Re: [sage-devel] Error installing package gap_packages-4.10.2.p1

[John H Palmieri]

The relevant ticket is https://trac.sagemath.org/ticket/30720, which has 
not yet been applied. (I'm guessing that this is because the problem was 
fixed recently and gap_packages is an optional package, so the ticket did 
not have super high priority.)

-- 
John


On Tuesday, October 27, 2020 at 5:11:44 PM UTC-7, François Bissey wrote:
>
> That’s a gcc-10 porting issue. I thought the fix from upstream had been 
> applied. 
> Someone more familiar with the ticket should comment. 
>
> > On 28/10/2020, at 12:22 PM, 'Peter Mueller' via sage-devel <
> sage-...@googlegroups.com > wrote: 
> > 
> > On a Lenovo ThinkPad with an up to date Manjaro Linux OS and Sage 9.2 
> successfully compiled from source I failed to install 
>  gap_packages-4.10.2.p1, while many other optional packages (like the huge 
> cbc) installed perfectly. Below I append the (hopefully) relevant piece of 
> the log file. 
> > 
> > -- Peter Mueller 
> > 
> > [...] 
> > gcc -c -O -fno-builtin nqmfns.c 
> > gcc -O -fno-builtin -o 
> ..//..//bin/x86_64-pc-linux-gnu-default64-kv3/nqmrun nqmd.o nqmp.o nqmfns.o 
> > /usr/bin/ld: nqmfns.o:(.bss+0x8): multiple definition of `ip'; 
> nqmp.o:(.bss+0x8): first defined here 
> > /usr/bin/ld: nqmfns.o:(.bss+0x0): multiple definition of `op'; 
> nqmp.o:(.bss+0x0): first defined here 
> > collect2: error: ld returned 1 exit status 
> > make[4]: *** [makefile:49: 
> ..//..//bin/x86_64-pc-linux-gnu-default64-kv3/nqmrun] Error 1 
> > make[3]: *** [Makefile:9: all] Error 2 
> > 
> 
>  
>
> > Error building gap_packages-4.10.2.p1 
> > [...] 
> > 
> > (I don't know if that matters, but the log also contains 201 warnings, 
> all about implicit declarations of functions.) 
> > 
> > 
> > -- 
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> Groups "sage-devel" group. 
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>  
>
>
>

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Re: [sage-devel] Error installing package gap_packages-4.10.2.p1

[François Bissey]

That’s a gcc-10 porting issue. I thought the fix from upstream had been applied.
Someone more familiar with the ticket should comment.

> On 28/10/2020, at 12:22 PM, 'Peter Mueller' via sage-devel 
>  wrote:
> 
> On a Lenovo ThinkPad with an up to date Manjaro Linux OS and Sage 9.2 
> successfully compiled from source I failed to install  
> gap_packages-4.10.2.p1, while many other optional packages (like the huge 
> cbc) installed perfectly. Below I append the (hopefully) relevant piece of 
> the log file.
> 
> -- Peter Mueller
> 
> [...]
> gcc -c -O -fno-builtin nqmfns.c 
> gcc -O -fno-builtin -o ..//..//bin/x86_64-pc-linux-gnu-default64-kv3/nqmrun 
> nqmd.o nqmp.o nqmfns.o
> /usr/bin/ld: nqmfns.o:(.bss+0x8): multiple definition of `ip'; 
> nqmp.o:(.bss+0x8): first defined here
> /usr/bin/ld: nqmfns.o:(.bss+0x0): multiple definition of `op'; 
> nqmp.o:(.bss+0x0): first defined here
> collect2: error: ld returned 1 exit status
> make[4]: *** [makefile:49: 
> ..//..//bin/x86_64-pc-linux-gnu-default64-kv3/nqmrun] Error 1
> make[3]: *** [Makefile:9: all] Error 2
> 
> Error building gap_packages-4.10.2.p1
> [...]
> 
> (I don't know if that matters, but the log also contains 201 warnings, all 
> about implicit declarations of functions.)
> 
> 
> -- 
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[sage-devel] Error installing package gap_packages-4.10.2.p1

['Peter Mueller' via sage-devel]

On a Lenovo ThinkPad with an up to date Manjaro Linux OS and Sage 9.2 
successfully compiled from source I failed to 
install  gap_packages-4.10.2.p1, while many other optional packages (like 
the huge cbc) installed perfectly. Below I append the (hopefully) relevant 
piece of the log file.

-- Peter Mueller

[...]
gcc -c -O -fno-builtin nqmfns.c 
gcc -O -fno-builtin -o ..//..//bin/x86_64-pc-linux-gnu-default64-kv3/nqmrun 
nqmd.o nqmp.o nqmfns.o
/usr/bin/ld: nqmfns.o:(.bss+0x8): multiple definition of `ip'; 
nqmp.o:(.bss+0x8): first defined here
/usr/bin/ld: nqmfns.o:(.bss+0x0): multiple definition of `op'; 
nqmp.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make[4]: *** [makefile:49: 
..//..//bin/x86_64-pc-linux-gnu-default64-kv3/nqmrun] Error 1
make[3]: *** [Makefile:9: all] Error 2

Error building gap_packages-4.10.2.p1
[...]

(I don't know if that matters, but the log also contains 201 warnings, all 
about implicit declarations of functions.)

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Re: [sage-devel] Building Sage 9.2 on Mac fails due to cysignals

[Matthias Koeppe]

>From config.log:

configure:5906: gcc -v >&5
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.21)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
configure:5917: $? = 0
...

configure:6029: gcc -o conftest  -I/usr/local/opt/llvm/include 
-L/usr/local/opt/llvm/lib conftest.c  >&5


This looks like an unsupported configuration - injecting these -L and -I 
flags via environment variables, but continuing to use Apple's gcc.
If you are trying to compile with homebrew's llvm, you should probably 
configure by setting CC and CXX as well. But this is also untested - I have 
created https://trac.sagemath.org/ticket/30835#ticket for testing such a 
configuration.


On Tuesday, October 27, 2020 at 3:46:10 AM UTC-7, Dima Pasechnik wrote:
>
> I'd have tried removing llvm and trying again. Perhaps this is a conflict 
> between Homebrew packages.
>
> On Tue, Oct 27, 2020 at 8:42 AM modp...@gmail.com  > wrote:
>
>> Please find config.log and cysignals-1.10.2.log attached. I already run 
>> "source .homebrew-build-env" before configuring.
>> And yes I also have llvm installed through Homebrew.
>>
>> On Monday, October 26, 2020 at 3:23:38 PM UTC+1 dim...@gmail.com wrote:
>>
>>> also note that you apparently have something in 
>>> -L/usr/local/opt/llvm/lib (installed from Homebrew ?) which might lead 
>>> to surprises. 
>>> Do you have some LDFLAGS set? 
>>> It would help if you also post logs/pkgs/cysignals-1.10.2.log 
>>>
>>> On Mon, Oct 26, 2020 at 2:15 PM Dima Pasechnik  
>>> wrote: 
>>> > 
>>> > also, if you have Homebrew, you should run 
>>> > 
>>> > source .homebrew-build-env 
>>> > 
>>> > before 
>>> > 
>>> > ./configure 
>>> > 
>>> > On Mon, Oct 26, 2020 at 1:50 PM Dima Pasechnik  
>>> wrote: 
>>> >> 
>>> >> please post the top-level config.log here 
>>> >> 
>>> >> On Mon, 26 Oct 2020, 13:45 modp...@gmail.com,  
>>> wrote: 
>>> >>> 
>>> >>> 
>>> >>> I'm building Sage 9.2 from source on macOS Catalina 10.15.7, 
>>> however, it fails 
>>> >>> when trying to install cysignals. More precisely, it throws the 
>>> following error: 
>>> >>> 
>>> >>> gcc -bundle -undefined dynamic_lookup -isysroot 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
>>>  
>>> -L/Users/myUser/app/sage-9.2/local/lib 
>>> -Wl,-rpath,/Users/myUser/app/sage-9.2/local/lib -L/usr/local/opt/llvm/lib 
>>> -I/usr/local/opt/llvm/include -Wp,-U_FORTIFY_SOURCE 
>>> build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals/signals.o 
>>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib 
>>> -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.15-x86_64-3.8/cysignals/
>>> signals.cpython-38-darwin.so -lpari -pthread 
>>> >>> ld: illegal thread local variable reference to regular symbol 
>>> _PARI_SIGINT_block for architecture x86_64 
>>> >>> clang: error: linker command failed with exit code 1 (use -v to see 
>>> invocation) 
>>> >>> error: command 'gcc' failed with exit status 1 
>>> >>> Building wheel for cysignals (setup.py): finished with status 
>>> 'error' 
>>> >>> ERROR: Failed building wheel for cysignals 
>>> >>> 
>>> >>> This is my compiler version: 
>>> >>> 
>>> >>> Configured with: 
>>> --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
>>>  
>>>
>>> >>> Apple clang version 12.0.0 (clang-1200.0.32.21) 
>>> >>> Target: x86_64-apple-darwin19.6.0 
>>> >>> Thread model: posix 
>>> >>> InstalledDir: 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>>  
>>>
>>> >>> 
>>> >>> Any idea what the problem might be, and how to solve it? 
>>> >>> 
>>> >>> -- 
>>> >>> You received this message because you are subscribed to the Google 
>>> Groups "sage-devel" group. 
>>> >>> To unsubscribe from this group and stop receiving emails from it, 
>>> send an email to sage-devel+...@googlegroups.com. 
>>> >>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/sage-devel/38ff74b7-a4bf-4118-8519-9f57736ba532n%40googlegroups.com.
>>>  
>>>
>>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
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>> email to sage-...@googlegroups.com .
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>>  
>> 
>> .
>>
>

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Re: [sage-devel] Building Sage 9.2 on Mac fails due to cysignals

[Dima Pasechnik]

I'd have tried removing llvm and trying again. Perhaps this is a conflict
between Homebrew packages.

On Tue, Oct 27, 2020 at 8:42 AM modp...@gmail.com 
wrote:

> Please find config.log and cysignals-1.10.2.log attached. I already run
> "source .homebrew-build-env" before configuring.
> And yes I also have llvm installed through Homebrew.
>
> On Monday, October 26, 2020 at 3:23:38 PM UTC+1 dim...@gmail.com wrote:
>
>> also note that you apparently have something in
>> -L/usr/local/opt/llvm/lib (installed from Homebrew ?) which might lead
>> to surprises.
>> Do you have some LDFLAGS set?
>> It would help if you also post logs/pkgs/cysignals-1.10.2.log
>>
>> On Mon, Oct 26, 2020 at 2:15 PM Dima Pasechnik  wrote:
>> >
>> > also, if you have Homebrew, you should run
>> >
>> > source .homebrew-build-env
>> >
>> > before
>> >
>> > ./configure
>> >
>> > On Mon, Oct 26, 2020 at 1:50 PM Dima Pasechnik 
>> wrote:
>> >>
>> >> please post the top-level config.log here
>> >>
>> >> On Mon, 26 Oct 2020, 13:45 modp...@gmail.com, 
>> wrote:
>> >>>
>> >>>
>> >>> I'm building Sage 9.2 from source on macOS Catalina 10.15.7, however,
>> it fails
>> >>> when trying to install cysignals. More precisely, it throws the
>> following error:
>> >>>
>> >>> gcc -bundle -undefined dynamic_lookup -isysroot
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
>> -L/Users/myUser/app/sage-9.2/local/lib
>> -Wl,-rpath,/Users/myUser/app/sage-9.2/local/lib -L/usr/local/opt/llvm/lib
>> -I/usr/local/opt/llvm/include -Wp,-U_FORTIFY_SOURCE
>> build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals/signals.o
>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib
>> -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.15-x86_64-3.8/cysignals/
>> signals.cpython-38-darwin.so -lpari -pthread
>> >>> ld: illegal thread local variable reference to regular symbol
>> _PARI_SIGINT_block for architecture x86_64
>> >>> clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> >>> error: command 'gcc' failed with exit status 1
>> >>> Building wheel for cysignals (setup.py): finished with status 'error'
>> >>> ERROR: Failed building wheel for cysignals
>> >>>
>> >>> This is my compiler version:
>> >>>
>> >>> Configured with:
>> --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
>>
>> >>> Apple clang version 12.0.0 (clang-1200.0.32.21)
>> >>> Target: x86_64-apple-darwin19.6.0
>> >>> Thread model: posix
>> >>> InstalledDir:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
>> >>>
>> >>> Any idea what the problem might be, and how to solve it?
>> >>>
>> >>> --
>> >>> You received this message because you are subscribed to the Google
>> Groups "sage-devel" group.
>> >>> To unsubscribe from this group and stop receiving emails from it,
>> send an email to sage-devel+...@googlegroups.com.
>> >>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/38ff74b7-a4bf-4118-8519-9f57736ba532n%40googlegroups.com.
>>
>>
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> 
> .
>

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