF1C95AE89AC3
Re: org-babel strange html print in R
Hello Jack, Thanks for taking the time to reply. > I think a more reliable implementation would be to avoid > `org-babel-comint-with-output', and take the approach used in the > ":results value" case, which reads the output from a temp file instead > of directly from the shell. I understand better now. Thanks > > Actually, that's the approach I use in my ob-session-async package [0], > which re-implements ob-R sessions to allow async evaluation. It doesn't > suffer from the bug you are reporting. I'll plan to extract that > implementation and submit it as a patch here. Your solution works just fine. I came across ob-session-async a recently and find it very interesting thanks again. #+begin_src R :results output html :cache no :async session library(xtable) x <- rnorm(100) y <- x + rnorm(100) a <- summary(lm(y ~ x)) print(xtable(a),type="html",comment=FALSE) #+end_src #+RESULTS: #+begin_export html Estimate Std. Error t value Pr(>|t|) (Intercept) 0.1249 0.0961 1.30 0.1969 x 0.9263 0.0879 10.53 0. #+end_export Best regards, Jeremie
Re: org-babel strange html print in R
Hi Jeremie, > Thanks for the info. > Unfortunately I couldn't identify the issue > I updated R and org (org 9.3.2, R 3.6.2). > but I'm still getting [the error] Sorry, I missed the initial property line where you set the ":session" header argument. When I set the ":session" header argument, I get the original buggy behavior that you report. It looks like the reason for this, is that the substrings like "tr>" match `comint-prompt-regexp', and so get stripped out by `org-babel-comint-with-output'. I think a more reliable implementation would be to avoid `org-babel-comint-with-output', and take the approach used in the ":results value" case, which reads the output from a temp file instead of directly from the shell. Actually, that's the approach I use in my ob-session-async package [0], which re-implements ob-R sessions to allow async evaluation. It doesn't suffer from the bug you are reporting. I'll plan to extract that implementation and submit it as a patch here. Long term, I am intending to contribute the full functionality in ob-session-async here, but that's still a ways off. [0] https://github.com/jackkamm/ob-session-async Jack
Re: org-babel strange html print in R
Hello, Jack Kamm writes: > Dominique Dumont writes: > >> On my system, org-mode 3.6.1 provides the expected table. > > My system produces the expected table as well (org 9.3.2, R 3.6.2). > > --Jack Thanks for the info. Unfortunately I couldn't identify the issue I updated R and org (org 9.3.2, R 3.6.2). launched > emacs -Q - executed the following commands (add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20200115.225") (add-to-list 'load-path "/home/djj/.emacs.d/elpa/julia-mode-20180816.2117") (require 'ess-site) (org-babel-do-load-languages 'org-babel-load-languages '( (R . t) )) but I'm still getting #+begin_src R :results output :cache no :session "R2" library(xtable) x <- rnorm(100) y <- x + rnorm(100) a <- summary(lm(y ~ x)) print(xtable(a),type="html") #+end_src #+RESULTS: #+begin_example < < < < #+end_example Best regards, Jeremie
Re: org-babel strange html print in R
On Friday, 7 February 2020 14:38:53 CET Bastien wrote: > This seems to be a *very* version of org-mode ;) Bummer... I remember that I've used org-version to get the version number. I guess I have cut'n'pasted an unrelated number :-/ For the record, I've tested R and html output on Org mode version 9.3.1 Sorry for the confusion. All the best Dod
Re: org-babel strange html print in R
Dominique Dumont writes: > On my system, org-mode 3.6.1 provides the expected table. My system produces the expected table as well (org 9.3.2, R 3.6.2). --Jack
Re: org-babel strange html print in R
Hi Dominique, Dominique Dumont writes: > On Thursday, 6 February 2020 19:23:36 CET Jeremie Juste wrote: >> I've found that some strange results when outputing html from R. >> Do you have some insights on a potential solution? > > On my system, org-mode 3.6.1 This seems to be a *very* version of org-mode ;) -- Bastien
Re: org-babel strange html print in R
On Thursday, 6 February 2020 19:23:36 CET Jeremie Juste wrote: > I've found that some strange results when outputing html from R. > Do you have some insights on a potential solution? On my system, org-mode 3.6.1 provides the expected table. All the best
org-babel strange html print in R
Hello, I've found that some strange results when outputing html from R. Do you have some insights on a potential solution? Best regards, Jeremie Org mode version 9.3.4 (9.3.4-elpa @ /home/djj/.emacs.d/elpa/org-20200206/) #+PROPERTY: header-args:R :eval yes :exports results :colnames yes :results output :output-dir images/:cache yes :session *R* #+begin_src R :results output html library(xtable) x <- rnorm(100) y <- x + rnorm(100) print(xtable(summary(lm(y ~ x))),type="html") #+end_src #+RESULTS: #+begin_export html < < < < #+end_export ** Expected results #+begin_export html Estimate Std. Error t value Pr(>|t|) (Intercept) -0.0130 0.1023 -0.13 0.8991 x 1.0011 0.0987 10.14 0. #+end_export
