This is fixed in R-rc_2017-04-19_r72555.tar.gz If you are affected by this issue then please test the RC tarball. This is the last chance to detect problems (including those created by the last-minute patch) before the release of R 3.4.0.
Martyn On Wed, 2017-04-19 at 12:19 +0000, Neumann, Steffen wrote: > Hi r-devel, > > a recent install of R-3.4.0 RC (2017-04-13 r72510) > on Linux (Ubuntu 16.04.1 LTS) x86_64-linux-gnu > with g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609 > (see http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-N > odeInfo.html for more) > results in CXXFLAGS not containing "-O2" as optimisation flag, > there is only " -Wall", while CFLAGS are happy with "-g -O2 > -Wall" > > This has an influence in at least one place > https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010733.html > where we have WARNINGS in R CMD check from "Found ‘abort’, > possibly from ‘abort’ (C)" in packages xcms/mzR. > The abort() call is not coming from XCMS, but rather > from the C++ code in the STL: > > [...] > # 1770 "/usr/include/c++/5/bits/stl_list.h" > void _M_check_equal_allocators(list& __x) { > if (_M_get_Node_allocator()) > __builtin_abort(); > } > > If we compile with -O2 optimisation, this getting rid of > the abort() symbol, as shown > in https://github.com/sneumann/xcms/issues/150#issuecomment-293545521 > > Martin Morgan created a minimum example that shows that > the symbol is indeed deep down in the STL (see below and in: > https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010837.html ) > > This raises several questions: > > 1) is there any way to avoid the WARNING / abort() inside > the STL list implementation ? Or just live with it ? > > 2) If not, is there a reason why the Bioconductor build farm > Ubuntu machine is not using -O2 as default CXXFLAG ? > BioC admins are trying to have a vanilla R installation with > defaults. > According to Herve Pages, CXXFLAGS without -O2 is default > since R-3.4 beta, but I don't know enough about the package > build logic to point to a particular R commit. > > 3) I thought about cheating the system and add -O2 > in the package CXXFLAGS, but Martin Morgan > recommends packages shouldn't mess and override system build > defaults > to mask and paper over the actual issue having a nasty abort() > lurking somewhere. > But I couldn't add PKG_CXXFLAGS=-O2 in first place, since that > triggers the different WARNING that -O2 is not portable. > > => Any help and input would be highly appreciated. > > Thanks in advance, > yours, > Steffen > > > tmp.cpp by Martin Morgan (also in above linked mail thread) > ------- > #include <list> > > int foo(int argc, const char *argv[]) { > std::list<int> l1, l2; > std::list<int>::iterator it; > > it = l1.begin(); > l1.splice (it, l2); // mylist1: 1 10 20 30 2 3 4 > > return 0; > } > ------- > > Test with > > rm -f tmp.o && R CMD SHLIB tmp.cpp && nm tmp.o | grep abort > > with compiler settings in ~/.R/Makevars with/without -O2 > ------------- > CXXFLAGS = -g -O0 > ------------- > > > > > > -- > 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 > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
