[babel] [BUG] table with header line as parameter

[babel] [BUG] table with header line as parameter

[Andreas Leha]

Hi all,

I do not know what could be the cause of this, but I can't have a
table with header as argument to a source block any more:

#+name: table_w_header
| one | two |
|-----+-----|
| 1   | 3   |

#+begin_src R :var tbl=table_w_header

#+end_src

If I do C-c C-v v on the above source block, I get this backtrace:

,----
| Debugger entered--Lisp error: (wrong-type-argument sequencep hline)
|   length(hline)
|   mapcar(length (("one" "two") hline (1 3)))
|   org-babel-R-assign-elisp(tbl (("one" "two") hline (1 3)) nil nil)
|   #[(pair) "\302\b@\bA\303\304	\"A\305\232\303\306	\"A\305\232$\207" [pair params org-babel-R-assign-elisp assoc :colnames "yes" :rownames] 7]((tbl ("one" "two") hline (1 3)))
|   mapcar(#[(pair) "\302\b@\bA\303\304	\"A\305\232\303\306	\"A\305\232$\207" [pair params org-babel-R-assign-elisp assoc :colnames "yes" :rownames] 7] ((tbl ("one" "two") hline (1 3))))
|   org-babel-variable-assignments:R(((:cache . "no") (:colname-names (tbl "one" "two")) (:comments . "") (:exports . "code") (:hlines . "no") (:noweb . "no") (:padline . "") (:padnewline . "yes") (:result-params "replace") (:result-type . value) (:results . "replace") (:rowname-names) (:session . "none") (:shebang . "") (:tangle . "no") (:var tbl (1 3))))
|   org-babel-expand-body:R("\n" ((:cache . "no") (:colname-names (tbl "one" "two")) (:comments . "") (:exports . "code") (:hlines . "no") (:noweb . "no") (:padline . "") (:padnewline . "yes") (:result-params "replace") (:result-type . value) (:results . "replace") (:rowname-names) (:session . "none") (:shebang . "") (:tangle . "no") (:var tbl (1 3))))
|   org-babel-expand-src-block()
|   call-interactively(org-babel-expand-src-block nil nil)
`----

I tested on with emacs -Q on
1. GNU Emacs 24.1.50.1 (x86_64-pc-linux-gnu, GTK+ Version 3.4.1) of 2012-05-02 on zelenka, modified by Debian
2. GNU Emacs 23.4.1 (x86_64-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-04-07 on trouble, modified by Debian

My org-version: Org-mode version 7.8.09 with last commit
,----
| commit 56520a6936351d6fcc149652e1ff30f50c43eb4e
| Merge: 505cc7a 0ebeb77
| Author: Nicolas Goaziou <n.goaziou@gmail.com>
| Date:   Wed May 9 23:34:05 2012 +0200
| 
|     Merge branch 'maint'
`----
So, the fix discussed in
[[https://lists.gnu.org/archive/html/emacs-orgmode/2011-02/msg01444.html]]
should be there.


Not sure if this could be connected:  I updated my emacs-snapshot (the
24 version) from [[http://emacs.naquadah.org]] today.


Any help is highly appreciated,
Andreas

Re: [babel] [BUG] table with header line as parameter

[Andreas Leha]

Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:

> Hi all,
>
> I do not know what could be the cause of this, but I can't have a
> table with header as argument to a source block any more:
>
> #+name: table_w_header
> | one | two |
> |-----+-----|
> | 1   | 3   |
>
> #+begin_src R :var tbl=table_w_header
>
> #+end_src
>
> If I do C-c C-v v on the above source block, I get this backtrace:
>
> ,----
> | Debugger entered--Lisp error: (wrong-type-argument sequencep hline)
> |   length(hline)
> |   mapcar(length (("one" "two") hline (1 3)))
> |   org-babel-R-assign-elisp(tbl (("one" "two") hline (1 3)) nil nil)
> |   #[(pair) "\302\b@\bA\303\304 \"A\305\232\303\306 \"A\305\232$\207"
> | [pair params org-babel-R-assign-elisp assoc :colnames "yes"
> | :rownames] 7]((tbl ("one" "two") hline (1 3)))
> |   mapcar(#[(pair) "\302\b@\bA\303\304 \"A\305\232\303\306
> | \"A\305\232$\207" [pair params org-babel-R-assign-elisp assoc
> | :colnames "yes" :rownames] 7] ((tbl ("one" "two") hline (1 3))))
> |   org-babel-variable-assignments:R(((:cache . "no") (:colname-names
> | (tbl "one" "two")) (:comments . "") (:exports . "code") (:hlines
> | . "no") (:noweb . "no") (:padline . "") (:padnewline . "yes")
> | (:result-params "replace") (:result-type . value) (:results
> | . "replace") (:rowname-names) (:session . "none") (:shebang . "")
> | (:tangle . "no") (:var tbl (1 3))))
> |   org-babel-expand-body:R("\n" ((:cache . "no") (:colname-names (tbl
> | "one" "two")) (:comments . "") (:exports . "code") (:hlines . "no")
> | (:noweb . "no") (:padline . "") (:padnewline . "yes")
> | (:result-params "replace") (:result-type . value) (:results
> | . "replace") (:rowname-names) (:session . "none") (:shebang . "")
> | (:tangle . "no") (:var tbl (1 3))))
> |   org-babel-expand-src-block()
> |   call-interactively(org-babel-expand-src-block nil nil)
> `----
>
> I tested on with emacs -Q on
> 1. GNU Emacs 24.1.50.1 (x86_64-pc-linux-gnu, GTK+ Version 3.4.1) of 2012-05-02 on zelenka, modified by Debian
> 2. GNU Emacs 23.4.1 (x86_64-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-04-07 on trouble, modified by Debian
>
> My org-version: Org-mode version 7.8.09 with last commit
> ,----
> | commit 56520a6936351d6fcc149652e1ff30f50c43eb4e
> | Merge: 505cc7a 0ebeb77
> | Author: Nicolas Goaziou <n.goaziou@gmail.com>
> | Date:   Wed May 9 23:34:05 2012 +0200
> | 
> |     Merge branch 'maint'
> `----
> So, the fix discussed in
> [[https://lists.gnu.org/archive/html/emacs-orgmode/2011-02/msg01444.html]]
> should be there.
>
>
> Not sure if this could be connected:  I updated my emacs-snapshot (the
> 24 version) from [[http://emacs.naquadah.org]] today.
>
>
> Any help is highly appreciated,
> Andreas


Hi all,

sorry for answering to my own message.

I thought, that I did not pull between working state and broken state, but
apparently I did.

So, in the end, =git bisect= now told me the responsible commit:
,----
| fb7ebd2dae66a7b42aecff695fe40461a33a76ed is the first bad commit
| commit fb7ebd2dae66a7b42aecff695fe40461a33a76ed
| Author: Eric Schulte <eric.schulte@gmx.com>
| Date:   Wed Apr 25 15:34:15 2012 -0400
| 
|     clean up the code implementing reads of irregular data into R
|     
|     * lisp/ob-R.el (org-babel-R-assign-elisp): Clean up the code
|       implementing reads of irregular data into R.
`----

This commit is revertable, and reverting this commit also solves the
described issue for me.

Cheers,
Andreas

Re: [babel] [BUG] table with header line as parameter

[Eric Schulte]

Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:

> Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:
>
>> Hi all,
>>
>> I do not know what could be the cause of this, but I can't have a
>> table with header as argument to a source block any more:
>>
>> #+name: table_w_header
>> | one | two |
>> |-----+-----|
>> | 1   | 3   |
>>
>> #+begin_src R :var tbl=table_w_header
>>
>> #+end_src
>>
>> If I do C-c C-v v on the above source block, I get this backtrace:
>>
>> ,----
>> | Debugger entered--Lisp error: (wrong-type-argument sequencep hline)
>> |   length(hline)
>> |   mapcar(length (("one" "two") hline (1 3)))
>> |   org-babel-R-assign-elisp(tbl (("one" "two") hline (1 3)) nil nil)
>> |   #[(pair) "\302\b@\bA\303\304 \"A\305\232\303\306 \"A\305\232$\207"
>> | [pair params org-babel-R-assign-elisp assoc :colnames "yes"
>> | :rownames] 7]((tbl ("one" "two") hline (1 3)))
>> |   mapcar(#[(pair) "\302\b@\bA\303\304 \"A\305\232\303\306
>> | \"A\305\232$\207" [pair params org-babel-R-assign-elisp assoc
>> | :colnames "yes" :rownames] 7] ((tbl ("one" "two") hline (1 3))))
>> |   org-babel-variable-assignments:R(((:cache . "no") (:colname-names
>> | (tbl "one" "two")) (:comments . "") (:exports . "code") (:hlines
>> | . "no") (:noweb . "no") (:padline . "") (:padnewline . "yes")
>> | (:result-params "replace") (:result-type . value) (:results
>> | . "replace") (:rowname-names) (:session . "none") (:shebang . "")
>> | (:tangle . "no") (:var tbl (1 3))))
>> |   org-babel-expand-body:R("\n" ((:cache . "no") (:colname-names (tbl
>> | "one" "two")) (:comments . "") (:exports . "code") (:hlines . "no")
>> | (:noweb . "no") (:padline . "") (:padnewline . "yes")
>> | (:result-params "replace") (:result-type . value) (:results
>> | . "replace") (:rowname-names) (:session . "none") (:shebang . "")
>> | (:tangle . "no") (:var tbl (1 3))))
>> |   org-babel-expand-src-block()
>> |   call-interactively(org-babel-expand-src-block nil nil)
>> `----
>>
>> I tested on with emacs -Q on
>> 1. GNU Emacs 24.1.50.1 (x86_64-pc-linux-gnu, GTK+ Version 3.4.1) of 2012-05-02 on zelenka, modified by Debian
>> 2. GNU Emacs 23.4.1 (x86_64-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-04-07 on trouble, modified by Debian
>>
>> My org-version: Org-mode version 7.8.09 with last commit
>> ,----
>> | commit 56520a6936351d6fcc149652e1ff30f50c43eb4e
>> | Merge: 505cc7a 0ebeb77
>> | Author: Nicolas Goaziou <n.goaziou@gmail.com>
>> | Date:   Wed May 9 23:34:05 2012 +0200
>> | 
>> |     Merge branch 'maint'
>> `----
>> So, the fix discussed in
>> [[https://lists.gnu.org/archive/html/emacs-orgmode/2011-02/msg01444.html]]
>> should be there.
>>
>>
>> Not sure if this could be connected:  I updated my emacs-snapshot (the
>> 24 version) from [[http://emacs.naquadah.org]] today.
>>
>>
>> Any help is highly appreciated,
>> Andreas
>
>
> Hi all,
>
> sorry for answering to my own message.
>
> I thought, that I did not pull between working state and broken state, but
> apparently I did.
>
> So, in the end, =git bisect= now told me the responsible commit:
> ,----
> | fb7ebd2dae66a7b42aecff695fe40461a33a76ed is the first bad commit
> | commit fb7ebd2dae66a7b42aecff695fe40461a33a76ed
> | Author: Eric Schulte <eric.schulte@gmx.com>
> | Date:   Wed Apr 25 15:34:15 2012 -0400
> | 
> |     clean up the code implementing reads of irregular data into R
> |     
> |     * lisp/ob-R.el (org-babel-R-assign-elisp): Clean up the code
> |       implementing reads of irregular data into R.
> `----
>
> This commit is revertable, and reverting this commit also solves the
> described issue for me.
>
> Cheers,
> Andreas
>
>

Hi Andreas,

Thanks for reporting and for bisecting (which made fixing much easier).
I've just pushed up a fix.

Please let me know if problems persist.

Best,

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/