[Rd] Verbose output from R CMD check

dpleydell David.Pleydell at antilles.inra.fr
Tue Apr 23 16:51:42 CEST 2013

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.

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.

many thanks

David Pleydell,
Domaine Duclos,
Prise D'eau,
97122 Petit Bourg,
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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