From: Rainer M Krug <Rainer@krugs.de>
To: "Charles C. Berry" <ccberry@ucsd.edu>
Cc: emacs-orgmode@gnu.org
Subject: [NEW PATCH] read.table in variable transfer caused sometimes "function not found" error - small change
Date: Thu, 09 Oct 2014 10:19:48 +0200 [thread overview]
Message-ID: <m2lhopvemz.fsf_-_@krugs.de> (raw)
In-Reply-To: <alpine.OSX.2.00.1410081426130.1655@charles-berrys-macbook.local> (Charles C. Berry's message of "Wed, 8 Oct 2014 14:34:49 -0700")
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"Charles C. Berry" <ccberry@ucsd.edu> writes:
> On Wed, 8 Oct 2014, Rainer M Krug wrote:
>
>> "Charles C. Berry" <ccberry@ucsd.edu> writes:
>>
>>> On Wed, 8 Oct 2014, Rainer M Krug wrote:
>>>
>>>> "Charles C. Berry" <ccberry@ucsd.edu> 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
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From 1eadbf6b44b8fc2fa5af29ea483383e9d137d19e Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
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
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>
> Chuck
>
>
--
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982
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next prev parent reply other threads:[~2014-10-09 8:22 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-10-06 12:00 [PATCH] read.table in variable transfer caused sometimes "function not found" error - small change Rainer M Krug
2014-10-07 20:51 ` Charles C. Berry
2014-10-08 9:54 ` Rainer M Krug
2014-10-08 15:43 ` Charles C. Berry
2014-10-08 18:39 ` Rainer M Krug
2014-10-08 21:34 ` Charles C. Berry
2014-10-09 8:19 ` Rainer M Krug [this message]
2014-10-09 8:25 ` [NEW PATCH] " Rainer M Krug
2014-10-10 4:21 ` Aaron Ecay
2014-10-10 7:43 ` Rainer M Krug
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