[O] [NEW PATCH] read.table in variable transfer caused sometimes "function not found" error - small change

[Rainer M Krug]

"Charles C. Berry" <address@hidden> writes:

> On Wed, 8 Oct 2014, Rainer M Krug wrote:
>
>> "Charles C. Berry" <address@hidden> writes:
>>
>>> On Wed, 8 Oct 2014, Rainer M Krug wrote:
>>>
>>>> "Charles C. Berry" <address@hidden> writes:
>>>>
>>>>> On Mon, 6 Oct 2014, Rainer M Krug wrote:
>>>>>
>>>>>> Hi
>>>>>>
>>>>>> The variable transfer of tables from org to R caused sometimes 'could
>>>>>> not find function "read.table"' errors (e.g. when the file was tangled
>>>>>> into a ./data directory which was loaded by the function
>>>>>> devtools::load_all("./")). This can easily be fixed by adding the package
>>>>>> name to the call in R, i.e. replacing =read.table()= with
>>>>>> =utils::read.table()= which is done in this patch.
>>>>>
>>>>> It does fix that one case.
>>>>>
>>>>> But I wonder if that is the best way.
>>>>>
>>>>> The heart of the matter is that load_all eventually calls sys.source,
>>>>> which can be persnickety about finding objects on the search path. See
>>>>> ?sys.source.
>>>>>
>>>>> If the src block you tangle to ./data/ has any code that uses any
>>>>> other objects from utils, stats, datasets or whatever, you will be in
>>>>> the same pickle.
>>>>
>>>> Exactly - that is true. But it is the same when putting this in a
>>>> package (as far as I am aware).
>>>>
>>>
>>> Do you mean that putting `x <- rnorm(10)' into a data/*.R file will
>>> fail when you try to build and check?
>>>
>>> In fact, `R CMD build' will execute it and save the result as a
>>> data/*.rda file. And check will go through.
>>>
>>> devtools::load_all (calling load_data) fails to do that. Which is why
>>> I think this is a devtools issue.
>>
>> OK - point taken. But I still think that the =utils::read.table()= would
>> not hurt, rather make the variable transfer safer.
>>
>
> What you want to change is in a defconst. So, the user can override
> with a file-local version.
>
> So, making the change really is harmless.
>
> Maybe add a note to the docstring to say that using
> utils::read.table' assures that `read.table' always can be found just
> in case anyone ever asks.

OK - done in attached patch.

Rainer

From 1eadbf6b44b8fc2fa5af29ea483383e9d137d19e Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <address@hidden>
Date: Mon, 6 Oct 2014 13:48:49 +0200
Subject: [PATCH] ob-R.el: Add package name to read.table call

* lisp/ob-R.el:
(ob-R-transfer-variable-table-with-header): Add package name to call
of R function read.table (now utils::read.table).  This clarifies the
call as well as avoids 'could not find function' error in R under
certain conditions.
---
 lisp/ob-R.el | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index ea33031..a64b647 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -101,7 +101,7 @@ this variable.")
      con <- textConnection(
        %S
      )
-     res <- read.table(
+     res <- utils::read.table(
        con,
        header    = %s,
        row.names = %s,
@@ -112,14 +112,17 @@ this variable.")
      res
    })"
   "R code used to transfer a table defined as a variable from org to R.
-This function is used when the table contains a header.")
+This function is used when the table contains a header. The usage
+of utils::read.table() ensures that the command read.table() can
+be found even in circumstances when the utils package is not in
+the search path from R.")
 
 (defconst ob-R-transfer-variable-table-without-header
   "%s <- local({
      con <- textConnection(
        %S
      )
-     res <- read.table(
+     res <- utils::read.table(
        con,
        header    = %s,
        row.names = %s,
-- 
2.1.2

>
> Chuck
>
>

-- 
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982

pgp_d6kxJgUjI.pgp
Description: PGP signature