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 ? Yours, Steffen Neumann -- Current job opportunities @ IPB Halle: For details, see: http://www.ipb-halle.de/en/career/job-vacancies/ * Department Head * LIMS-Manager / Data manager ---------------------------------------------------------- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
