[Rd] Verbose output from R CMD check

Simon Urbanek simon.urbanek at r-project.org
Tue Apr 23 17:21:17 CEST 2013

On Apr 23, 2013, at 10:51 AM, dpleydell wrote:

> I've been developing a package called foobar for a couple of years now. It has evolved through various versions, but has always contained compiled C code. Recently, R CMD check has started generating the following message
> R CMD check foobar_1.7.5.tar.gz
> * using log directory ‘/home/david/foobar/package/foobar.Rcheck’
> * using R version 2.15.2 (2012-10-26)
> * using platform: x86_64-unknown-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘foobar/DESCRIPTION’ ... OK
> * checking compiled code ... NOTE
> File ‘/home/david/foobar/package/foobar.Rcheck/foobar/libs/foobar.so’:
>  Found ‘putchar’, possibly from ‘putchar’ (C)
>    Object: ‘foobar.o’
>  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
>    Object: ‘foobar.o’
> Compiled code should not call functions which might terminate R nor write to stdout/stderr instead of to the console.
> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
> * checking examples ... OK
> * checking PDF version of manual ... OK
> NOTE: There was 1 note.
> See ‘/home/david/foobar/package/foobar.Rcheck/00check.log’ for details.
> This message is recent, but appears even when I re-compile and check old versions of the package which previously passed the check without any such warning messages.
> My understanding is that since R 2.15.0 R CMD check has undergone numerous modifications, and as a result it is now identifying a "problem" that wasn't being identified previously. I'm currently running R 2.15.2.
> Identifying the source of the message is a non-trivial problem because there are a large number of calls to printf and fprintf etc in several thousands of lines of code spread over many different *.c files.

There should be none, so apparently you have broken the rules quite a lot ;). This is not a new rule, R just got better at identifying the transgressions. Number of lines in your code is quite irrelevant - that's why there is grep and the search function in editors.

> So my question... is there a way to obtain a more verbose output that could point me to the lines of code that generate the message? Without this information debugging is rendered unnecessarily hard, time consuming and frustrating.

It's not "unnecessarily hard" - it fact it's much easier to find this out from the sources than the compiled code which is how R has to identify it which makes it impossible to track the source (because it could have been from a static library, for example).


> many thanks
> David
> -- 
> David Pleydell,
> UMR-1351 CMAEE,
> Domaine Duclos,
> Prise D'eau,
> 97122 Petit Bourg,
> Guadeloupe
> dpleydell at antilles.inra.fr
> pleydell at cirad.fr
> Tel +33 5 90 25 54 42
> Fax +33 5 90 94 03 96
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