Re: [O] bug: orgtbl-to-tsv: premature end of table
Hi all, "Charles C. Berry" writes: > On Wed, 22 Jul 2015, Nicolas Goaziou wrote: > >> Hello, >> >> "Charles C. Berry" writes: >> >>> Not a bug IMO. >> >> Notwithstanding the R issue, I think trimming the output of a radio >> table is a bit aggressive. We cannot know if trailing (and leading) >> spaces are significant in the output format the user defined. >> >> I removed the trimming part in commit >> bf37cd09b128b4431e1dd1a538fbcc4be3615042. >> >> Let me know if you disagree with that change. > > I don't think the change broke anything that wasn't already broken. > > And my diagnosis was wrong - I was confused by a problem that remains: > > `org-babel-R-assign-elisp' is broken. Ragged rows in a table are filled > with "" in each missing field; `org-table-to-lisp' returns a list of lists > of common length. > > `org-babel-R-assign-elisp' inspects that list to see if any element vary > in length. But they do not, and therefore `max' and `min' in the let* > varlist are equal and later on `ob-R-transfer-variable-table-with-header' > is always used. > > I think lom pik's example would not have failed had max and min differed > as `ob-R-transfer-variable-table-without-header' would have been used > instead. > > R src blocks ought to render missing elements due to ragged rows in a > table as NA, but this isnt the current behavior for this table: > > #+NAME: tbl-ragged > | 1 | 2 | a | > > | 8 | 9 | | > > It seems like the fix for this would be to prune any "" at the ends of > lists in the value arg when beginning `org-babel-R-assign-elisp'. > > But I am tired, so I'll defer trying this till another time. > > Best, > > Chuck Thank you all for looking into this. I have seen this as well and the manual work-around (to put sth into the last cell) was getting really annoying -- especially if the table was auto-generated by sth else. While looking at handling tables, could I suggest to switch to csv instead of tsv for the table passing? I still see issues with tables not separated. (This happens only in preview (C-c C-v v) and not when executing the block.) I never had time to track this down, but I get caught now and then. Using csv should be more robust in this regard. Thanks, Andreas
Re: [O] bug: orgtbl-to-tsv: premature end of table
On Wed, 22 Jul 2015, Nicolas Goaziou wrote: Hello, "Charles C. Berry" writes: Not a bug IMO. Notwithstanding the R issue, I think trimming the output of a radio table is a bit aggressive. We cannot know if trailing (and leading) spaces are significant in the output format the user defined. I removed the trimming part in commit bf37cd09b128b4431e1dd1a538fbcc4be3615042. Let me know if you disagree with that change. I don't think the change broke anything that wasn't already broken. And my diagnosis was wrong - I was confused by a problem that remains: `org-babel-R-assign-elisp' is broken. Ragged rows in a table are filled with "" in each missing field; `org-table-to-lisp' returns a list of lists of common length. `org-babel-R-assign-elisp' inspects that list to see if any element vary in length. But they do not, and therefore `max' and `min' in the let* varlist are equal and later on `ob-R-transfer-variable-table-with-header' is always used. I think lom pik's example would not have failed had max and min differed as `ob-R-transfer-variable-table-without-header' would have been used instead. R src blocks ought to render missing elements due to ragged rows in a table as NA, but this isnt the current behavior for this table: #+NAME: tbl-ragged | 1 | 2 | a | | 8 | 9 | | It seems like the fix for this would be to prune any "" at the ends of lists in the value arg when beginning `org-babel-R-assign-elisp'. But I am tired, so I'll defer trying this till another time. Best, Chuck
Re: [O] bug: orgtbl-to-tsv: premature end of table
Hi > removed the trimming part in commit > bf37cd09b128b4431e1dd1a538fbcc4be3615042. With this commit, issue is gone. This did not happen in previous org-mode releases although all other proposed workarounds worked as well. Regards. lompik On Wed, Jul 22, 2015 at 5:41 PM, Nicolas Goaziou wrote: > Hello, > > "Charles C. Berry" writes: > > > Not a bug IMO. > > Notwithstanding the R issue, I think trimming the output of a radio > table is a bit aggressive. We cannot know if trailing (and leading) > spaces are significant in the output format the user defined. > > I removed the trimming part in commit > bf37cd09b128b4431e1dd1a538fbcc4be3615042. > > Let me know if you disagree with that change. > > > Regards, > > -- > Nicolas Goaziou >
Re: [O] bug: orgtbl-to-tsv: premature end of table
Hello, "Charles C. Berry" writes: > Not a bug IMO. Notwithstanding the R issue, I think trimming the output of a radio table is a bit aggressive. We cannot know if trailing (and leading) spaces are significant in the output format the user defined. I removed the trimming part in commit bf37cd09b128b4431e1dd1a538fbcc4be3615042. Let me know if you disagree with that change. Regards, -- Nicolas Goaziou
Re: [O] bug: orgtbl-to-tsv: premature end of table
On Tue, 14 Jul 2015, lom pik wrote:
Hi,
-- this was only tested with the current git version
I was trying to export a table as a variable to R via babel evaluation.
However it seems that is the rows are empty , the exported table ends at
the last non-empty value.
For example,the second row of tbl-issue defined below ends with 2 columns
[8,9]. The next table however works ok. I've narrowed down the cause to the
orgtbl-to-tsv function as highlighted below.
Not a bug IMO.
See the R documentation page for `read.table'. Note `fill'.
#+NAME: tbl-issue
| 1 | 2 | 3 | 5 | 6 | 7 |
| 8 | 9 | | | | |
#+BEGIN_SRC R :session *R* :var df2=tbl-issue :results value## won't
work
print(df2)
#+END_SRC
You have two options (at least):
1. Place `NA' in the last cell of the last line
2. add ' , fill=TRUE ' like this:
#+BEGIN_SRC emacs-lisp
(setq
ob-R-transfer-variable-table-with-header
"%s <- local({
con <- textConnection(
%S
)
res <- utils::read.table(
con,
header= %s,
row.names = %s,
sep = \"\\t\",
as.is = TRUE, fill=TRUE
)
close(con)
res
})")
#+END_SRC
Either way you will get:
#+RESULTS:
| 1 | 2 | 3 | 5 | 6 | 7 |
| 8 | 9 | nil | nil | nil | nil |
HTH,
Chuck
[O] bug: orgtbl-to-tsv: premature end of table
Hi, -- this was only tested with the current git version I was trying to export a table as a variable to R via babel evaluation. However it seems that is the rows are empty , the exported table ends at the last non-empty value. For example,the second row of tbl-issue defined below ends with 2 columns [8,9]. The next table however works ok. I've narrowed down the cause to the orgtbl-to-tsv function as highlighted below. #+NAME: tbl-issue | 1 | 2 | 3 | 5 | 6 | 7 | | 8 | 9 | | | | | #+BEGIN_SRC R :session *R* :var df2=tbl-issue :results value## won't work print(df2) #+END_SRC (orgtbl-to-tsv '( (1 2 #1="" #1# #1# #1# ) ) '(:fmt org-babel-R-quote-tsv-field)) -> "\"1\"\"2\"" #+NAME: tlb-ok | 1 | 2 | 3 | 5 | 6 | 7 | | 8 | 9 | | | | 10 | #+BEGIN_SRC R :session *R* :var df2=tbl-ok :results value # work ok print(df2) #+END_SRC (orgtbl-to-tsv '( (1 2 #1="" #1# #1# #1# 10) ) '(:fmt org-babel-R-quote-tsv-field)) -> "\"1\"\"2\"\"1\"" Emacs 24.5 with Org-mode version 8.3beta (release_8.3beta-1286-g20795f.dirty ) Regards, lompik
[O] [BUG] orgtbl-to-tsv: premature end of table
Hi, -- this was only tested with the git version I was trying to export a table as a variable to R via babel evaluation. However it seems that is the rows are empty , the exported table ends at the last non-empty value. For example,the second row of tbl-issue defined below ends with 2 columns [8,9]. The next table however works ok. I've narrowed down the cause to the orgtbl-to-tsv function as highlighted below. #+NAME: tbl-issue | 1 | 2 | 3 | 5 | 6 | 7 | | 8 | 9 | | | | | #+BEGIN_SRC R :session *R* :var df2=tbl-issue :results value## won't work print(df2) #+END_SRC (orgtbl-to-tsv '( (1 2 #1="" #1# #1# #1# ) ) '(:fmt org-babel-R-quote-tsv-field)) -> "\"1\"\"2\"" #+NAME: tlb-ok | 1 | 2 | 3 | 5 | 6 | 7 | | 8 | 9 | | | | 10 | #+BEGIN_SRC R :session *R* :var df2=tbl-ok :results value # work ok print(df2) #+END_SRC (orgtbl-to-tsv '( (1 2 #1="" #1# #1# #1# 10) ) '(:fmt org-babel-R-quote-tsv-field)) -> "\"1\"\"2\"\"1\"" Emacs 24.5 with Org-mode version 8.3beta (release_8.3beta-1286-g20795f.dirty ) Regards, lompik
