Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Bastien b...@gnu.org writes: Hi Rainer, Rainer M Krug rai...@krugs.de writes: Amended patches attached. Applied, thanks, Thanks, Rainer -- 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 pgpaSMV6WtrTp.pgp Description: PGP signature
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Hi Rainer, Rainer M Krug rai...@krugs.de writes: Amended patches attached. Applied, thanks, -- Bastien
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Rainer M Krug Rainer at krugs.de writes: Nicolas Goaziou mail at nicolasgoaziou.fr writes: Hello, Rainer M Krug Rainer at krugs.de writes: [snip] Amended patches attached. AFAICS, these patches are good to go. Can they be applied, please? Chuck
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Rainer M Krug rai...@krugs.de writes: Just to ping these patches for application. Cheers, Rainer Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Rainer M Krug rai...@krugs.de writes: Attached please find two patches ready for application to fix that table variables were not usable adter tangling as temporary files were used. These patches were discussed in the thread [babel][PATCHES] ob-R patches for review I have not much to say about the feature, since I don't use R. Usual nitpicking follows. +(if (integerp value) (format %s - %s name (concat (number-to-string value) L)) + (if (floatp value) (format %s - %s name value) + (if (stringp value) (format %s - %S name value) + (format %s - %S name (prin1-to-string value))) I think a `cond' would be more readable here. Amended patches attached. Regards, -- 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 pgpUyiBKyFB1K.pgp Description: PGP signature
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Rainer M Krug rai...@krugs.de writes: Attached please find two patches ready for application to fix that table variables were not usable adter tangling as temporary files were used. These patches were discussed in the thread [babel][PATCHES] ob-R patches for review I have not much to say about the feature, since I don't use R. Usual nitpicking follows. +(if (integerp value) (format %s - %s name (concat (number-to-string value) L)) + (if (floatp value) (format %s - %s name value) +(if (stringp value) (format %s - %S name value) + (format %s - %S name (prin1-to-string value))) I think a `cond' would be more readable here. Agreed - my emacs lisp knowledge is growing daily... Will send the revised patch later, Rainer Regards, -- 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 pgpYisJfteTnT.pgp Description: PGP signature
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Nicolas Goaziou m...@nicolasgoaziou.fr writes:
Hello,
Rainer M Krug rai...@krugs.de writes:
Attached please find two patches ready for application to fix that table
variables were not usable adter tangling as temporary files were used.
These patches were discussed in the thread [babel][PATCHES] ob-R
patches for review
I have not much to say about the feature, since I don't use R. Usual
nitpicking follows.
+(if (integerp value) (format %s - %s name (concat (number-to-string
value) L))
+ (if (floatp value) (format %s - %s name value)
+(if (stringp value) (format %s - %S name value)
+ (format %s - %S name (prin1-to-string value)))
I think a `cond' would be more readable here.
Amended patches attached.
Regards,
--
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
From 38c029b38c85d9f9d35d0867b332eebc3daf1aca 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 1/2] 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 | 52
1 file changed, 32 insertions(+), 20 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index a3ae1ec..c77a103 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -190,32 +190,44 @@ 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
From 551d003d15c5cc9d3792909a12247fca58ae8d84 Mon Sep 17 00:00:00 2001
From: Rainer M. Krug r.m.k...@gmail.com
Date: Mon, 23 Jun 2014 12:11:59 +0200
Subject: [PATCH 2/2] Make transfer of values from R type aware
* lisp/ob-R.el (org-babel-R-assign-elisp): Added different cases for
transfer of integer, float, string and other variables to R so that
now integer values are transferred as integers (L) and
[O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Hi
Attached please find two patches ready for application to fix that table
variables were not usable adter tangling as temporary files were used.
These patches were discussed in the thread [babel][PATCHES] ob-R
patches for review
Thanks,
RainerFrom 38c029b38c85d9f9d35d0867b332eebc3daf1aca 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 1/2] 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 | 52
1 file changed, 32 insertions(+), 20 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index a3ae1ec..c77a103 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -190,32 +190,44 @@ 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
From e62a75e7227027c406d23fa9f8ac594db2ce81d6 Mon Sep 17 00:00:00 2001
From: Rainer M. Krug r.m.k...@gmail.com
Date: Mon, 23 Jun 2014 12:11:59 +0200
Subject: [PATCH 2/2] Make transfer of values from R type aware
* lisp/ob-R.el (org-babel-R-assign-elisp): Added different cases for
transfer of integer, float, string and other variables to R so that
now integer values are transferred as integers (L) and stored in R as
such. This change is backward compatible as integer values are
numerical values in R.
Moved definition of R functions for transfer of tables into defconst
ob-R-transfer-variable-table-with-header and
ob-R-transfer-variable-table-without-header.
---
lisp/ob-R.el | 78
1 file changed, 47 insertions(+), 31 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index c77a103..92c1dbc 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -93,6 +93,44 @@ this variable.)
(when (and session (string-match ^\\*\\(.+?\\)\\*$ session))
(save-match-data (org-babel-R-initiate-session session nil)
+(defconst ob-R-transfer-variable-table-with-header
+ %s - local({
+ con - textConnection(
+ %S
+ )
+ res - read.table(
+ con,
+ header= %s,
+ row.names = %s,
+ sep = \\\t\,
+ as.is
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Hello, Rainer M Krug rai...@krugs.de writes: Attached please find two patches ready for application to fix that table variables were not usable adter tangling as temporary files were used. These patches were discussed in the thread [babel][PATCHES] ob-R patches for review I have not much to say about the feature, since I don't use R. Usual nitpicking follows. +(if (integerp value) (format %s - %s name (concat (number-to-string value) L)) + (if (floatp value) (format %s - %s name value) + (if (stringp value) (format %s - %S name value) + (format %s - %S name (prin1-to-string value))) I think a `cond' would be more readable here. Regards, -- Nicolas Goaziou
