[R-sig-Debian] LTO flags in 4.1.0 Ubuntu 21.04 Makeconf

[Karl Dunkle Werner]

Hello Dirk,

Thanks for the very helpful response!


Answering the points you made, not in order:

> | Would it be possible to remove the flags -flto=auto and -ffat-lto-objects?
>
> Not likely for the package I ship. I tend to not second guess upstream, and
> have followed R Core pretty much without changes to the program for 20 years.
>
> If you think you need a locally modified version I may be able to help you
> build one.
Got it, and thank you for the offer! I can edit my Makeconf (everything 
works when I remove the LTO-related flags). I was hoping to make 
installation smoother for other Arrow and Ubuntu users, but maybe that's 
something users or the Arrow developers will need to tackle.



> but I would be interested to hear how others fared on Debian or Ubuntu systems.
In my experience, installing Arrow has gotten a lot better over time 
(including the reinstall requirement; see 
https://cran.r-project.org/web/packages/arrow/vignettes/install.html). 
It's still the most finicky of the packages I install, but substantially 
improved.




I think I'm confused by this comment (because I don't know much about 
the packaging process).
> - the Debian and hence derived Ubuntu package of R 4.1.0 does*not*  enable
>    LTO yet, in other words I have not yet add --enable-lto to the configure
>    call and we use to default of 'nope'
I'm confused because the R 4.1.0 Debian versions have flags like:
CXX11FLAGS = -g -O2 
-ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.1.0=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g $(LTO)

The R 4.1.0 Ubuntu 20.10 flags are:
CXX11FLAGS = -g -O2 
-fdebug-prefix-map=/build/r-base-2Aokdc/r-base-4.1.0=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g $(LTO)

While the R 4.1.0 Ubuntu 21.04 flags are:
CXX11FLAGS = -g -O2 
-ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto 
-ffat-lto-objects -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)

Should the Ubuntu 21.04 LTO flags be different than the others?


> That is something you may need to discuss with either R Core upstream (for
> the Makeconf), or maybe with the Arrow team for how they build the
> package. And there could of course be a bug but I remind you that Arrow
> itself is on CRAN.
The GCC docs note that the -flto flag will enable LTO, but it can be 
disabled by passing -fno-lto in the link command 
(https://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html#index-flto). 
I'll see if the Arrow folks are able to set -fno-lto.



If it's at all helpful, here's a reproducible example using Rocker 
(thank you for making this easy to troubleshoot across R installations).

1. Download the Makeconf file with these LTO flags 
(https://issues.apache.org/jira/secure/attachment/13025950/Makeconf_local) 
or extract it from the Ubuntu 21.04 deb file 
(https://cloud.r-project.org/bin/linux/ubuntu/hirsute-cran40/r-base-core_4.1.0-1.2104.0_amd64.deb).
2. Start docker: docker run -e "LIBARROW_BINARY=false" -e 
"ARROW_R_DEV=true" -e "LIBARROW_MINIMAL=true" --rm -ti rocker/r-base:4.1.0
3. In a different terminal, find the docker container ID: docker ps
4. Copy Makeconf: docker cp Makeconf_local <container ID>:/etc/R/Makeconf
5. In the docker R:
     tools::Rcmd("config CXX11FLAGS") to see the new flags
     install.packages("arrow") now fails

My challenges are with the Makeconf flags packaged with Ubuntu 21.04's R 
4.1.0, but the example above also fails when the same Makeconf file is 
copied into the rocker/r-base:4.0.5 image.


Thanks,
Karl



On 6/1/21 3:50 PM, Dirk Eddelbuettel wrote:
> Two more follow-ups if I may:
>
> - the Debian and hence derived Ubuntu package of R 4.1.0 does *not* enable
>    LTO yet, in other words I have not yet add --enable-lto to the configure
>    call and we use to default of 'nope'
> - my dev box is still 20.10; I only run 21.04 on one small machine where I
>    have not tried to build arrow; but under 20.10 + R 4.1.0 + arrow 4.0.? the
>    two step dance that they force on us works
>
> Dirk
>


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