[ This is a crazy bug where you have to increase optimization. ] I some to add here. I am involved in at least two packages which requires overriding the optimization switch to downgrade optimization. You have an additional problem where you need to add additional flags.
The solution in affxparser (see the source) is a custom compiler call where we place -O0 before the system/package compiler flags. This is not a great solution as it assumes that the compiler knows about -O notation (which is true for GCC but not a true assumption everywhere). In Rgraphviz I have the same problem (but not solved yet because of ... time). The issue here is that recent GCCs (v8 and higher) cannot be used with -O3 but needs -O2. I have started to think about a better solution than affxparser, to be used by the community, but have been a bit stumped. Preferably I would like to use autoconf macro for detecting GCC, but when we compile a package we are using the compiler encoded in R (aka $CC). So somehow I want to run autoconf "detect which compiler is used" but for a specific compiler. This is probably possible, but I don't know how right now. Then, conditional on GCC I plan to do a regex which replaces -O3 with -O2. This is not perfect either because the different -O3 optimizations can be supplied as individual flags, and I don't know which flag it is which breaks GCC. But it is must closer to the right solution. I don't know if regex/sed'ing is better than overriding by changing the order as in affxparser, but having the ability to do a conditional in Makevars would be good. Of course, the autoconf route does not address Windows, but I think we can assume / count on the fact that the RTools pipeline is used (aka, it is always GCC). I would be happy to communicate more on this, to get this sorted out. It has been a todo list item for me, for a while, and I should really try to resolve it. But for a quick fix, look at affxparser. Best, Kasper On Fri, May 24, 2019 at 10:16 AM Ramon Diaz-Uriarte <rdia...@gmail.com> wrote: > > Dear All, > > For a package we develop, OncoSimulR > (https://bioconductor.org/packages/release/bioc/html/OncoSimulR.html), we > have added new functionality > (https://github.com/rdiaz02/OncoSimul/tree/freq-dep-fitness) that uses the > ExprTk library[1] for parsing and evaluation of mathematical > expressions. This works fine under Linux. But it is known[2] that ExprTk > can fail when using MinGW with the "too many sections" error. > > > A solution that has been suggested is to use -Wa,-mbig-obj with -O3 [3]. > But I am unable to have R compile the package with -O3; -O3 is never > placed at the right of the default -O2 no matter what I set in > Makevars.win[4]. > > > > Any suggestions? > > Thanks, > > > R. > > > > [1] http://www.partow.net/programming/exprtk/index.html > [2] https://sourceforge.net/p/mingw-w64/discussion/723797/thread/c6b70624/ > . > [3] https://github.com/MrKepzie/Natron/blob/master/Engine/ExprTk.cpp > "// exprtk requires -Wa,-mbig-obj on mingw, but there is a bug that > prevents linking if not using -O3" > > See also, for example, > https://discourse.mc-stan.org/t/too-many-sections/6261 > > [4] > > https://stackoverflow.com/questions/23414448/r-makevars-file-to-overwrite-r-cmds-default-g-options > > Our package has > > CXX_STD = CXX11 > > > And I've tried: > > > ## To the left of -O2 > PKG_CXXFLAGS = -Wa,-mbig-obj -O3 > > ## To the left of -O2 > PKG_CXXFLAGS += -Wa,-mbig-obj -O3 > > > ## Also to the left of -O2 > PKG_CPPFLAGS = -Wa,-mbig-obj -O3 > > ## Also to the left of -O2 > PKG_CPPFLAGS += -Wa,-mbig-obj -O3 > > ## Ignored > PKG_CXX11FLAGS = -Wa,-mbig-obj -O3 > ## Ignored > PKG_CXX11FLAGS += -Wa,-mbig-obj -O3 > > > > > -- > Ramon Diaz-Uriarte > Department of Biochemistry, Lab B-25 > Facultad de Medicina > Universidad Autónoma de Madrid > Arzobispo Morcillo, 4 > 28029 Madrid > Spain > > Phone: +34-91-497-2412 > > Email: rdia...@gmail.com > ramon.d...@iib.uam.es > > http://ligarto.org/rdiaz > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
