[Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

Neumann, Steffen sneumann at ipb-halle.de
Sun Apr 2 12:52:33 CEST 2017


in preparation for the release, we are hunting down WARNINGS
"Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
The abort() call is not coming from XCMS, but rather 
from the C++ code in the STL, and we have no idea 
how to get rid of it.

We are tracking this in: https://github.com/sneumann/xcms/issues/150

In a nutshell, the standard tenplate library (STL) that comes 
with g++-5.4.0 has a snippet:


# 1770 "/usr/include/c++/5/bits/stl_list.h"
void _M_check_equal_allocators(list& __x) {
 if (_M_get_Node_allocator())

You can also check this by looking at the compiler output 
after the preprocess step:

g++ -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-
protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g  -c massifquant/TrMgr.cpp -E | less

The same applies to mzR, where the same stl_list.h is included
in two files (Found ‘abort’, possibly from ‘abort’ (C)
    Objects: ‘./boost/libs/regex/src/instances.o’,

=> Since we don't want to patch the STL, we have no idea 
   how to fix that WARNING. Is there a way to get an exception, 
   or patch/whitelist this call in R CMD check ?

Steffen Neumann

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IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
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