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PostPosted: Tue Nov 14, 2017 8:47 pm 
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Joined: Fri Jan 20, 2017 5:29 pm
Posts: 37
Location: Graduate School of Oceanography,URI
Hi all,
I tried to install PyCNAL on anaconda, I followed the direction of https://github.com/ESMG/PyCNAL, but at the step check the paths in the install script and see if it runs..., I got errors , I have installed gfortran_osx-64,Is there any one having suggestions?
Code:
installing pycnal...

running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_py
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "pycnal._interp" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._obs_interp" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
  adding 'build/src.macosx-10.6-x86_64-3.5/pycnal/_obs_interp-f2pywrappers.f' to sources.
building extension "pycnal._remapping" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._remapping_fast" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._remapping_fast_weighted" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._iso" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
build_src: building npy-pkg config files
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /Users/xiaohuizhou/anaconda3/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
Warning: distutils distribution has been initialized, it may be too late to add an extension _interpWarning: distutils distribution has been initialized, it may be too late to add an extension _obs_interpWarning: distutils distribution has been initialized, it may be too late to add an extension _remappingWarning: distutils distribution has been initialized, it may be too late to add an extension _remapping_fastWarning: distutils distribution has been initialized, it may be too late to add an extension _remapping_fast_weightedWarning: distutils distribution has been initialized, it may be too late to add an extension _isorunning install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_py
running install_lib
running install_egg_info
Removing /Users/xiaohuizhou/python/lib/python3.5/site-packages/pycnal-0.1.0-py3.5.egg-info
Writing /Users/xiaohuizhou/python/lib/python3.5/site-packages/pycnal-0.1.0-py3.5.egg-info
running install_clib
customize UnixCCompiler
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "pycnal._interp" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._obs_interp" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
  adding 'build/src.macosx-10.6-x86_64-3.5/pycnal/_obs_interp-f2pywrappers.f' to sources.
building extension "pycnal._remapping" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._remapping_fast" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._remapping_fast_weighted" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
building extension "pycnal._iso" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pycnal' to include_dirs.
build_src: building npy-pkg config files
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /Users/xiaohuizhou/anaconda3/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
running install_lib
running install_egg_info
Removing /Users/xiaohuizhou/python/lib/python3.5/site-packages/pycnal-0.0.0-py3.5.egg-info
Writing /Users/xiaohuizhou/python/lib/python3.5/site-packages/pycnal-0.0.0-py3.5.egg-info
running install_clib
customize UnixCCompiler
Warning: distutils distribution has been initialized, it may be too late to add an extension _interpWarning: distutils distribution has been initialized, it may be too late to add an extension _obs_interpWarning: distutils distribution has been initialized, it may be too late to add an extension _remappingWarning: distutils distribution has been initialized, it may be too late to add an extension _remapping_fastWarning: distutils distribution has been initialized, it may be too late to add an extension _remapping_fast_weightedWarning: distutils distribution has been initialized, it may be too late to add an extension _isoinstalling external libraries...
installing gridgen...
Using prefix /Users/xiaohuizhou/python
Using libdir /Users/xiaohuizhou/python/lib
checking for gcc... gcc
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking for ar... ar
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for main in -lm... yes
checking for realloc... yes
checking for strtod... yes
checking for strtok... yes
checking for hypot... yes
checking for -fno-force-mem option... no
configure: creating ./config.status
config.status: creating makefile
config.status: creating config.h
config.status: config.h is unchanged
/bin/sh mkinstalldirs /Users/xiaohuizhou/python/bin /Users/xiaohuizhou/python/lib /Users/xiaohuizhou/python/include
for i in libnn.a; do \
      /usr/bin/install -c -m 644 $i /Users/xiaohuizhou/python/lib/$i; \
   done
for i in nn.h; do \
      /usr/bin/install -c -m 644 $i /Users/xiaohuizhou/python/include; \
   done
for i in minell nnbathy; do \
      fname=`basename $i`; \
      /usr/bin/install -c $i /Users/xiaohuizhou/python/bin; \
   done
Using prefix /Users/xiaohuizhou/python
Using libdir /Users/xiaohuizhou/python/lib
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking for ar... ar
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for main in -lm... yes
checking for realloc... yes
checking for hypot... yes
checking for copysign... yes
configure: creating ./config.status
config.status: creating makefile
config.status: creating config.h
config.status: config.h is unchanged
/bin/sh mkinstalldirs /Users/xiaohuizhou/python/bin /Users/xiaohuizhou/python/lib /Users/xiaohuizhou/python/include
for i in libcsa.a; do \
      /usr/bin/install -c -m 644 $i /Users/xiaohuizhou/python/lib/$i; \
   done
for i in csa.h; do \
      /usr/bin/install -c -m 644 $i /Users/xiaohuizhou/python/include; \
   done
for i in csabathy; do \
      fname=`basename $i`; \
      /usr/bin/install -c $i /Users/xiaohuizhou/python/bin; \
   done
Using prefix /Users/xiaohuizhou/python
Using libdir /Users/xiaohuizhou/python/lib
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking for ar... ar
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking nn.h usability... yes
checking nn.h presence... yes
checking for nn.h... yes
checking csa.h usability... yes
checking csa.h presence... yes
checking for csa.h... yes
checking for main in -lm... yes
checking for main in -lnn... yes
checking for main in -lcsa... yes
checking for ANSI C header files... (cached) yes
checking for strcasecmp... yes
checking for strerror... yes
checking for isnan... yes
configure: creating ./config.status
config.status: creating makefile
config.status: creating gridutilsconfig.h
config.status: gridutilsconfig.h is unchanged
  installing libgu.a
  installing libgu.so
  installing gridmap.h
  installing gucommon.h
  installing gridnodes.h
  installing getbound
  installing getnodes
  installing insertgrid
  installing setbathy
  installing subgrid
  installing xy2ij
  installing gridbathy
Using prefix /Users/xiaohuizhou/python
Using libdir /Users/xiaohuizhou/python/lib
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking for ar... ar
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for main in -lm... yes
checking for tgamma... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for clog... yes
checking for cexp... yes
-n checking for keyword _Complex...
yes
checking gridnodes.h usability... yes
checking gridnodes.h presence... yes
checking for gridnodes.h... yes
checking for gridnodes_readnextpoint in -lgu... yes
configure: creating ./config.status
config.status: creating makefile
config.status: creating config.h
config.status: config.h is unchanged
make: Nothing to be done for `lib'.
make: Nothing to be done for `shlib'.
  installing gridgen
  installing gridgen.h
  installing libgridgen.a
  installing libgridgen.so
installing scrip...
gfortran -g -fdefault-real-8 -ffixed-form -O2 -fPIC -Inf-config not yet implemented for cmake builds/include -c ./kinds_mod.f
gfortran: error: not: No such file or directory
gfortran: error: yet: No such file or directory
gfortran: error: implemented: No such file or directory
gfortran: error: for: No such file or directory
gfortran: error: cmake: No such file or directory
gfortran: error: builds/include: No such file or directory
make: *** [kinds_mod.o] Error 1
gfortran -g -fdefault-real-8 -ffixed-form -O2 -fPIC -Inf-config not yet implemented for cmake builds/include -c ./kinds_mod.f
gfortran: error: not: No such file or directory
gfortran: error: yet: No such file or directory
gfortran: error: implemented: No such file or directory
gfortran: error: for: No such file or directory
gfortran: error: cmake: No such file or directory
gfortran: error: builds/include: No such file or directory
make: *** [kinds_mod.o] Error 1
/bin/cp ./scrip /Users/xiaohuizhou/python/bin
cp: ./scrip: No such file or directory
make: *** [install] Error 1
cp: scrip*.so*: No such file or directory

Done installing pycnal...
pycnal make use of the so-called gridid file to store
grid information like the path to the grid file, the
number of vertical level, the vertical transformation
use, ...
Please set the environment variable PYCNAL_GRIDID_FILE
to point to your gridid file. A gridid file template
is available here:
/Users/xiaohuizhou/Documents/python_tools/PyCNAL-master/pycnal/pycnal/gridid.txt
Press any key to continue or Ctrl+C to quit this install


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