Compilation failures in f2py

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Compilation failures in f2py

Samuel Dupree-2
I'm attempting to wrap a Fortran-77 source member library using f2py.
I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro
(2019) under Mac OS X Big Sur (ver. 11.1). The version of Xcode.app I'm
running is 12.3. The version of NumPy I'm running is 1.18.3.

The errors I'm getting are from header files the compiler can't find as
captured in the attached log file. A sample of the kind of errors I'm
seeing are captured below.

compile options:
'-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7
-I/Users/user/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include
-I/Users/user/opt/anaconda3/include/python3.7m -c'
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/fortranobject.c
In file included from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/syslimits.h:7,
                  from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:34,
                  from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:11,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:195:61:
error: no include path in which to search for limits.h
   195 | #include_next <limits.h>  /* recurse down to the real one */
|                                                             ^
In file included from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:25,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/stdio.h:78:10:
fatal error: _stdio.h: No such file or directory
    78 | #include <_stdio.h>
       |          ^~~~~~~~~~
compilation terminated.

Any suggestions?

Sam Dupree.



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Re: Compilation failures in f2py

Christopher Albert
Hi Sam,

looks like the XCode command line tools containing standard headers are either not installed or updated. Try xcode-select --install or manually download them from https://developer.apple.com/download/more/ and maybe uninstall/reinstall them in case updates don't work. Check with 

find /Library/Developer/CommandLineTools/ -name _stdio.h

which should give /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/_stdio.h (besides possible older versions of MacOSX)

Best,

Chris




Am Sa., 9. Jan. 2021 um 03:02 Uhr schrieb Samuel Dupree <[hidden email]>:
I'm attempting to wrap a Fortran-77 source member library using f2py.
I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro
(2019) under Mac OS X Big Sur (ver. 11.1). The version of Xcode.app I'm
running is 12.3. The version of NumPy I'm running is 1.18.3.

The errors I'm getting are from header files the compiler can't find as
captured in the attached log file. A sample of the kind of errors I'm
seeing are captured below.

compile options:
'-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7
-I/Users/user/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include
-I/Users/user/opt/anaconda3/include/python3.7m -c'
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/fortranobject.c
In file included from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/syslimits.h:7,
                  from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:34,
                  from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:11,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:195:61:
error: no include path in which to search for limits.h
   195 | #include_next <limits.h>  /* recurse down to the real one */
|                                                             ^
In file included from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:25,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/stdio.h:78:10:
fatal error: _stdio.h: No such file or directory
    78 | #include <_stdio.h>
       |          ^~~~~~~~~~
compilation terminated.

Any suggestions?

Sam Dupree.


_______________________________________________
NumPy-Discussion mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/numpy-discussion

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Re: Compilation failures in f2py

Samuel Dupree-2

Chris,

Thank you for responding to my post. I uninstalled and then reinstalled CommandLineTools per your suggestion. I'm still getting the same error. It appears that gcc is not seeing any of the CommandLineTools directories. When I ran the command

find /Library/Developer/CommandLineTools/ -name _stdio.h

I got:

(base) user@Mac-Pro ~ % find /Library/Developer/CommandLineTools/ -name _stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/xlocale/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/secure/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/xlocale/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/secure/_stdio.h

Any suggestions?

Sam Dupree.




On January/12/2021 05:11:50, Christopher Albert wrote:
Hi Sam,

looks like the XCode command line tools containing standard headers are either not installed or updated. Try xcode-select --install or manually download them from https://developer.apple.com/download/more/ and maybe uninstall/reinstall them in case updates don't work. Check with 

find /Library/Developer/CommandLineTools/ -name _stdio.h

which should give /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/_stdio.h (besides possible older versions of MacOSX)

Best,

Chris




Am Sa., 9. Jan. 2021 um 03:02 Uhr schrieb Samuel Dupree <[hidden email]>:
I'm attempting to wrap a Fortran-77 source member library using f2py.
I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro
(2019) under Mac OS X Big Sur (ver. 11.1). The version of Xcode.app I'm
running is 12.3. The version of NumPy I'm running is 1.18.3.

The errors I'm getting are from header files the compiler can't find as
captured in the attached log file. A sample of the kind of errors I'm
seeing are captured below.

compile options:
'-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7
-I/Users/user/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include
-I/Users/user/opt/anaconda3/include/python3.7m -c'
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/fortranobject.c
In file included from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/syslimits.h:7,
                  from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:34,
                  from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:11,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:195:61:
error: no include path in which to search for limits.h
   195 | #include_next <limits.h>  /* recurse down to the real one */
|                                                             ^
In file included from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:25,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/stdio.h:78:10:
fatal error: _stdio.h: No such file or directory
    78 | #include <_stdio.h>
       |          ^~~~~~~~~~
compilation terminated.

Any suggestions?

Sam Dupree.


_______________________________________________
NumPy-Discussion mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/numpy-discussion

_______________________________________________
NumPy-Discussion mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/numpy-discussion


_______________________________________________
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[hidden email]
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Re: Compilation failures in f2py

Christopher Albert
Sam,

the last suggestion from my side would be to upgrade or reinstall macports from https://www.macports.org/install.php and/or set your gcc compiler version to the latest one via port select. Then I'm out of clues too. 

Best,

Chris


Am Sa., 23. Jan. 2021 um 21:22 Uhr schrieb Samuel Dupree <[hidden email]>:

Chris,

Thank you for responding to my post. I uninstalled and then reinstalled CommandLineTools per your suggestion. I'm still getting the same error. It appears that gcc is not seeing any of the CommandLineTools directories. When I ran the command

find /Library/Developer/CommandLineTools/ -name _stdio.h

I got:

(base) user@Mac-Pro ~ % find /Library/Developer/CommandLineTools/ -name _stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/xlocale/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/secure/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/xlocale/_stdio.h
/Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/secure/_stdio.h

Any suggestions?

Sam Dupree.




On January/12/2021 05:11:50, Christopher Albert wrote:
Hi Sam,

looks like the XCode command line tools containing standard headers are either not installed or updated. Try xcode-select --install or manually download them from https://developer.apple.com/download/more/ and maybe uninstall/reinstall them in case updates don't work. Check with 

find /Library/Developer/CommandLineTools/ -name _stdio.h

which should give /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/_stdio.h (besides possible older versions of MacOSX)

Best,

Chris




Am Sa., 9. Jan. 2021 um 03:02 Uhr schrieb Samuel Dupree <[hidden email]>:
I'm attempting to wrap a Fortran-77 source member library using f2py.
I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro
(2019) under Mac OS X Big Sur (ver. 11.1). The version of Xcode.app I'm
running is 12.3. The version of NumPy I'm running is 1.18.3.

The errors I'm getting are from header files the compiler can't find as
captured in the attached log file. A sample of the kind of errors I'm
seeing are captured below.

compile options:
'-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7
-I/Users/user/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include
-I/Users/user/opt/anaconda3/include/python3.7m -c'
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c
gcc:
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/fortranobject.c
In file included from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/syslimits.h:7,
                  from
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:34,
                  from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:11,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:195:61:
error: no include path in which to search for limits.h
   195 | #include_next <limits.h>  /* recurse down to the real one */
|                                                             ^
In file included from
/Users/user/opt/anaconda3/include/python3.7m/Python.h:25,
                  from
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14:
/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/stdio.h:78:10:
fatal error: _stdio.h: No such file or directory
    78 | #include <_stdio.h>
       |          ^~~~~~~~~~
compilation terminated.

Any suggestions?

Sam Dupree.


_______________________________________________
NumPy-Discussion mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/numpy-discussion

_______________________________________________
NumPy-Discussion mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/numpy-discussion


_______________________________________________
NumPy-Discussion mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/numpy-discussion