R devel - May 2023 - R-4.2.3 build from source on Windows (w Rtools42) - lto1.exe error

Windows 11 PRO Version??10.0.22621 Build 22621
Processor: Intel(R) Core(TM) i7-1065G7 "Icelake-client"
```
?svn info	
Path: .
Working Copy Root Path: /d/R_DEV/R-4/R42/R-4-2-branch
URL: https://svn.r-project.org/R/branches/R-4-2-branch
Relative URL: ^/branches/R-4-2-branch
Repository Root: https://svn.r-project.org/R
Repository UUID: 00db46b3-68df-0310-9c12-caf00c1e9a41
Revision: 84417
Node Kind: directory
Schedule: normal
Last Changed Author: kalibera
Last Changed Rev: 84249
Last Changed Date: 2023-04-13 07:12:24 +0000 (Thu, 13 Apr 2023)
```

Only adaptation done in MkRules.local was adding: `EOPTS = -march=native`  -
that's why I included the cpu-type info above;
running make all recommended? fails at/with:
```
gcc -shared -s -static-libgcc -o utils.dll tmp.def init.o io.o size.o sock.o
stubs.o utils.o hashtab.o windows/dataentry.o windows/dialogs.o
windows/registry.o windows/util.o windows/widgets.o
../../../gnuwin32/dllversion.o -lRgraphapp -lversion
-L/x86_64-w64-mingw32.static.posix/lib/x64 -llzma
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -L../../../../bin/x64 -lR

lto1.exe: fatal error: bytecode stream in file 'windows/dataentry.o'
generated with LTO version 9.3 instead of the expected 9.4
compilation terminated.

lto-wrapper.exe: fatal error:
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\gcc.exe returned 1 exit status
compilation terminated.
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: error: lto-wrapper
failed
collect2.exe: error: ld returned 1 exit status
cp: cannot stat 'utils.dll': No such file or directory
make[4]: *** [Makefile.win:36: shlib] Error 1
make[3]: *** [../../../share/make/basepkg.mk:145: mksrc-win2] Error 1
make[2]: *** [Makefile.win:24: all] Error 2
make[1]: *** [Makefile.win:34: R] Error 1
make: *** [Makefile:18: all] Error 2
```
Any hints/ideas on how to fix this? I guess I could 
gcc -c -flto ... windows/dataentry.c -o windows/dataentry.o 
with the exact path of that fiile ... 
and it hopefully will fix that but I guess it would make sense to add a Revision
to update that LTO version mismatch there, and I don't know yet if this is
the only one?

Greetings,
W

Hi. 

Are you sure you have the most up-to-date version of the libraries? It should be
version 5550. Tomas updates the entire toolchain semi-regularly. If you call ?
cat /x86_64-w64-mingw32.static.posix/.version? and it?s not 5550, try updating
the libraries as per
https://cran.r-project.org/bin/windows/base/howto-R-devel.html.

Hope that helps,

Avi

Sent from my iPhone
> On May 10, 2023, at 9:07 PM, Gmail <walter.djuric at gmail.com>
wrote:
> 
> ?Windows 11 PRO Version??10.0.22621 Build 22621
> Processor: Intel(R) Core(TM) i7-1065G7 "Icelake-client"
> ```
> ?svn info    
> Path: .
> Working Copy Root Path: /d/R_DEV/R-4/R42/R-4-2-branch
> URL: https://svn.r-project.org/R/branches/R-4-2-branch
> Relative URL: ^/branches/R-4-2-branch
> Repository Root: https://svn.r-project.org/R
> Repository UUID: 00db46b3-68df-0310-9c12-caf00c1e9a41
> Revision: 84417
> Node Kind: directory
> Schedule: normal
> Last Changed Author: kalibera
> Last Changed Rev: 84249
> Last Changed Date: 2023-04-13 07:12:24 +0000 (Thu, 13 Apr 2023)
> ```
> 
> Only adaptation done in MkRules.local was adding: `EOPTS = -march=native` 
- that's why I included the cpu-type info above;
> running make all recommended? fails at/with:
> ```
> gcc -shared -s -static-libgcc -o utils.dll tmp.def init.o io.o size.o
sock.o stubs.o utils.o hashtab.o windows/dataentry.o windows/dialogs.o
windows/registry.o windows/util.o windows/widgets.o
../../../gnuwin32/dllversion.o -lRgraphapp -lversion
-L/x86_64-w64-mingw32.static.posix/lib/x64 -llzma
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -L../../../../bin/x64 -lR
> 
> lto1.exe: fatal error: bytecode stream in file
'windows/dataentry.o' generated with LTO version 9.3 instead of the
expected 9.4
> compilation terminated.
> 
> lto-wrapper.exe: fatal error:
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\gcc.exe returned 1 exit status
> compilation terminated.
> C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: error: lto-wrapper
failed
> collect2.exe: error: ld returned 1 exit status
> cp: cannot stat 'utils.dll': No such file or directory
> make[4]: *** [Makefile.win:36: shlib] Error 1
> make[3]: *** [../../../share/make/basepkg.mk:145: mksrc-win2] Error 1
> make[2]: *** [Makefile.win:24: all] Error 2
> make[1]: *** [Makefile.win:34: R] Error 1
> make: *** [Makefile:18: all] Error 2
> ```
> Any hints/ideas on how to fix this? I guess I could 
> gcc -c -flto ... windows/dataentry.c -o windows/dataentry.o 
> with the exact path of that fiile ... 
> and it hopefully will fix that but I guess it would make sense to add a
Revision to update that LTO version mismatch there, and I don't know yet if
this is the only one?
> 
> Greetings,
> W
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
	[[alternative HTML version deleted]]

Initial comments

- R 4.2.3 is not current

- -flto does not seem to be the default in src/gnuwin32/MkRules.

- LTO versions in GCC are tied to the compiler version, and in recent 
GCC are the same as the compiler version.  The recommended toolchain for 
R 4.2.x is Rtools42 which according to NEWS is based on GCC 10 not 9.

- LTO mismatches in my experience are most often seen in incremental 
builds, so first do an ab initio build.  (Not so long ago they were not 
detected during linking but gave segfaults.)

Assuming it is important to use LTO, I would first build without LTO to 
isolate the issue.  And be aware of the following in the NEWS for R 4.3.0:

     ? The Rcomplex definition (in header R_ext/Complex.h) has been
       extended to prevent possible mis-compilation when interfacing
       with Fortran (PR#18430).

AFAIR that "possible mis-compilation" is most likely using LTO.


On 11/05/2023 02:07, Gmail wrote:
> Windows 11 PRO Version??10.0.22621 Build 22621
> Processor: Intel(R) Core(TM) i7-1065G7 "Icelake-client"
> ```
> ?svn info	
> Path: .
> Working Copy Root Path: /d/R_DEV/R-4/R42/R-4-2-branch
> URL: https://svn.r-project.org/R/branches/R-4-2-branch
> Relative URL: ^/branches/R-4-2-branch
> Repository Root: https://svn.r-project.org/R
> Repository UUID: 00db46b3-68df-0310-9c12-caf00c1e9a41
> Revision: 84417
> Node Kind: directory
> Schedule: normal
> Last Changed Author: kalibera
> Last Changed Rev: 84249
> Last Changed Date: 2023-04-13 07:12:24 +0000 (Thu, 13 Apr 2023)
> ```
> 
> Only adaptation done in MkRules.local was adding: `EOPTS = -march=native` 
- that's why I included the cpu-type info above;
> running make all recommended? fails at/with:
> ```
> gcc -shared -s -static-libgcc -o utils.dll tmp.def init.o io.o size.o
sock.o stubs.o utils.o hashtab.o windows/dataentry.o windows/dialogs.o
windows/registry.o windows/util.o windows/widgets.o
../../../gnuwin32/dllversion.o -lRgraphapp -lversion
-L/x86_64-w64-mingw32.static.posix/lib/x64 -llzma
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -L../../../../bin/x64 -lR
> 
> lto1.exe: fatal error: bytecode stream in file
'windows/dataentry.o' generated with LTO version 9.3 instead of the
expected 9.4
> compilation terminated.
> 
> lto-wrapper.exe: fatal error:
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\gcc.exe returned 1 exit status
> compilation terminated.
> C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: error: lto-wrapper
failed
> collect2.exe: error: ld returned 1 exit status
> cp: cannot stat 'utils.dll': No such file or directory
> make[4]: *** [Makefile.win:36: shlib] Error 1
> make[3]: *** [../../../share/make/basepkg.mk:145: mksrc-win2] Error 1
> make[2]: *** [Makefile.win:24: all] Error 2
> make[1]: *** [Makefile.win:34: R] Error 1
> make: *** [Makefile:18: all] Error 2
> ```
> Any hints/ideas on how to fix this? I guess I could
> gcc -c -flto ... windows/dataentry.c -o windows/dataentry.o
> with the exact path of that fiile ...
> and it hopefully will fix that but I guess it would make sense to add a
Revision to update that LTO version mismatch there, and I don't know yet if
this is the only one?
> 
> Greetings,
> W
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

On 5/11/23 03:07, Gmail wrote:
> Windows 11 PRO Version??10.0.22621 Build 22621
> Processor: Intel(R) Core(TM) i7-1065G7 "Icelake-client"
> ```
> ?svn info	
> Path: .
> Working Copy Root Path: /d/R_DEV/R-4/R42/R-4-2-branch
> URL: https://svn.r-project.org/R/branches/R-4-2-branch
> Relative URL: ^/branches/R-4-2-branch
> Repository Root: https://svn.r-project.org/R
> Repository UUID: 00db46b3-68df-0310-9c12-caf00c1e9a41
> Revision: 84417
> Node Kind: directory
> Schedule: normal
> Last Changed Author: kalibera
> Last Changed Rev: 84249
> Last Changed Date: 2023-04-13 07:12:24 +0000 (Thu, 13 Apr 2023)
> ```
>
> Only adaptation done in MkRules.local was adding: `EOPTS = -march=native` 
- that's why I included the cpu-type info above;
> running make all recommended? fails at/with:
> ```
> gcc -shared -s -static-libgcc -o utils.dll tmp.def init.o io.o size.o
sock.o stubs.o utils.o hashtab.o windows/dataentry.o windows/dialogs.o
windows/registry.o windows/util.o windows/widgets.o
../../../gnuwin32/dllversion.o -lRgraphapp -lversion
-L/x86_64-w64-mingw32.static.posix/lib/x64 -llzma
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64
-LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -L../../../../bin/x64 -lR
>
> lto1.exe: fatal error: bytecode stream in file
'windows/dataentry.o' generated with LTO version 9.3 instead of the
expected 9.4
> compilation terminated.
>
> lto-wrapper.exe: fatal error:
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\gcc.exe returned 1 exit status
> compilation terminated.
> C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: error: lto-wrapper
failed
> collect2.exe: error: ld returned 1 exit status
> cp: cannot stat 'utils.dll': No such file or directory
> make[4]: *** [Makefile.win:36: shlib] Error 1
> make[3]: *** [../../../share/make/basepkg.mk:145: mksrc-win2] Error 1
> make[2]: *** [Makefile.win:24: all] Error 2
> make[1]: *** [Makefile.win:34: R] Error 1
> make: *** [Makefile:18: all] Error 2
> ```
> Any hints/ideas on how to fix this? I guess I could
> gcc -c -flto ... windows/dataentry.c -o windows/dataentry.o
> with the exact path of that fiile ...
All of the object files are generated on your system during the build. 
If dataentry.o is generated using an older version than other object 
files, maybe there is some configuration problem on the system. It might 
be worth checking the compilers and linkers from Rtools42 are used, and 
then running "make distclean", and then trying the build again.

I never tried building R with LTO on Windows myself, I don't know if 
that works even on a system set up according to the documentation for R 
4.2 (https://cran.r-project.org/bin/windows/base/howto-R-4.2.html).
> and it hopefully will fix that but I guess it would make sense to add a
Revision to update that LTO version mismatch there, and I don't know yet if
this is the only one?
Perhaps it is better to use Rtools43 and R-devel if you can, so that if 
you find some problem in either, it can still be fixed.
> Greetings,
> W
Best,
Tomas
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel