[Bioc-devel] use -Wa, -mbig-obj -O3 when building package under Windows

[Ramon Diaz-Uriarte]

Dear Kasper,

Thank you very much. Using what you do in affxparser I can have the -O
settings at will.

(It turns out that did not solve the "too many sections" problem though, as
now the linker never exists; but that is a different story ---I am
currently trying to see if I can get it to work with Rtools 40).


Thanks again,


R.


On Fri, 24-May-2019, at 16:31:31, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> wrote:
> [ 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 <rdiaz02 using 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: rdiaz02 using gmail.com
>>        ramon.diaz using iib.uam.es
>>
>> http://ligarto.org/rdiaz
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>


--
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: rdiaz02 using gmail.com
       ramon.diaz using iib.uam.es

http://ligarto.org/rdiaz