On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
Hi,
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:
https://github.com/gcc-mirror/gcc/blob/1cb6c2eb3b8361d850be8e8270c59727
0a1a7967/libstdc%2B%2B-v3/include/bits/stl_list.h#L1825
...
# 1770 "/usr/include/c++/5/bits/stl_list.h"
void _M_check_equal_allocators(list& __x) {
if (_M_get_Node_allocator())
__builtin_abort();
}
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’,
‘./boost/libs/regex/src/winstances.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 ?
I don't think Bioconductor can help with this; maybe the Rcpp or R-devel
mailing lists?
Presumably there is a minimal example that generates the warning? It
would be convenient to communicate that (maybe a package as github
repo?) rather than the prospect of mzR / xcms installation & debugging.
Martin
Yours,
Steffen Neumann
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