Hi All,
I would really like to script my daily SPM analysis but I can't seem to get
Gwyddion with pygwy to install.
*First Macports:*
<Error: org.macports.destroot for port gwyddion returned: error renaming
"/opt/local/var/macports/build/_opt_local_var_macports_sourc
es_rsync.macports.org_release_tarballs_ports_science_gwyddion/gwyddion/work/
destroot/opt/local/lib/python2.7/site-packages/gwy.so": no such file or
directory>
navigating to find files: bla/destroot/opt/local/lib/python2.7 does not
exist at all
ran: sudo port clean gwyddion so as to hopefully not effect compiling
*Compiling from source:*
No matter what options and or flags are set (I tried a bunch of stuff but
probably missed something key), output of ./configure gives:
< Python interface (pygwy): no (needs libpython2.7)>
libpython2.7.dylib does exist in /opt/local/lib
Attached is full output
*Other Notes/Thoughts:*
All dependancies are installed via Macports
Are these errors related? Is the issue stemming from not finding the
libpython2.7?
Am I just missing something entirely straight forward?
I have attempted to follow and try all that was in the the discussion in
the 2014 on pygwy via macports
<https://sourceforge.net/p/gwyddion/mailman/gwyddion-users/thread/20140427111002.GA10822%40physics.muni.cz/#msg32273589>
thread
but no luck.
Any help is appreciated.
Thank you,
Austin
Austin Fox
*Graduate Assistant*
*Multi-functional Thin Film Materials Group, Materials Science*
*School of Mechanical, Industrial, & Manufacturing Engineering*
*Oregon State University*
204 Rogers Hall | Corvallis, OR 97331 | Tel: *(717)-371-3077*
*www.openafox.com <http://www.openafox.com/>*
CPPFLAGS="-I/opt/local/include" \
| => LDFLAGS="-L/opt/local/lib" \
| => ./configure
checking build system type... x86_64-apple-darwin16.4.0
checking host system type... x86_64-apple-darwin16.4.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports nested variables... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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 whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /opt/local/bin/gsed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc...
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker
(/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld)
is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm -B
checking the name lister (/opt/local/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin16.4.0 file names to
x86_64-apple-darwin16.4.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin16.4.0 file names to toolchain
format... func_convert_file_noop
checking for
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... dlltool
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /opt/local/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker
(/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld)
supports shared libraries... yes
checking dynamic linker characteristics... darwin16.4.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++...
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker
(/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld)
is GNU ld... no
checking whether the g++ linker
(/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld)
supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker
(/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld)
supports shared libraries... yes
checking dynamic linker characteristics... darwin16.4.0 dyld
checking how to hardcode library paths into programs... immediate
checking for xsltproc... xsltproc
checking for epydoc... no
checking for pkg-config... /opt/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking whether to build gtk-doc documentation... no
checking size of void*... 8
checking for native Microsoft Windows... no
checking for Darwin... yes
checking for update-desktop-database... update-desktop-database
checking for update-mime-database... update-mime-database
checking for gconftool-2... no
checking for a Python interpreter with version >= 2.4... python
checking for python... /opt/local/bin/python
checking for python version... 2.7
checking for python platform... darwin
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory...
${exec_prefix}/lib/python2.7/site-packages
checking size of pid_t... 4
checking for python build option BASECFLAGS... -fno-strict-aliasing -fno-common
-dynamic
checking for python build option LDFLAGS... -L/opt/local/lib
-Wl,-headerpad_max_install_names -L/opt/local/lib/db48
checking for python build option CCSHARED...
checking for python build option LINKFORSHARED... -u _PyMac_Error
Python.framework/Versions/2.7/Python
checking for python build option LIBDIR...
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib
checking for PyRun_String in -lpython2.7... no
checking for perl5... /opt/local/bin/perl5
checking for pod2man... /opt/local/bin/pod2man
checking for ruby... /Users/towel/.rvm/rubies/ruby-2.3.3/bin/ruby
checking if ruby version >= 1.8... yes
checking for ruby narray module... no
checking for fpc... no
checking whether gcc knows -Wno-format-zero-length... yes
checking whether gcc knows -Wno-system-headers... yes
checking whether gcc knows -Wno-pointer-sign... yes
checking whether gcc knows -Wno-unused-parameter... yes
checking whether gcc knows -Werror=implicit-function-declaration... yes
checking whether gcc knows -Werror=return-type... yes
checking whether gcc knows -Wdeclaration-after-statement... yes
checking whether gcc knows -Wredundant-decls... yes
checking whether gcc knows -Wno-missing-field-initializers... yes
checking whether gcc knows -fno-trapping-math... yes
checking whether gcc knows -fno-math-errno... yes
checking whether gcc knows -fexcess-precision=fast... yes
checking whether gcc knows -fno-strict-aliasing... yes
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for GTK_BASE... yes
checking for GOBJECT... yes
checking for GMODULE... yes
checking for GIO... yes
checking for Gdk target... x11
checking for XmuClientWindow in -lXmu... yes
checking X11/Xmu/WinUtil.h usability... yes
checking X11/Xmu/WinUtil.h presence... yes
checking for X11/Xmu/WinUtil.h... yes
checking for GTK... yes
checking for FFTW3... yes
checking for FFTW3_1... yes
checking for GTKGLEXT... yes
checking for inflate in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for BZ2_bzopen in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for MINIZIP... no
checking for LIBZIP... yes
checking for PNG... yes
checking for WEBP... yes
checking if the C++ compiler is a real thing... yes
checking for EXR... yes
checking for CFITSIO... no
checking for XML2... yes
checking for UNIQUE... no
checking for anyone actually reading this nonsense... no
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for GL/glext.h... yes
checking for cbrt... yes
checking for hypot... yes
checking for pow10... no
checking for acosh... yes
checking for asinh... yes
checking for atanh... yes
checking for isinf... yes
checking for isnan... yes
checking for sincos... no
checking for memrchr... no
checking for memmem... yes
checking whether NLS is requested... yes
checking for msgfmt... /opt/local/bin/msgfmt
checking for gmsgfmt... /opt/local/bin/msgfmt
checking for xgettext... /opt/local/bin/xgettext
checking for msgmerge... /opt/local/bin/msgmerge
checking for ld used by gcc...
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker
(/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld)
is GNU ld... no
checking for shared library run path origin... done
checking for CFPreferencesCopyAppValue... yes
checking for CFLocaleCopyCurrent... yes
checking for GNU gettext in libc... no
checking for iconv... yes
checking how to link with libiconv... -liconv
checking for GNU gettext in libintl... yes
checking whether to use NLS... yes
checking where the gettext function comes from... external libintl
checking how to link with libintl... -lintl -Wl,-framework -Wl,CoreFoundation
checking whether we are using the GNU C Library 2.1 or newer... no
configure: fixing msgmerge to work on Darwin
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating m4/Makefile
config.status: creating app/Makefile
config.status: creating libdraw/Makefile
config.status: creating libgwyddion/Makefile
config.status: creating libgwyddion/gwyversion.h
config.status: creating libgwydgets/Makefile
config.status: creating libgwymodule/Makefile
config.status: creating libprocess/Makefile
config.status: creating modules/Makefile
config.status: creating modules/file/Makefile
config.status: creating modules/graph/Makefile
config.status: creating modules/layer/Makefile
config.status: creating modules/process/Makefile
config.status: creating modules/pygwy/Makefile
config.status: creating modules/tools/Makefile
config.status: creating modules/volume/Makefile
config.status: creating modules/xyz/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/file/Makefile
config.status: creating plugins/process/Makefile
config.status: creating pixmaps/Makefile
config.status: creating po/Makefile.in
config.status: creating perl/Makefile
config.status: creating python/Makefile
config.status: creating ruby/Makefile
config.status: creating data/Makefile
config.status: creating data/glmaterials/Makefile
config.status: creating data/gradients/Makefile
config.status: creating utils/Makefile
config.status: creating utils/bundler
config.status: creating utils/mkosxlauncher
config.status: creating thumbnailer/Makefile
config.status: creating devel-docs/Makefile
config.status: creating devel-docs/libgwyapp/Makefile
config.status: creating devel-docs/libgwyapp/releaseinfo.xml
config.status: creating devel-docs/libgwyddion/Makefile
config.status: creating devel-docs/libgwyddion/releaseinfo.xml
config.status: creating devel-docs/libgwydgets/Makefile
config.status: creating devel-docs/libgwydgets/releaseinfo.xml
config.status: creating devel-docs/libgwydraw/Makefile
config.status: creating devel-docs/libgwydraw/releaseinfo.xml
config.status: creating devel-docs/libgwymodule/Makefile
config.status: creating devel-docs/libgwymodule/releaseinfo.xml
config.status: creating devel-docs/libgwyprocess/Makefile
config.status: creating devel-docs/libgwyprocess/releaseinfo.xml
config.status: creating gwyddion.spec
config.status: creating data/gwyddion.pc
config.status: creating data/gwyddion.nsit
config.status: creating data/mingw-gwyddion-libs.spec
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing po-directories commands
config.status: creating po/POTFILES
config.status: creating po/Makefile
config.status: executing gwyconfig.h commands
config.status: executing osx-chmod commands
=================================================================
Configuration:
FFTW3: yes
OpenGL 3D widgets: yes
Remote control: x11
Optional file formats included: NanoObserver, NanoScanTech, OpenGPS, PLUX,
APE DAX, OpenEXR, Createc zlib compression, NRRD zlib compression, RHK SM4 PRM
metadata compression, SPML, NRRD bzip2 compression, high-depth PNG
Optional file formats excluded: FITS
Thumbnailers to build: manual
Python interface (pygwy): no (needs libpython2.7)
Desktop integration files go to: prefix
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