Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-14 Thread Dima Pasechnik 
Thanks. Now the only conclusion we have about 10.15 that it's hard to
predict the outcome of
building Sage on it...

On Mon, Oct 14, 2019 at 7:42 AM David Coudert  wrote:
>
> Since it’s cleaner, I tried, and after a make distclean and the removal of 
> MacOSX10.14.sdk, I was able to build Sage !
>
> Thanks,
> David.
>
>
> Le 14 oct. 2019 à 01:29, Volker Braun  a écrit :
>
> I just tried the latest Xcode and gfortran fails to build for me, too...
>>>
>>>
>
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>
>
> 
> David Coudert
> Equipe-Projet COATI
> Centre de Recherche INRIA Sophia Antipolis - Méditerranée
> Université Côte d’Azur, Inria, CNRS, I3S, France
> http://www-sop.inria.fr/members/David.Coudert
>
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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-14 Thread David Coudert 
Since it’s cleaner, I tried, and after a make distclean and the removal of 
MacOSX10.14.sdk, I was able to build Sage !

Thanks,
David.


> Le 14 oct. 2019 à 01:29, Volker Braun  a écrit :
> 
> I just tried the latest Xcode and gfortran fails to build for me, too...
> 
> 
> -- 
> You received this message because you are subscribed to a topic in the Google 
> Groups "sage-devel" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/sage-devel/TsdmX1ozkq0/unsubscribe 
> .
> To unsubscribe from this group and all its topics, send an email to 
> sage-devel+unsubscr...@googlegroups.com 
> .
> To view this discussion on the web visit 
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>  
> .


David Coudert
Equipe-Projet COATI
Centre de Recherche INRIA Sophia Antipolis - Méditerranée
Université Côte d’Azur, Inria, CNRS, I3S, France
http://www-sop.inria.fr/members/David.Coudert

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Volker Braun 
I just tried the latest Xcode and gfortran fails to build for me, too...

>
>>

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
On Sun, 13 Oct 2019, 20:57 David Coudert,  wrote:

>
>
> Le 13 oct. 2019 à 20:24, Dima Pasechnik  a écrit :
>
> On Sun, Oct 13, 2019 at 4:57 PM David Coudert 
> wrote:
>
>
> It’s working ! I can now complete compilation.
>
> Thanks both of you for the help.
>
> Now I have to remember to remove MacOSX10.14.sdk when it will no longer be
> needed, but when…
>
>
>
>
> hmm, so does this mean that you didn't do a full rebuild of Sage after
> OS upgrade?
> Cause you are on 10.15 now, no?
>
>
> I had to reformat my hard drive, so I reinstalled / rebuilt everything
> from scratch, including Sagemath.
> I’m currently with Mojave 10.14.6.
> However, I did an update Xcode 2-3 days ago (app store said I should
> update Xcode…) but didn’t do full rebuild. Should I ?
>

well, this upgrade did break gfortran.
I presume building gfortran from scratch does not need that Xcode hack by
Isuru...



> D.
>
>
>
> David.
>
> Le 13 oct. 2019 à 17:32, Isuru Fernando  a écrit :
>
> You have the same issue as
> https://github.com/sagemath/binary-pkg/issues/19
>
> Can you try downloading 10.14 SDK from
> https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
> extracting it inside
> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`
>
> Isuru
>
> On Sun, Oct 13, 2019 at 10:27 AM David Coudert 
> wrote:
>
>
> No, but MacOSX10.15.sdk
>
> confetti:lib dcoudert$ ll
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> ls:
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
> No such file or directory
> confetti:lib dcoudert$ ll
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
> total 0
> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
>
>
> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
>
> Hi,
>
> Do you have the folder
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> ?
>
> Isuru
>
> On Sun, Oct 13, 2019 at 10:14 AM David Coudert 
> wrote:
>
>
> here it is.
>
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran
> -print-prog-name=ld
> ld
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> Using built-in specs.
> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>
> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
> Target: x86_64-apple-darwin18.6.0
> Configured with: ../src/configure
> --prefix=/Users/dcoudert/sage3/sage/local
> --with-local-prefix=/Users/dcoudert/sage3/sage/local
> --with-gmp=/Users/dcoudert/sage3/sage/local
> --with-mpfr=/Users/dcoudert/sage3/sage/local
> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib
> --without-isl --disable-multilib --disable-nls --disable-libitm
> --with-build-config=bootstrap-debug --without-isl --without-cloog
> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> --disable-bootstrap --enable-languages=fortran
> Thread model: posix
> gcc version 7.4.0 (GCC)
>
>
> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>
> Hi,
>
> This is a problem with gfortran using an incorrect linker.
>
> Can you post the output of,
>
> /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>
> /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>
> Isuru
>
>
> On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
> wrote:
>
>
> confetti:lib dcoudert$ otool -L libfflas.dylib
> libfflas.dylib:
> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
> version 2.0.0, current version 2.0.0)
> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
> version 11.0.0, current version 11.1.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
> version 24.0.0, current version 24.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
> version 13.0.0, current version 13.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
> (compatibility version 0.0.0, current version 0.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
> 400.9.4)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1252.250.1)
>
>
> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>
> oops sorry, your gfortran is ok.
> how about fflas* package, it is probably broken...
>
> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>
>
> are you building gfortran in Sage, or using a prebuilt one?
>
> it might be that its libgfortran got broken
>
> On Sun, 13 Oct 2019, 13:01 David Coudert,  wrote:
>
>
>
>
> confetti:lib dcoudert$ pwd
>
> /Users/dcoudert/sage3/sage/local/lib
>
> confetti:lib dcoudert$ otool

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 


> Le 13 oct. 2019 à 20:24, Dima Pasechnik  a écrit :
> 
> On Sun, Oct 13, 2019 at 4:57 PM David Coudert  > wrote:
>> 
>> It’s working ! I can now complete compilation.
>> 
>> Thanks both of you for the help.
>> 
>> Now I have to remember to remove MacOSX10.14.sdk when it will no longer be 
>> needed, but when…
> 
> 
> 
> hmm, so does this mean that you didn't do a full rebuild of Sage after
> OS upgrade?
> Cause you are on 10.15 now, no?

I had to reformat my hard drive, so I reinstalled / rebuilt everything from 
scratch, including Sagemath.
I’m currently with Mojave 10.14.6. 
However, I did an update Xcode 2-3 days ago (app store said I should update 
Xcode…) but didn’t do full rebuild. Should I ?

D.



>> David.
>> 
>> Le 13 oct. 2019 à 17:32, Isuru Fernando  a écrit :
>> 
>> You have the same issue as https://github.com/sagemath/binary-pkg/issues/19
>> 
>> Can you try downloading 10.14 SDK from 
>> https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
>>  extracting it inside 
>> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`
>> 
>> Isuru
>> 
>> On Sun, Oct 13, 2019 at 10:27 AM David Coudert  
>> wrote:
>>> 
>>> No, but MacOSX10.15.sdk
>>> 
>>> confetti:lib dcoudert$ ll 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>> ls: 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
>>>  No such file or directory
>>> confetti:lib dcoudert$ ll 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
>>> total 0
>>> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
>>> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
>>> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
>>> 
>>> 
>>> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
>>> 
>>> Hi,
>>> 
>>> Do you have the folder 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>>  ?
>>> 
>>> Isuru
>>> 
>>> On Sun, Oct 13, 2019 at 10:14 AM David Coudert  
>>> wrote:
 
 here it is.
 
 confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
 -print-prog-name=ld
 ld
 confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
 Using built-in specs.
 COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
 COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
 Target: x86_64-apple-darwin18.6.0
 Configured with: ../src/configure 
 --prefix=/Users/dcoudert/sage3/sage/local 
 --with-local-prefix=/Users/dcoudert/sage3/sage/local 
 --with-gmp=/Users/dcoudert/sage3/sage/local 
 --with-mpfr=/Users/dcoudert/sage3/sage/local 
 --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib 
 --without-isl --disable-multilib --disable-nls --disable-libitm 
 --with-build-config=bootstrap-debug --without-isl --without-cloog 
 --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
  --disable-bootstrap --enable-languages=fortran
 Thread model: posix
 gcc version 7.4.0 (GCC)
 
 
 Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
 
 Hi,
 
 This is a problem with gfortran using an incorrect linker.
 
 Can you post the output of,
 
 /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
 
 /Users/dcoudert/sage3/sage/local/bin/gfortran -v
 
 Isuru
 
 
 On Sun, Oct 13, 2019 at 8:21 AM David Coudert  
 wrote:
> 
> confetti:lib dcoudert$ otool -L libfflas.dylib
> libfflas.dylib:
> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
> version 2.0.0, current version 2.0.0)
> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
> version 11.0.0, current version 11.1.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
> version 24.0.0, current version 24.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
> version 13.0.0, current version 13.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
> (compatibility version 0.0.0, current version 0.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
> 400.9.4)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 
> 1252.250.1)
> 
> 
> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
> 
> oops sorry, your gfortran is ok.
> how about fflas* package, it is probably broken...
> 
> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>> 
>> are you building gfortran in Sage, or using a prebuilt one?
>>

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
On Sun, Oct 13, 2019 at 4:57 PM David Coudert  wrote:
>
> It’s working ! I can now complete compilation.
>
> Thanks both of you for the help.
>
> Now I have to remember to remove MacOSX10.14.sdk when it will no longer be 
> needed, but when…



hmm, so does this mean that you didn't do a full rebuild of Sage after
OS upgrade?
Cause you are on 10.15 now, no?

>
>
> David.
>
> Le 13 oct. 2019 à 17:32, Isuru Fernando  a écrit :
>
> You have the same issue as https://github.com/sagemath/binary-pkg/issues/19
>
> Can you try downloading 10.14 SDK from 
> https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
>  extracting it inside 
> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`
>
> Isuru
>
> On Sun, Oct 13, 2019 at 10:27 AM David Coudert  wrote:
>>
>> No, but MacOSX10.15.sdk
>>
>> confetti:lib dcoudert$ ll 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>> ls: 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
>>  No such file or directory
>> confetti:lib dcoudert$ ll 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
>> total 0
>> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
>> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
>> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
>>
>>
>> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
>>
>> Hi,
>>
>> Do you have the folder 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>  ?
>>
>> Isuru
>>
>> On Sun, Oct 13, 2019 at 10:14 AM David Coudert  
>> wrote:
>>>
>>> here it is.
>>>
>>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
>>> -print-prog-name=ld
>>> ld
>>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>> Using built-in specs.
>>> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>>> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
>>> Target: x86_64-apple-darwin18.6.0
>>> Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
>>> --with-local-prefix=/Users/dcoudert/sage3/sage/local 
>>> --with-gmp=/Users/dcoudert/sage3/sage/local 
>>> --with-mpfr=/Users/dcoudert/sage3/sage/local 
>>> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib 
>>> --without-isl --disable-multilib --disable-nls --disable-libitm 
>>> --with-build-config=bootstrap-debug --without-isl --without-cloog 
>>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>>  --disable-bootstrap --enable-languages=fortran
>>> Thread model: posix
>>> gcc version 7.4.0 (GCC)
>>>
>>>
>>> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>>>
>>> Hi,
>>>
>>> This is a problem with gfortran using an incorrect linker.
>>>
>>> Can you post the output of,
>>>
>>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>>>
>>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>>
>>> Isuru
>>>
>>>
>>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert  
>>> wrote:

 confetti:lib dcoudert$ otool -L libfflas.dylib
 libfflas.dylib:
 /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
 version 2.0.0, current version 2.0.0)
 /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
 version 11.0.0, current version 11.1.0)
 /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
 version 24.0.0, current version 24.3.0)
 /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
 version 13.0.0, current version 13.3.0)
 /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
 (compatibility version 0.0.0, current version 0.0.0)
 /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
 400.9.4)
 /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 
 1252.250.1)


 Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :

 oops sorry, your gfortran is ok.
 how about fflas* package, it is probably broken...

 On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>
> are you building gfortran in Sage, or using a prebuilt one?
>
> it might be that its libgfortran got broken
>
> On Sun, 13 Oct 2019, 13:01 David Coudert,  wrote:
>>
>>
>>
>> confetti:lib dcoudert$ pwd
>>
>> /Users/dcoudert/sage3/sage/local/lib
>>
>> confetti:lib dcoudert$ otool -L libgfortran.dylib
>>
>> libgfortran.dylib:
>>
>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
>> version 5.0.0, current version 5.0.0)
>>
>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 
It’s working ! I can now complete compilation.

Thanks both of you for the help.

Now I have to remember to remove MacOSX10.14.sdk when it will no longer be 
needed, but when…

David.

> Le 13 oct. 2019 à 17:32, Isuru Fernando  a écrit :
> 
> You have the same issue as https://github.com/sagemath/binary-pkg/issues/19 
> 
> 
> Can you try downloading 10.14 SDK from 
> https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
>  
> 
>  extracting it inside 
> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`
> 
> Isuru
> 
> On Sun, Oct 13, 2019 at 10:27 AM David Coudert  > wrote:
> No, but MacOSX10.15.sdk
> 
> confetti:lib dcoudert$ ll 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>  
> ls: 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
>  No such file or directory
> confetti:lib dcoudert$ ll 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
> total 0
> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
> 
> 
>> Le 13 oct. 2019 à 17:16, Isuru Fernando > > a écrit :
>> 
>> Hi,
>> 
>> Do you have the folder 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>  ?
>> 
>> Isuru
>> 
>> On Sun, Oct 13, 2019 at 10:14 AM David Coudert > > wrote:
>> here it is.
>> 
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
>> -print-prog-name=ld
>> ld
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>> Using built-in specs.
>> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
>> Target: x86_64-apple-darwin18.6.0
>> Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
>> --with-local-prefix=/Users/dcoudert/sage3/sage/local 
>> --with-gmp=/Users/dcoudert/sage3/sage/local 
>> --with-mpfr=/Users/dcoudert/sage3/sage/local 
>> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib --without-isl 
>> --disable-multilib --disable-nls --disable-libitm 
>> --with-build-config=bootstrap-debug --without-isl --without-cloog 
>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>  --disable-bootstrap --enable-languages=fortran  
>> Thread model: posix
>> gcc version 7.4.0 (GCC) 
>> 
>> 
>>> Le 13 oct. 2019 à 16:47, Isuru Fernando >> > a écrit :
>>> 
>>> Hi,
>>> 
>>> This is a problem with gfortran using an incorrect linker.
>>> 
>>> Can you post the output of,
>>> 
>>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>>> 
>>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>> 
>>> Isuru
>>> 
>>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert >> > wrote:
>>> confetti:lib dcoudert$ otool -L libfflas.dylib
>>> libfflas.dylib:
>>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
>>> version 2.0.0, current version 2.0.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
>>> version 11.0.0, current version 11.1.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
>>> version 24.0.0, current version 24.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
>>> version 13.0.0, current version 13.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
>>> (compatibility version 0.0.0, current version 0.0.0)
>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
>>> 400.9.4)
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>>> version 1252.250.1)
>>> 
>>> 
 Le 13 oct. 2019 à 15:19, Dima Pasechnik >>> > a écrit :
 
 oops sorry, your gfortran is ok.
 how about fflas* package, it is probably broken...
 
 On Sun, 13 Oct 2019, 14:17 Dima Pasechnik, >>> > wrote:
 are you building gfortran in Sage, or using a prebuilt one?
 
 it might be that its libgfortran got broken
 
 On Sun, 13 Oct 2019, 13:01 David Coudert, >>> > wrote:
 
 
 confetti:lib dcoudert$ pwd
 
 /Users/dcoudert/sage3/sage/local/lib
 
 confetti:lib dcoudert$ otool -L libgfortran.dylib 
 
 libgfortran.dylib:

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Isuru Fernando 
You have the same issue as https://github.com/sagemath/binary-pkg/issues/19

Can you try downloading 10.14 SDK from
https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
extracting it inside
`/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`

Isuru

On Sun, Oct 13, 2019 at 10:27 AM David Coudert 
wrote:

> No, but MacOSX10.15.sdk
>
> confetti:lib dcoudert$ ll
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> ls:
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
> No such file or directory
> confetti:lib dcoudert$ ll
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
> total 0
> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
>
>
> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
>
> Hi,
>
> Do you have the folder 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> ?
>
> Isuru
>
> On Sun, Oct 13, 2019 at 10:14 AM David Coudert 
> wrote:
>
>> here it is.
>>
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran
>> -print-prog-name=ld
>> ld
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>> Using built-in specs.
>> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>>
>> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
>> Target: x86_64-apple-darwin18.6.0
>> Configured with: ../src/configure
>> --prefix=/Users/dcoudert/sage3/sage/local
>> --with-local-prefix=/Users/dcoudert/sage3/sage/local
>> --with-gmp=/Users/dcoudert/sage3/sage/local
>> --with-mpfr=/Users/dcoudert/sage3/sage/local
>> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib
>> --without-isl --disable-multilib --disable-nls --disable-libitm
>> --with-build-config=bootstrap-debug --without-isl --without-cloog
>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>> --disable-bootstrap --enable-languages=fortran
>> Thread model: posix
>> gcc version 7.4.0 (GCC)
>>
>>
>> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>>
>> Hi,
>>
>> This is a problem with gfortran using an incorrect linker.
>>
>> Can you post the output of,
>>
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>>
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>
>> Isuru
>>
>>
>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
>> wrote:
>>
>>> confetti:lib dcoudert$ otool -L libfflas.dylib
>>> libfflas.dylib:
>>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
>>> version 2.0.0, current version 2.0.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
>>> version 11.0.0, current version 11.1.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
>>> version 24.0.0, current version 24.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
>>> version 13.0.0, current version 13.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
>>> (compatibility version 0.0.0, current version 0.0.0)
>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
>>> 400.9.4)
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>>> 1252.250.1)
>>>
>>>
>>> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>>>
>>> oops sorry, your gfortran is ok.
>>> how about fflas* package, it is probably broken...
>>>
>>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>>>
 are you building gfortran in Sage, or using a prebuilt one?

 it might be that its libgfortran got broken

 On Sun, 13 Oct 2019, 13:01 David Coudert, 
 wrote:

>
>
> confetti:lib dcoudert$ pwd
>
> /Users/dcoudert/sage3/sage/local/lib
>
> confetti:lib dcoudert$ otool -L libgfortran.dylib
>
> libgfortran.dylib:
>
> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib
> (compatibility version 5.0.0, current version 5.0.0)
>
> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
>
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1252.250.1)
>
> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
> version 1.0.0, current version 1.0.0)
>
>
> but I don't have the 2 others
>
> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>
> confetti:sage dcoudert$ pwd
>
> /Users/dcoudert/sage3/sage
>
>
>
>
>
> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>>
>>

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 
No, but MacOSX10.15.sdk

confetti:lib dcoudert$ ll 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
 
ls: 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
 No such file or directory
confetti:lib dcoudert$ ll 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
total 0
drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk


> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
> 
> Hi,
> 
> Do you have the folder 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>  ?
> 
> Isuru
> 
> On Sun, Oct 13, 2019 at 10:14 AM David Coudert  > wrote:
> here it is.
> 
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
> -print-prog-name=ld
> ld
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> Using built-in specs.
> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
> Target: x86_64-apple-darwin18.6.0
> Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
> --with-local-prefix=/Users/dcoudert/sage3/sage/local 
> --with-gmp=/Users/dcoudert/sage3/sage/local 
> --with-mpfr=/Users/dcoudert/sage3/sage/local 
> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib --without-isl 
> --disable-multilib --disable-nls --disable-libitm 
> --with-build-config=bootstrap-debug --without-isl --without-cloog 
> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>  --disable-bootstrap --enable-languages=fortran  
> Thread model: posix
> gcc version 7.4.0 (GCC) 
> 
> 
>> Le 13 oct. 2019 à 16:47, Isuru Fernando > > a écrit :
>> 
>> Hi,
>> 
>> This is a problem with gfortran using an incorrect linker.
>> 
>> Can you post the output of,
>> 
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>> 
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>> 
>> Isuru
>> 
>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert > > wrote:
>> confetti:lib dcoudert$ otool -L libfflas.dylib
>> libfflas.dylib:
>>  /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
>> version 2.0.0, current version 2.0.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
>> version 11.0.0, current version 11.1.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
>> version 24.0.0, current version 24.3.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
>> version 13.0.0, current version 13.3.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
>> (compatibility version 0.0.0, current version 0.0.0)
>>  /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
>> 400.9.4)
>>  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>> version 1252.250.1)
>> 
>> 
>>> Le 13 oct. 2019 à 15:19, Dima Pasechnik >> > a écrit :
>>> 
>>> oops sorry, your gfortran is ok.
>>> how about fflas* package, it is probably broken...
>>> 
>>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik, >> > wrote:
>>> are you building gfortran in Sage, or using a prebuilt one?
>>> 
>>> it might be that its libgfortran got broken
>>> 
>>> On Sun, 13 Oct 2019, 13:01 David Coudert, >> > wrote:
>>> 
>>> 
>>> confetti:lib dcoudert$ pwd
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib
>>> 
>>> confetti:lib dcoudert$ otool -L libgfortran.dylib 
>>> 
>>> libgfortran.dylib:
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
>>> version 5.0.0, current version 5.0.0)
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
>>> version 1.0.0, current version 1.0.0)
>>> 
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>>> version 1252.250.1)
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
>>> version 1.0.0, current version 1.0.0)
>>> 
>>> 
>>> 
>>> but I don't have the 2 others
>>> 
>>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>>> 
>>> confetti:sage dcoudert$ pwd
>>> 
>>> 
>>> /Users/dcoudert/sage3/sage
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>>> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
>>> being incorrectly linked/broken. 
>>> 
>>> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
>>> "otool -L" on each of them 
>>> to see if they are OK. 
>>>

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Isuru Fernando 
Hi,

Do you have the folder
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
?

Isuru

On Sun, Oct 13, 2019 at 10:14 AM David Coudert 
wrote:

> here it is.
>
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran
> -print-prog-name=ld
> ld
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> Using built-in specs.
> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>
> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
> Target: x86_64-apple-darwin18.6.0
> Configured with: ../src/configure
> --prefix=/Users/dcoudert/sage3/sage/local
> --with-local-prefix=/Users/dcoudert/sage3/sage/local
> --with-gmp=/Users/dcoudert/sage3/sage/local
> --with-mpfr=/Users/dcoudert/sage3/sage/local
> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib
> --without-isl --disable-multilib --disable-nls --disable-libitm
> --with-build-config=bootstrap-debug --without-isl --without-cloog
> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> --disable-bootstrap --enable-languages=fortran
> Thread model: posix
> gcc version 7.4.0 (GCC)
>
>
> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>
> Hi,
>
> This is a problem with gfortran using an incorrect linker.
>
> Can you post the output of,
>
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>
> Isuru
>
>
> On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
> wrote:
>
>> confetti:lib dcoudert$ otool -L libfflas.dylib
>> libfflas.dylib:
>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
>> version 2.0.0, current version 2.0.0)
>> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
>> version 11.0.0, current version 11.1.0)
>> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
>> version 24.0.0, current version 24.3.0)
>> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
>> version 13.0.0, current version 13.3.0)
>> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
>> (compatibility version 0.0.0, current version 0.0.0)
>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
>> 400.9.4)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>> 1252.250.1)
>>
>>
>> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>>
>> oops sorry, your gfortran is ok.
>> how about fflas* package, it is probably broken...
>>
>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>>
>>> are you building gfortran in Sage, or using a prebuilt one?
>>>
>>> it might be that its libgfortran got broken
>>>
>>> On Sun, 13 Oct 2019, 13:01 David Coudert, 
>>> wrote:
>>>


 confetti:lib dcoudert$ pwd

 /Users/dcoudert/sage3/sage/local/lib

 confetti:lib dcoudert$ otool -L libgfortran.dylib

 libgfortran.dylib:

 /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility
 version 5.0.0, current version 5.0.0)

 /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility
 version 1.0.0, current version 1.0.0)

 /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
 version 1252.250.1)

 /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
 version 1.0.0, current version 1.0.0)


 but I don't have the 2 others

 confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib

 confetti:sage dcoudert$ pwd

 /Users/dcoudert/sage3/sage





 Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>
> I gather that the error comes from one of  -ldfftpack -lfftpack
> -lgfortran
> being incorrectly linked/broken.
>
> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
> "otool -L" on each of them
> to see if they are OK.
>
>
> On Sun, Oct 13, 2019 at 12:43 PM David Coudert 
> wrote:
> >
> > it's an incremental build from 9.0.beta0.
> > I upgraded my OS in July after a system crash. So I had to reinstall
> everything from scratch.
> >
> > In case, I have Xcode Version 11.1 (11A1027).
> >
> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
>
> >>
> >> Is this a build from scratch?
> >> (after an OS upgrade, incremental builds may break)
> >>
> >>
> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert 
> wrote:
> >> >
> >> >
> >> >
> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a
> écrit :
> >> >>
> >> >> We have already seen that puzzling
> >> >>
> >> >> ld: library not found for -lSystem
> >> >>
> >> >> error message.
> >> >>
> >> >> Is there a /usr/lib/libSystem.dylib present?

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 
here it is.

confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
-print-prog-name=ld
ld
confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
Using built-in specs.
COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
Target: x86_64-apple-darwin18.6.0
Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
--with-local-prefix=/Users/dcoudert/sage3/sage/local 
--with-gmp=/Users/dcoudert/sage3/sage/local 
--with-mpfr=/Users/dcoudert/sage3/sage/local 
--with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib --without-isl 
--disable-multilib --disable-nls --disable-libitm 
--with-build-config=bootstrap-debug --without-isl --without-cloog 
--with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
 --disable-bootstrap --enable-languages=fortran  
Thread model: posix
gcc version 7.4.0 (GCC) 


> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
> 
> Hi,
> 
> This is a problem with gfortran using an incorrect linker.
> 
> Can you post the output of,
> 
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
> 
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> 
> Isuru
> 
> On Sun, Oct 13, 2019 at 8:21 AM David Coudert  > wrote:
> confetti:lib dcoudert$ otool -L libfflas.dylib
> libfflas.dylib:
>   /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
> version 2.0.0, current version 2.0.0)
>   /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
> version 11.0.0, current version 11.1.0)
>   /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
> version 24.0.0, current version 24.3.0)
>   /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
> version 13.0.0, current version 13.3.0)
>   /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
> (compatibility version 0.0.0, current version 0.0.0)
>   /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
> 400.9.4)
>   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 1252.250.1)
> 
> 
>> Le 13 oct. 2019 à 15:19, Dima Pasechnik > > a écrit :
>> 
>> oops sorry, your gfortran is ok.
>> how about fflas* package, it is probably broken...
>> 
>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik, > > wrote:
>> are you building gfortran in Sage, or using a prebuilt one?
>> 
>> it might be that its libgfortran got broken
>> 
>> On Sun, 13 Oct 2019, 13:01 David Coudert, > > wrote:
>> 
>> 
>> confetti:lib dcoudert$ pwd
>> 
>> /Users/dcoudert/sage3/sage/local/lib
>> 
>> confetti:lib dcoudert$ otool -L libgfortran.dylib 
>> 
>> libgfortran.dylib:
>> 
>>  /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
>> version 5.0.0, current version 5.0.0)
>> 
>>  /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
>> version 1.0.0, current version 1.0.0)
>> 
>>  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>> version 1252.250.1)
>> 
>>  /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
>> version 1.0.0, current version 1.0.0)
>> 
>> 
>> 
>> but I don't have the 2 others
>> 
>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>> 
>> confetti:sage dcoudert$ pwd
>> 
>> 
>> /Users/dcoudert/sage3/sage
>> 
>> 
>> 
>> 
>> 
>> 
>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
>> being incorrectly linked/broken. 
>> 
>> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
>> "otool -L" on each of them 
>> to see if they are OK. 
>> 
>> 
>> On Sun, Oct 13, 2019 at 12:43 PM David Coudert > 
>> wrote: 
>> > 
>> > it's an incremental build from 9.0.beta0. 
>> > I upgraded my OS in July after a system crash. So I had to reinstall 
>> > everything from scratch. 
>> > 
>> > In case, I have Xcode Version 11.1 (11A1027). 
>> > 
>> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit : 
>> >> 
>> >> Is this a build from scratch? 
>> >> (after an OS upgrade, incremental builds may break) 
>> >> 
>> >> 
>> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert > 
>> >> wrote: 
>> >> > 
>> >> > 
>> >> > 
>> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
>> >> >> 
>> >> >> We have already seen that puzzling 
>> >> >> 
>> >> >> ld: library not found for -lSystem 
>> >> >> 
>> >> >> error message. 
>> >> >> 
>> >> >> Is there a /usr/lib/libSystem.dylib present? 
>> >> > 
>> >> > 
>> >> > Yes: 
>> >> > 
>> >> > 
>> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
>> >> > 
>> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Isuru Fernando 
Hi,

This is a problem with gfortran using an incorrect linker.

Can you post the output of,

 /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld

 /Users/dcoudert/sage3/sage/local/bin/gfortran -v

Isuru


On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
wrote:

> confetti:lib dcoudert$ otool -L libfflas.dylib
> libfflas.dylib:
> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
> version 2.0.0, current version 2.0.0)
> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
> version 11.0.0, current version 11.1.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
> version 24.0.0, current version 24.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
> version 13.0.0, current version 13.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
> (compatibility version 0.0.0, current version 0.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
> 400.9.4)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1252.250.1)
>
>
> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>
> oops sorry, your gfortran is ok.
> how about fflas* package, it is probably broken...
>
> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>
>> are you building gfortran in Sage, or using a prebuilt one?
>>
>> it might be that its libgfortran got broken
>>
>> On Sun, 13 Oct 2019, 13:01 David Coudert,  wrote:
>>
>>>
>>>
>>> confetti:lib dcoudert$ pwd
>>>
>>> /Users/dcoudert/sage3/sage/local/lib
>>>
>>> confetti:lib dcoudert$ otool -L libgfortran.dylib
>>>
>>> libgfortran.dylib:
>>>
>>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility
>>> version 5.0.0, current version 5.0.0)
>>>
>>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility
>>> version 1.0.0, current version 1.0.0)
>>>
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>>> 1252.250.1)
>>>
>>> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
>>> version 1.0.0, current version 1.0.0)
>>>
>>>
>>> but I don't have the 2 others
>>>
>>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>>>
>>> confetti:sage dcoudert$ pwd
>>>
>>> /Users/dcoudert/sage3/sage
>>>
>>>
>>>
>>>
>>>
>>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :

 I gather that the error comes from one of  -ldfftpack -lfftpack
 -lgfortran
 being incorrectly linked/broken.

 please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
 "otool -L" on each of them
 to see if they are OK.


 On Sun, Oct 13, 2019 at 12:43 PM David Coudert 
 wrote:
 >
 > it's an incremental build from 9.0.beta0.
 > I upgraded my OS in July after a system crash. So I had to reinstall
 everything from scratch.
 >
 > In case, I have Xcode Version 11.1 (11A1027).
 >
 > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
 >>
 >> Is this a build from scratch?
 >> (after an OS upgrade, incremental builds may break)
 >>
 >>
 >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert 
 wrote:
 >> >
 >> >
 >> >
 >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit
 :
 >> >>
 >> >> We have already seen that puzzling
 >> >>
 >> >> ld: library not found for -lSystem
 >> >>
 >> >> error message.
 >> >>
 >> >> Is there a /usr/lib/libSystem.dylib present?
 >> >
 >> >
 >> > Yes:
 >> >
 >> >
 >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib
 >> >
 >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15
 /usr/lib/libSystem.dylib -> libSystem.B.dylib
 >> >
 >> >
 >> >
 >> >>
 >> >> If yes, then I guess this means a broken dependency of scipy, more

 >> >> specifically, a broken dylib, built
 >> >> along the way.
 >> >> or Xcode that needs to be reinstalled...
 >> >>
 >> >> Can you do
 >> >> ./sage --python
 >> >> >> import numpy
 >> >>
 >> >> without an error?
 >> >
 >> >
 >> > yes too:
 >> >
 >> > confetti:sage dcoudert$ ./sage --python
 >> >
 >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13)
 >> >
 >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin
 >> >
 >> > Type "help", "copyright", "credits" or "license" for more
 information.
 >> >
 >> > >>> import numpy
 >> >
 >> > >>>
 >> >
 >> >
 >> >
 >> >
 >> > --
 >> > 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-...@googlegroups.com.
 >> > To view this discussion on the web visit
 https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com
 .
 >
 >

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 
confetti:lib dcoudert$ otool -L libfflas.dylib
libfflas.dylib:
/Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
version 2.0.0, current version 2.0.0)
/Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
version 11.0.0, current version 11.1.0)
/Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
version 24.0.0, current version 24.3.0)
/Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
version 13.0.0, current version 13.3.0)
/Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
(compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
400.9.4)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 1252.250.1)


> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
> 
> oops sorry, your gfortran is ok.
> how about fflas* package, it is probably broken...
> 
> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  > wrote:
> are you building gfortran in Sage, or using a prebuilt one?
> 
> it might be that its libgfortran got broken
> 
> On Sun, 13 Oct 2019, 13:01 David Coudert,  > wrote:
> 
> 
> confetti:lib dcoudert$ pwd
> 
> /Users/dcoudert/sage3/sage/local/lib
> 
> confetti:lib dcoudert$ otool -L libgfortran.dylib 
> 
> libgfortran.dylib:
> 
>   /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
> version 5.0.0, current version 5.0.0)
> 
>   /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
> version 1.0.0, current version 1.0.0)
> 
>   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 1252.250.1)
> 
>   /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
> version 1.0.0, current version 1.0.0)
> 
> 
> 
> but I don't have the 2 others
> 
> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
> 
> confetti:sage dcoudert$ pwd
> 
> 
> /Users/dcoudert/sage3/sage
> 
> 
> 
> 
> 
> 
> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
> being incorrectly linked/broken. 
> 
> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
> "otool -L" on each of them 
> to see if they are OK. 
> 
> 
> On Sun, Oct 13, 2019 at 12:43 PM David Coudert > wrote: 
> > 
> > it's an incremental build from 9.0.beta0. 
> > I upgraded my OS in July after a system crash. So I had to reinstall 
> > everything from scratch. 
> > 
> > In case, I have Xcode Version 11.1 (11A1027). 
> > 
> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit : 
> >> 
> >> Is this a build from scratch? 
> >> (after an OS upgrade, incremental builds may break) 
> >> 
> >> 
> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert > 
> >> wrote: 
> >> > 
> >> > 
> >> > 
> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
> >> >> 
> >> >> We have already seen that puzzling 
> >> >> 
> >> >> ld: library not found for -lSystem 
> >> >> 
> >> >> error message. 
> >> >> 
> >> >> Is there a /usr/lib/libSystem.dylib present? 
> >> > 
> >> > 
> >> > Yes: 
> >> > 
> >> > 
> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
> >> > 
> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
> >> > libSystem.B.dylib 
> >> > 
> >> > 
> >> > 
> >> >> 
> >> >> If yes, then I guess this means a broken dependency of scipy, more 
> >> >> specifically, a broken dylib, built 
> >> >> along the way. 
> >> >> or Xcode that needs to be reinstalled... 
> >> >> 
> >> >> Can you do 
> >> >> ./sage --python 
> >> >> >> import numpy 
> >> >> 
> >> >> without an error? 
> >> > 
> >> > 
> >> > yes too: 
> >> > 
> >> > confetti:sage dcoudert$ ./sage --python 
> >> > 
> >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13) 
> >> > 
> >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin 
> >> > 
> >> > Type "help", "copyright", "credits" or "license" for more information. 
> >> > 
> >> > >>> import numpy 
> >> > 
> >> > >>> 
> >> > 
> >> > 
> >> > 
> >> > 
> >> > -- 
> >> > 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-...@googlegroups.com <>. 
> >> > To view this discussion on the web visit 
> >> > https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com
> >> >  
> >> > .
> >> >  
> > 
> > -- 
> > 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-...@googlegroups.com <>. 
> > To view this discussion on

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
oops sorry, your gfortran is ok.
how about fflas* package, it is probably broken...

On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:

> are you building gfortran in Sage, or using a prebuilt one?
>
> it might be that its libgfortran got broken
>
> On Sun, 13 Oct 2019, 13:01 David Coudert,  wrote:
>
>>
>>
>> confetti:lib dcoudert$ pwd
>>
>> /Users/dcoudert/sage3/sage/local/lib
>>
>> confetti:lib dcoudert$ otool -L libgfortran.dylib
>>
>> libgfortran.dylib:
>>
>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility
>> version 5.0.0, current version 5.0.0)
>>
>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility
>> version 1.0.0, current version 1.0.0)
>>
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>> 1252.250.1)
>>
>> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
>> version 1.0.0, current version 1.0.0)
>>
>>
>> but I don't have the 2 others
>>
>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>>
>> confetti:sage dcoudert$ pwd
>>
>> /Users/dcoudert/sage3/sage
>>
>>
>>
>>
>>
>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>>>
>>> I gather that the error comes from one of  -ldfftpack -lfftpack
>>> -lgfortran
>>> being incorrectly linked/broken.
>>>
>>> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
>>> "otool -L" on each of them
>>> to see if they are OK.
>>>
>>>
>>> On Sun, Oct 13, 2019 at 12:43 PM David Coudert 
>>> wrote:
>>> >
>>> > it's an incremental build from 9.0.beta0.
>>> > I upgraded my OS in July after a system crash. So I had to reinstall
>>> everything from scratch.
>>> >
>>> > In case, I have Xcode Version 11.1 (11A1027).
>>> >
>>> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
>>> >>
>>> >> Is this a build from scratch?
>>> >> (after an OS upgrade, incremental builds may break)
>>> >>
>>> >>
>>> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert 
>>> wrote:
>>> >> >
>>> >> >
>>> >> >
>>> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit
>>> :
>>> >> >>
>>> >> >> We have already seen that puzzling
>>> >> >>
>>> >> >> ld: library not found for -lSystem
>>> >> >>
>>> >> >> error message.
>>> >> >>
>>> >> >> Is there a /usr/lib/libSystem.dylib present?
>>> >> >
>>> >> >
>>> >> > Yes:
>>> >> >
>>> >> >
>>> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib
>>> >> >
>>> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib
>>> -> libSystem.B.dylib
>>> >> >
>>> >> >
>>> >> >
>>> >> >>
>>> >> >> If yes, then I guess this means a broken dependency of scipy, more
>>> >> >> specifically, a broken dylib, built
>>> >> >> along the way.
>>> >> >> or Xcode that needs to be reinstalled...
>>> >> >>
>>> >> >> Can you do
>>> >> >> ./sage --python
>>> >> >> >> import numpy
>>> >> >>
>>> >> >> without an error?
>>> >> >
>>> >> >
>>> >> > yes too:
>>> >> >
>>> >> > confetti:sage dcoudert$ ./sage --python
>>> >> >
>>> >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13)
>>> >> >
>>> >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin
>>> >> >
>>> >> > Type "help", "copyright", "credits" or "license" for more
>>> information.
>>> >> >
>>> >> > >>> import numpy
>>> >> >
>>> >> > >>>
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > --
>>> >> > 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-...@googlegroups.com.
>>> >> > To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>>>
>>> >
>>> > --
>>> > 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-...@googlegroups.com.
>>> > To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-devel/752fcf51-af9a-4315-b62d-f15dab05f4ea%40googlegroups.com.
>>>
>>>
>> --
>> 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+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/0e66a999-c1d3-47e4-9ff6-2a929c4d820a%40googlegroups.com
>> 
>> .
>>
>

-- 
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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
are you building gfortran in Sage, or using a prebuilt one?

it might be that its libgfortran got broken

On Sun, 13 Oct 2019, 13:01 David Coudert,  wrote:

>
>
> confetti:lib dcoudert$ pwd
>
> /Users/dcoudert/sage3/sage/local/lib
>
> confetti:lib dcoudert$ otool -L libgfortran.dylib
>
> libgfortran.dylib:
>
> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility
> version 5.0.0, current version 5.0.0)
>
> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility
> version 1.0.0, current version 1.0.0)
>
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1252.250.1)
>
> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
> version 1.0.0, current version 1.0.0)
>
>
> but I don't have the 2 others
>
> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>
> confetti:sage dcoudert$ pwd
>
> /Users/dcoudert/sage3/sage
>
>
>
>
>
> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>>
>> I gather that the error comes from one of  -ldfftpack -lfftpack
>> -lgfortran
>> being incorrectly linked/broken.
>>
>> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
>> "otool -L" on each of them
>> to see if they are OK.
>>
>>
>> On Sun, Oct 13, 2019 at 12:43 PM David Coudert 
>> wrote:
>> >
>> > it's an incremental build from 9.0.beta0.
>> > I upgraded my OS in July after a system crash. So I had to reinstall
>> everything from scratch.
>> >
>> > In case, I have Xcode Version 11.1 (11A1027).
>> >
>> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
>> >>
>> >> Is this a build from scratch?
>> >> (after an OS upgrade, incremental builds may break)
>> >>
>> >>
>> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert 
>> wrote:
>> >> >
>> >> >
>> >> >
>> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit :
>> >> >>
>> >> >> We have already seen that puzzling
>> >> >>
>> >> >> ld: library not found for -lSystem
>> >> >>
>> >> >> error message.
>> >> >>
>> >> >> Is there a /usr/lib/libSystem.dylib present?
>> >> >
>> >> >
>> >> > Yes:
>> >> >
>> >> >
>> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib
>> >> >
>> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib
>> -> libSystem.B.dylib
>> >> >
>> >> >
>> >> >
>> >> >>
>> >> >> If yes, then I guess this means a broken dependency of scipy, more
>> >> >> specifically, a broken dylib, built
>> >> >> along the way.
>> >> >> or Xcode that needs to be reinstalled...
>> >> >>
>> >> >> Can you do
>> >> >> ./sage --python
>> >> >> >> import numpy
>> >> >>
>> >> >> without an error?
>> >> >
>> >> >
>> >> > yes too:
>> >> >
>> >> > confetti:sage dcoudert$ ./sage --python
>> >> >
>> >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13)
>> >> >
>> >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin
>> >> >
>> >> > Type "help", "copyright", "credits" or "license" for more
>> information.
>> >> >
>> >> > >>> import numpy
>> >> >
>> >> > >>>
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > 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-...@googlegroups.com.
>> >> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>>
>> >
>> > --
>> > 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-...@googlegroups.com.
>> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/752fcf51-af9a-4315-b62d-f15dab05f4ea%40googlegroups.com.
>>
>>
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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 


confetti:lib dcoudert$ pwd

/Users/dcoudert/sage3/sage/local/lib

confetti:lib dcoudert$ otool -L libgfortran.dylib 

libgfortran.dylib:

/Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
version 5.0.0, current version 5.0.0)

/Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
version 1.0.0, current version 1.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 
1252.250.1)

/Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
version 1.0.0, current version 1.0.0)


but I don't have the 2 others

confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib

confetti:sage dcoudert$ pwd

/Users/dcoudert/sage3/sage





Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>
> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
> being incorrectly linked/broken. 
>
> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
> "otool -L" on each of them 
> to see if they are OK. 
>
>
> On Sun, Oct 13, 2019 at 12:43 PM David Coudert  > wrote: 
> > 
> > it's an incremental build from 9.0.beta0. 
> > I upgraded my OS in July after a system crash. So I had to reinstall 
> everything from scratch. 
> > 
> > In case, I have Xcode Version 11.1 (11A1027). 
> > 
> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit : 
> >> 
> >> Is this a build from scratch? 
> >> (after an OS upgrade, incremental builds may break) 
> >> 
> >> 
> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert  
> wrote: 
> >> > 
> >> > 
> >> > 
> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
> >> >> 
> >> >> We have already seen that puzzling 
> >> >> 
> >> >> ld: library not found for -lSystem 
> >> >> 
> >> >> error message. 
> >> >> 
> >> >> Is there a /usr/lib/libSystem.dylib present? 
> >> > 
> >> > 
> >> > Yes: 
> >> > 
> >> > 
> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
> >> > 
> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib 
> -> libSystem.B.dylib 
> >> > 
> >> > 
> >> > 
> >> >> 
> >> >> If yes, then I guess this means a broken dependency of scipy, more 
> >> >> specifically, a broken dylib, built 
> >> >> along the way. 
> >> >> or Xcode that needs to be reinstalled... 
> >> >> 
> >> >> Can you do 
> >> >> ./sage --python 
> >> >> >> import numpy 
> >> >> 
> >> >> without an error? 
> >> > 
> >> > 
> >> > yes too: 
> >> > 
> >> > confetti:sage dcoudert$ ./sage --python 
> >> > 
> >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13) 
> >> > 
> >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin 
> >> > 
> >> > Type "help", "copyright", "credits" or "license" for more 
> information. 
> >> > 
> >> > >>> import numpy 
> >> > 
> >> > >>> 
> >> > 
> >> > 
> >> > 
> >> > 
> >> > -- 
> >> > 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-...@googlegroups.com. 
> >> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>  
>
> > 
> > -- 
> > 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-...@googlegroups.com . 
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/752fcf51-af9a-4315-b62d-f15dab05f4ea%40googlegroups.com.
>  
>
>

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran
being incorrectly linked/broken.

please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
"otool -L" on each of them
to see if they are OK.


On Sun, Oct 13, 2019 at 12:43 PM David Coudert  wrote:
>
> it's an incremental build from 9.0.beta0.
> I upgraded my OS in July after a system crash. So I had to reinstall 
> everything from scratch.
>
> In case, I have Xcode Version 11.1 (11A1027).
>
> Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
>>
>> Is this a build from scratch?
>> (after an OS upgrade, incremental builds may break)
>>
>>
>> On Sun, Oct 13, 2019 at 12:19 PM David Coudert  wrote:
>> >
>> >
>> >
>> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit :
>> >>
>> >> We have already seen that puzzling
>> >>
>> >> ld: library not found for -lSystem
>> >>
>> >> error message.
>> >>
>> >> Is there a /usr/lib/libSystem.dylib present?
>> >
>> >
>> > Yes:
>> >
>> >
>> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib
>> >
>> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
>> > libSystem.B.dylib
>> >
>> >
>> >
>> >>
>> >> If yes, then I guess this means a broken dependency of scipy, more
>> >> specifically, a broken dylib, built
>> >> along the way.
>> >> or Xcode that needs to be reinstalled...
>> >>
>> >> Can you do
>> >> ./sage --python
>> >> >> import numpy
>> >>
>> >> without an error?
>> >
>> >
>> > yes too:
>> >
>> > confetti:sage dcoudert$ ./sage --python
>> >
>> > Python 3.7.3 (default, Oct 13 2019, 02:06:13)
>> >
>> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin
>> >
>> > Type "help", "copyright", "credits" or "license" for more information.
>> >
>> > >>> import numpy
>> >
>> > >>>
>> >
>> >
>> >
>> >
>> > --
>> > 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-...@googlegroups.com.
>> > To view this discussion on the web visit 
>> > https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>
> --
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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 
it's an incremental build from 9.0.beta0.
I upgraded my OS in July after a system crash. So I had to reinstall 
everything from scratch.

In case, I have Xcode Version 11.1 (11A1027).

Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
>
> Is this a build from scratch? 
> (after an OS upgrade, incremental builds may break) 
>
>
> On Sun, Oct 13, 2019 at 12:19 PM David Coudert  > wrote: 
> > 
> > 
> > 
> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
> >> 
> >> We have already seen that puzzling 
> >> 
> >> ld: library not found for -lSystem 
> >> 
> >> error message. 
> >> 
> >> Is there a /usr/lib/libSystem.dylib present? 
> > 
> > 
> > Yes: 
> > 
> > 
> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
> > 
> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
> libSystem.B.dylib 
> > 
> > 
> > 
> >> 
> >> If yes, then I guess this means a broken dependency of scipy, more 
> >> specifically, a broken dylib, built 
> >> along the way. 
> >> or Xcode that needs to be reinstalled... 
> >> 
> >> Can you do 
> >> ./sage --python 
> >> >> import numpy 
> >> 
> >> without an error? 
> > 
> > 
> > yes too: 
> > 
> > confetti:sage dcoudert$ ./sage --python 
> > 
> > Python 3.7.3 (default, Oct 13 2019, 02:06:13) 
> > 
> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin 
> > 
> > Type "help", "copyright", "credits" or "license" for more information. 
> > 
> > >>> import numpy 
> > 
> > >>> 
> > 
> > 
> > 
> > 
> > -- 
> > 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-...@googlegroups.com . 
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>  
>
>

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
Is this a build from scratch?
(after an OS upgrade, incremental builds may break)


On Sun, Oct 13, 2019 at 12:19 PM David Coudert  wrote:
>
>
>
> Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit :
>>
>> We have already seen that puzzling
>>
>> ld: library not found for -lSystem
>>
>> error message.
>>
>> Is there a /usr/lib/libSystem.dylib present?
>
>
> Yes:
>
>
> confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib
>
> lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
> libSystem.B.dylib
>
>
>
>>
>> If yes, then I guess this means a broken dependency of scipy, more
>> specifically, a broken dylib, built
>> along the way.
>> or Xcode that needs to be reinstalled...
>>
>> Can you do
>> ./sage --python
>> >> import numpy
>>
>> without an error?
>
>
> yes too:
>
> confetti:sage dcoudert$ ./sage --python
>
> Python 3.7.3 (default, Oct 13 2019, 02:06:13)
>
> [Clang 11.0.0 (clang-1100.0.33.8)] on darwin
>
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> import numpy
>
> >>>
>
>
>
>
> --
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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread David Coudert 


Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit :
>
> We have already seen that puzzling 
>
> ld: library not found for -lSystem 
>
> error message. 
>
> Is there a /usr/lib/libSystem.dylib present? 
>

Yes:


confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib

lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
libSystem.B.dylib

 

> If yes, then I guess this means a broken dependency of scipy, more 
> specifically, a broken dylib, built 
> along the way. 
> or Xcode that needs to be reinstalled... 
>
> Can you do 
> ./sage --python 
> >> import numpy 
>
> without an error? 
>

yes too:

confetti:sage dcoudert$ ./sage --python

Python 3.7.3 (default, Oct 13 2019, 02:06:13) 

[Clang 11.0.0 (clang-1100.0.33.8)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import numpy

>>> 

 

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

2019-10-13 Thread Dima Pasechnik 
We have already seen that puzzling

ld: library not found for -lSystem

error message.

Is there a /usr/lib/libSystem.dylib present?

If yes, then I guess this means a broken dependency of scipy, more
specifically, a broken dylib, built
along the way.
or Xcode that needs to be reinstalled...

Can you do
./sage --python
>> import numpy

without an error?

On Sun, Oct 13, 2019 at 11:36 AM David Coudert  wrote:
>
> While compiling 9.0.beta1 with python3 on a macbook air with macOS mojave, I 
> got an error building scipy 1.2.0.
> The log file attached.
>
> Any help is more than welcome.
> Thanks,
> David.
>
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