From edd at debian.org  Tue Nov  4 15:42:08 2014
From: edd at debian.org (Dirk Eddelbuettel)
Date: Tue, 4 Nov 2014 08:42:08 -0600
Subject: [Rd] Linking to the BH package introduces CRAN warnings
In-Reply-To: <5458D68D.3070102@gmail.com>
References: <5458D68D.3070102@gmail.com>
Message-ID: <21592.58816.359652.109459@max.nulle.part>


On 4 November 2014 at 14:37, kaveh wrote:
| Dear all,
| 
| I'm working on a project that links to the BH package
| (http://cran.r-project.org/web/packages/BH/index.html).
| 
| My packages doesn't call entry points which might terminate R nor
| write to stdout/stderr instead of to the console.
| 
| However, it seems some of the codes in the BH package
| might. At any rate, when I include some boost headers such as
| boost/math/distributions/ through BH, I get the following warnings
|   when  submitting to the win-builder page:
| 
| 
|    Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| 
|    Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| 
|    Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| 
|    Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| 
| 
|   Furthermore, these warnings disappear when remove the boost
|   headers and replace the call to boost functions by constants.
| 
| Looking at the CRAN-check diagnostics of some other packages that link to
| BH, I do not see similar warnings, so I suppose it is possible to fix 
| this issue.
| Looking at their source code, it is not clear to me how these authors have
| managed to do this, but this might be because I'm not that familiar with
| boost to begin with. Can someone point me to some solution to this problem?

Briefly:

i) Your subject line is wrong.  You do not "link" to BH, you use it to
include headers at compile time. That may seem like a small difference, but
it is not. You generally want to avoid linking as much as you can, if only
for cross-OS portability,

ii) This the R-devel list for R question. You have a package question. You
are generally advised to contact __the package authors__ and/or the package
mailing list. And yes, BH has one in

    http://lists.r-forge.r-project.org/pipermail/boostheaders-devel/

though I grant you that it is not as well advertised as it should be. I just
opened a ticket at https://github.com/eddelbuettel/bh/issues/3 to remind
myself to improve that.

iii) As for your problem, only you and some careful bisections can help you
there as we do not have your sources.  I too have packages including BH
headers, but they do not pull in abort() or other things the CRAN gatekeepers
prohibit us from deploying.

Dirk
aka your friendly neighborhood BH maintainer

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org



[Rd] Linking to the BH package introduces CRAN warnings
Dirk Eddelbuettel