cannot compile with R 4.3.2 under Fedora 38 about rwcs HOT 11 CLOSED

@rtobar These are the CFLAGS for each compilation: one has the lto, the other does not:

4.3.2

• CFLAGS: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer

4.2.3

• CFLAGS: -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection

from rwcs.

Thanks @cnaw for confirming the issue can be bypassed with the -fno-lto option. I'll still follow this up on our side, users shouldn't need to do/remove compilation flags for our package to be installed.

from rwcs.

@cnaw Thanks for reporting this.

This seems to be a clash between R and wcslib both choosing to name a global variable CAR. C doesn't provide namespaces, so unless you prefix your global names, or make them static so they don't escape your translation unit, they'll prevent others from using those names.

The ideal solution is that this clash doesn't happen. There's no point on trying to change R's internals, that's an uphill battle most probably due to many reasons. But we might have a better chance changing wcslib. I'll check if this is something that an be changed upstream, but worst-case scenario we can patch our embedded sources to prevent the issue.

While I haven't looked into the header differences, if they don't affect the definition of CAR then there must be another explanation as to why this didn't happen before. One possibility is that, in your system, R 4.3 compiles extensions with LTO, but 4.2 doesn't, but I can't tell if the latter is true from your message. Could you confirm that's the case? Thanks!

from rwcs.

Awesome, that makes sense then.

As a workaround, and if you need to compile for 4.3.2 in your system, you could pass -flto=no (I'm assuming the value "no", maybe it's a different one) in your CXXFLAGS / CXX11FLAGS in your ~/.R/Makevars to override the LTO behaviour and hopefully get a successful compilation.

from rwcs.

Thanks for the tip. I have been trying with -flto -flto=no and the code still does not compile. This is an example :
Installing package into ‘/home/cnaw/R/x86_64-redhat-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)

• installing source package ‘Rwcs’ ...
  ** using staged installation

• Running configure on Linux
• R_HOME: /usr/lib64/R
• R_ARCH:
• R_ARCH_BIN:
• CC: gcc
• CFLAGS: -O3 -Wall -mtune=native -march=native -Ofast -std=gnu99 -flto
• AR:
  checking build system type... x86_64-pc-linux-gnu
  checking host system type... x86_64-pc-linux-gnu
  checking for flex... flex
  configure: Using Flex version 2.6.4.
  checking for gcc... gcc
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... configure: error: in /tmp/RtmpLiPEWb/R.INSTALL19d1173a0d4be/Rwcs/src/wcslib': configure: error: cannot run C compiled programs. If you meant to cross compile, use --host'.
  See `config.log' for more details
  ERROR: configuration failed for package ‘Rwcs’

• removing ‘/home/cnaw/R/x86_64-redhat-linux-gnu-library/4.3/Rwcs’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpOa1vbt/file19c937957190f/Rwcs_1.7.0.tar.gz’ had non-zero exit status
  ...
  I cannot find the "config.log" to understand what is the error - I have the impression that it is stored in the /tmp file which gets erased. Is there any additional parameter that I should be adding to ~/.R/Makevars ?

from rwcs.

What about -fno-lto? That's apparently the correct syntax, sorry for the wrong guess earlier.

from rwcs.

Another update: I edited my ~/.R/Makevars to:

CXXFLAGS=-Wall -O3 -g -flto
CXX11FLAGS=-Wall -O3 -g -flto
CFLAGS=-Wall -O3 -g -flto

and that reproduced the issue. I then edited it like this:

CXXFLAGS=-Wall -O3 -g -flto -fno-lto
CXX11FLAGS=-Wall -O3 -g -flto -fno-lto
CFLAGS=-Wall -O3 -g -flto -fno-lto

and the problem was gone.

from rwcs.

Thanks, this did make the magic work!
These are the contents of ~/.R/Makevars that make the compilation successful:

CC = gcc
CXX = g++
CXX1X = g++
CXX11 = g++

CXXFLAGS=-Wall -O3 -g -flto -fno-lto
CXX11FLAGS=-Wall -O3 -g -flto -fno-lto
CFLAGS=-Wall -O3 -g -flto -fno-lto -fexceptions -g -grecord-gcc-switches -pipe -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer

I had to do this as a normal user rather than running sudo R.
(any potential future users be aware that CFLAGS is a single line, e.g. -Wp,-U_FORTIFY_SOURCE, etc.)
Thanks a lot for your help! I will close the issue.

from rwcs.

@cnaw if you have some time, could you try compiling the lto-fix branch of this repository with R 4.3.2 without the extra compilation flags? After that's successful I'll merge to master. Note that I've also asked Mark Callabreta to upstream this change in wcslib itself for good measure.

from rwcs.

@rtobar I did this as a user:

git clone -b lto-fix https://github.com/asgr/Rwcs.git
tar -zcvf Rwcs_1.70_fix.tar.gz Rwcs
mv ~/.R/Makevars ~/.R/org_Makevars
cd R
R
library(devtools)
install.packages("/home/cnaw/Rwcs_1.70_fix.tar.gz",repos=NULL,type="source")
...

• CFLAGS: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer
  ...

• DONE (Rwcs)
  ...
  To have an independent confirmation that the new fixes work I tried again, this time as superuser (yesterday the installation failed as su). With the new fixes it works! Thank you for keeping on top of this!

from rwcs.

Great, thanks for the confirmation @cnaw, I've merged the fix to master now.

from rwcs.