Attached please find =the reworked patch. 1) uses local() and closes connection 2) does not leave a variable cal;led file behind
Cheers, Rainer
From 2989c5890736099521a077d3b15d2ccc37c88b67 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <r.m.k...@gmail.com>
Date: Fri, 20 Jun 2014 22:19:59 +0200
Subject: [PATCH] lisp/ob-R.el: Fix tangling with tables
* lisp/ob-R.el (org-babel-R-assign-elisp): Fix variable transfer of
tables by using text connections in R instead of files. Variable
transfer of tables does not depend on files anymore, i.e. works also
when tangling.
---
lisp/ob-R.el | 42 ++++++++++++++++++++++--------------------
1 file changed, 22 insertions(+), 20 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index a3ae1ec..7f366c4 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -190,32 +190,34 @@ This function is called by `org-babel-execute-src-block'."
(if (listp value)
(let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
(max (if lengths (apply 'max lengths) 0))
- (min (if lengths (apply 'min lengths) 0))
- (transition-file (org-babel-temp-file "R-import-")))
+ (min (if lengths (apply 'min lengths) 0)))
;; Ensure VALUE has an orgtbl structure (depth of at least 2).
(unless (listp (car value)) (setq value (list value)))
- (with-temp-file transition-file
- (insert
- (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
- "\n"))
- (let ((file (org-babel-process-file-name transition-file 'noquote))
+ (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
(header (if (or (eq (nth 1 value) 'hline) colnames-p)
"TRUE" "FALSE"))
(row-names (if rownames-p "1" "NULL")))
(if (= max min)
- (format "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE)" name file header row-names)
- (format "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE,
- fill=TRUE,
- col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
- name file header row-names max))))
+ (format "%s <- local({
+ con <- textConnection(%S)
+ res <- read.table(con,
+ header = %s,
+ row.names = %s,
+ sep = \"\\t\",
+ as.is = TRUE)
+ close(con)
+ res})" name file header row-names)
+ (format "%s <- local({
+ con <- textConnection(%S)
+ res <- read.table(con,
+ header = %s,
+ row.names = %s,
+ sep = \"\\t\",
+ as.is = TRUE,
+ fill = TRUE,
+ col.names = paste(\"V\", seq_len(%d), sep =\"\"))
+ close(con)
+ res})" name file header row-names max))))
(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
--
2.0.0
Rainer M Krug <rai...@krugs.de> writes:
> Charles Berry <ccbe...@ucsd.edu> writes:
>
>> Aaron Ecay <aaronecay <at> gmail.com> writes:
>>
>>>
>>> Hi Rainer,
>>>
>>> I have not tested the patch (I rarely use :var), but here are some
>>> comments from reading the patch.
>>>
>> [snip]
>>>
>>> > (header (if (or (eq (nth 1 value) 'hline) colnames-p)
>>> > "TRUE" "FALSE"))
>>> > (row-names (if rownames-p "1" "NULL")))
>>> > (if (= max min)
>>> > - (format "%s <- read.table(\"%s\",
>>> > + (format "%s <- read.table(textConnection('%s'),
>>>
>>> This will fail if ‘file’ contains an apostrophe character. I guess you
>>> need to escape apostrophes in ‘file’.
>>>
>>
>> There are a bunch of issues with the textConnection - the point Aaron
>> makes, the nasty name (try showConnections() to see), and close()-ing it.
>>
>> I think you need something more like this:
>>
>> ====
>> (header (if (or (eq (nth 1 value) 'hline) colnames-p)
>> "TRUE" "FALSE"))
>> (row-names (if rownames-p "1" "NULL")))
>> (if (= max min)
>> (format "
>> %s <-
>> local({con.object <-
>> %S
>> con <- textConnection(con.object)
>> res <- read.table(con,
>> header=%s,
>> row.names=%s,
>> sep=\"\\t\",
>> as.is=TRUE)
>> close(con)
>> res})"
>> name file header row-names)
>>
>> ====
>>
>> Notes: %S handles Aaron's quoting issue.
>> local() keeps unwanted objects out of user's way.
>> This worked on a couple of simple tests
>
> I agree completely here - thanks for the %S (didn't know about it - now
> I do) and haven't thought about the local() - I think it is a very good
> idea to use it in the context of the variable transfer.
>
>>
>> If you have `:session :results output' headers your session
>> transcript will have `file' dumped into it, which might be an annoyance.
>
> Not only annoyance - can cause overwriting of the data. Will look into
> this.
>
> Thanks a lot,
>
> Rainer
>
>>
>> HTH,
>>
>> Chuck
>>
>>
>>
>>
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
pgpVsaq6SD16N.pgp
Description: PGP signature
