Hello,
With the following patch the link to graphics output is finally back on
with R source code. Note that on top of the "graphics" parameter the
"file" parameter have to be used for the org-link to work out of the
box. I will try to remove the need for a second "file" parameter in the
future.
#+begin_src R :results output graphics file :file test2.pdf :session *local*
:cache no :dir "~/Documents/images"
plot(rnorm(100))
#+end_src
#+RESULTS:
[[file:images/test2.pdf]]
The link also works for R remote sessions. Comments are welcome. The
next steps
- Remove second the need for a second file parameter
- Add tests to avoid regression
- implement async in ob-R
>From e3d37da7b643990dc70ee42528051f1323fa5cae Mon Sep 17 00:00:00 2001
From: Jeremie Juste <jeremieju...@gmail.com>
Date: Wed, 23 Jun 2021 23:58:26 +0200
Subject: [PATCH 1/4] ob-R.el: Remove redundant argument to function
* lisp/ob-R.el (org-babel-R-construct-graphics-device-call): Modify
function to take only 'params' and not 'graphics-file'. The parameter
graphics-file can be extracted from params.
---
lisp/ob-R.el | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 2d9073cee..8266dc4ae 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -170,8 +170,7 @@ This function is called by `org-babel-execute-src-block'."
(mapconcat 'identity
(if graphics-file
(append
- (list (org-babel-R-construct-graphics-device-call
- graphics-file params))
+ (list (org-babel-R-construct-graphics-device-call params))
inside
(list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
inside)
@@ -311,13 +310,16 @@ Each member of this list is a list with three members:
3. the name of the argument to this function which specifies the
file to write to (typically \"file\" or \"filename\")")
-(defun org-babel-R-construct-graphics-device-call (out-file params)
+(defun org-babel-R-construct-graphics-device-call (params)
"Construct the call to the graphics device."
(let* ((allowed-args '(:width :height :bg :units :pointsize
:antialias :quality :compression :res
:type :family :title :fonts :version
:paper :encoding :pagecentre :colormodel
:useDingbats :horizontal))
+
+ (out-file (cdr (assq :file params)))
+
(device (file-name-extension out-file))
(device-info (or (assq (intern (concat ":" device))
org-babel-R-graphics-devices)
--
2.20.1
>From 589eab5d98a4156b46943c7201404300f0ae6ca0 Mon Sep 17 00:00:00 2001
From: Jeremie Juste <jeremieju...@gmail.com>
Date: Thu, 24 Jun 2021 00:04:59 +0200
Subject: [PATCH 2/4] ob-R.el: New function to construct org-link
* lisp/ob-R.el (org-babel-output-link-path:R): New function to
contruct org-link from 'params'.
---
lisp/ob-R.el | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 8266dc4ae..c325c9cfa 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -185,6 +185,13 @@ This function is called by `org-babel-execute-src-block'."
(org-babel-pick-name
(cdr (assq :rowname-names params)) rownames-p)))))
(if graphics-file nil result))))
+(defun org-babel-output-link-path:R (params)
+ "format org-link to file from PARAMS"
+
+ (format "[[file:%s]]" (concat (cdr (assq :dir params))
+ "/"
+ (cdr (assq :file params)))))
+
(defun org-babel-prep-session:R (session params)
"Prepare SESSION according to the header arguments specified in PARAMS."
--
2.20.1
>From b55148df0da94312e1a3e5709263ed9b66355384 Mon Sep 17 00:00:00 2001
From: Jeremie Juste <jeremieju...@gmail.com>
Date: Thu, 24 Jun 2021 00:07:39 +0200
Subject: [PATCH 3/4] ob-R.el: Return link if graphics parameter is used
* lisp/ob-R.el (org-babel-execute:R): Return org-link instead of nil if graphics
parameter is used.
---
lisp/ob-R.el | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index c325c9cfa..9f32db97a 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -184,7 +184,9 @@ This function is called by `org-babel-execute-src-block'."
(or (equal "yes" rownames-p)
(org-babel-pick-name
(cdr (assq :rowname-names params)) rownames-p)))))
- (if graphics-file nil result))))
+ (if graphics-file (org-babel-output-link-path:R params)
+ result))))
+
(defun org-babel-output-link-path:R (params)
"format org-link to file from PARAMS"
--
2.20.1
>From 12a06671415a55c726975d6e0297a20aefbbce62 Mon Sep 17 00:00:00 2001
From: Jeremie Juste <jeremieju...@gmail.com>
Date: Thu, 24 Jun 2021 00:11:10 +0200
Subject: [PATCH 4/4] ob-R.el: Handle graphics file path for remote R session
* lisp/ob-R.el (org-babel-R-construct-graphics-device-call): If R
session is remote, remove "/ssh:" part in file path before writing the
graph to file on remote host.
---
lisp/ob-R.el | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 9f32db97a..2769804a4 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -336,6 +336,11 @@ Each member of this list is a list with three members:
(extra-args (cdr (assq :R-dev-args params))) filearg args)
(setq device (nth 1 device-info))
(setq filearg (nth 2 device-info))
+ (setq out-file-path (concat
+ (replace-regexp-in-string "/ssh:.*?:" "" (cdr (assq :dir params)))
+ "/"
+ out-file))
+
(setq args (mapconcat
(lambda (pair)
(if (member (car pair) allowed-args)
@@ -344,7 +349,7 @@ Each member of this list is a list with three members:
(cdr pair)) ""))
params ""))
(format "%s(%s=\"%s\"%s%s%s); tryCatch({"
- device filearg out-file args
+ device filearg out-file-path args
(if extra-args "," "") (or extra-args ""))))
(defconst org-babel-R-eoe-indicator "'org_babel_R_eoe'")
--
2.20.1
Best regards,
--
Jeremie Juste
