ctffind 4.1.5 compile on a mac

Submitted by dominika on Thu, 2017-01-05 21:09

Forums

ctffind & ctftilt

Hi guys,
Anyone managed to compile ctffind 4.1.5 on a mac? We have newest g++ compilers, wxwidgets and fftw3.3.5, it's still not working.
Previous versions compile just fine.
Thanks!

timgrant Fri, 2017-01-13 06:33

Hi Dominka,

What is the error you are getting? If it is about missing headers, please can you remove lines 59-62 from the src/core/core_headers.h.

these lines should read :-

#include "refinement_package.h"
#include "refinement.h"
#include "database.h"
#include "project.h"

Hopefully this will help.

Tim

hael Tue, 2017-01-24 22:02

Hi:

The headers look fine in the version 4.1.6 tar ball we got from Alexis and it compiles fine on my Mac but bugs out upon execution:

@!#> ./ctffind
./src/common/cmdline.cpp(254): assert "GetShortOptionName(shrt.begin(), shrt.end()).Len() == shrt.Len()" failed in wxCmdLineArgImpl(): Short option contains invalid characters

HTH

Alexis Fri, 2017-03-17 14:17

Took me a while, but I've now confirmed that the next version (4.1.7) compiles & runs correctly on Mac (we've tested on 3 different macs, with different OSes).

Please contact me directly to request the latest tar ball. Here are the basic steps:

1) Install Homebrew (https://brew.sh/)
2) brew install wxmac
3) brew install fftw
4) tar -xvf ctffind*.tar.gz
5) cd ctffind*
6) mkdir build
7) cd build
8) ../configure CXXFLAGS="-I/usr/local/include -L/usr/local/lib"
9) You must use the system gcc (/usr/bin/gcc)
If necessary, you may need to specify CC=/usr/bin/gcc

lucajovine Thu, 2017-10-19 03:10

Hello, I've tried the above procedure to try installing 4.1.8 under Mac OS 10.12. However:

OSX> cd /usr/local/ctffind/ctffind-4.1.8/build
OSX> make clean
OSX> ../configure CC=/usr/bin/gcc CXXFLAGS="-I/usr/local/include -I/usr/local/include/wx-3.0 -I/usr/local/lib/wx/include/osx_cocoa-unicode-3.0 -L/usr/local/lib"
OSX> make
(...)
/bin/sh ./libtool --tag=CXX --mode=link g++ -I/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/lib/wx/include/osx_cocoa-unicode-3.0 -I/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/include/wx-3.0 -D_FILE_OFFSET_BITS=64 -DWXUSINGDLL -D__WXMAC__ -D__WXOSX__ -D__WXOSX_COCOA__ -DwxUSE_GUI=0 -I/usr/local/include -I/usr/local/include/wx-3.0 -I/usr/local/lib/wx/include/osx_cocoa-unicode-3.0 -L/usr/local/lib -DNDEBUG -funroll-loops -O3 -Wall -pipe -fexpensive-optimizations -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -L/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/lib -framework IOKit -framework Carbon -framework Cocoa -framework AudioToolbox -framework System -framework OpenGL -lwx_osx_cocoau-3.0 -o ctffind src/programs/ctffind/ctffind-ctffind.o src/core/ctffind-functions.o src/core/ctffind-globals.o src/core/ctffind-randomnumbergenerator.o src/core/ctffind-userinput.o src/core/ctffind-curve.o ctffind-image_trim.o src/core/ctffind-matrix.o src/core/ctffind-symmetry_matrix.o src/core/ctffind-abstract_image_file.o src/core/ctffind-mrc_header.o src/core/ctffind-mrc_file.o src/core/ctffind-tiff_file.o src/core/ctffind-dm_file.o src/core/ctffind-image_file.o src/core/ctffind-job_packager.o src/core/ctffind-job_tracker.o src/core/ctffind-run_profiles.o src/core/ctffind-myapp.o src/core/ctffind-empirical_distribution.o src/core/ctffind-ctf.o src/core/ctffind-numeric_text_file.o src/core/ctffind-progressbar.o src/core/ctffind-downhill_simplex.o src/core/ctffind-brute_force_search.o src/core/ctffind-va04.o src/core/ctffind-conjugate_gradient.o -ltiff -ldl -lfftw3f
libtool: link: g++ -I/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/lib/wx/include/osx_cocoa-unicode-3.0 -I/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/include/wx-3.0 -D_FILE_OFFSET_BITS=64 -DWXUSINGDLL -D__WXMAC__ -D__WXOSX__ -D__WXOSX_COCOA__ -DwxUSE_GUI=0 -I/usr/local/include -I/usr/local/include/wx-3.0 -I/usr/local/lib/wx/include/osx_cocoa-unicode-3.0 -DNDEBUG -funroll-loops -O3 -Wall -pipe -fexpensive-optimizations -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ctffind src/programs/ctffind/ctffind-ctffind.o src/core/ctffind-functions.o src/core/ctffind-globals.o src/core/ctffind-randomnumbergenerator.o src/core/ctffind-userinput.o src/core/ctffind-curve.o ctffind-image_trim.o src/core/ctffind-matrix.o src/core/ctffind-symmetry_matrix.o src/core/ctffind-abstract_image_file.o src/core/ctffind-mrc_header.o src/core/ctffind-mrc_file.o src/core/ctffind-tiff_file.o src/core/ctffind-dm_file.o src/core/ctffind-image_file.o src/core/ctffind-job_packager.o src/core/ctffind-job_tracker.o src/core/ctffind-run_profiles.o src/core/ctffind-myapp.o src/core/ctffind-empirical_distribution.o src/core/ctffind-ctf.o src/core/ctffind-numeric_text_file.o src/core/ctffind-progressbar.o src/core/ctffind-downhill_simplex.o src/core/ctffind-brute_force_search.o src/core/ctffind-va04.o src/core/ctffind-conjugate_gradient.o -Wl,-bind_at_load -L/usr/local/lib -L/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/lib -framework IOKit -framework Carbon -framework Cocoa -framework AudioToolbox -framework System -framework OpenGL -lwx_osx_cocoau-3.0 -ltiff -ldl -lfftw3f
ld: warning: directory not found for option '-L/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/install/lib'
ld: warning: text-based stub file /System/Library/Frameworks//AudioToolbox.framework/AudioToolbox.tbd and library file /System/Library/Frameworks//AudioToolbox.framework/AudioToolbox are out of sync. Falling back to library file for linking.
ld: library not found for -lwx_osx_cocoau-3.0
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Makefile:629: ctffind] Error 1
OSX>

And indeed, the only instances of libwx_osx_cocoau-3.0*.dylib I can find on my system are have nothing to wit the brew installation of wxmac:

/usr/local/phenix/phenix-dev-2926/base/lib/libwx_osx_cocoau-3.0.0.2.0.dylib
/Applications/ccp4-7.0/lib/libwx_osx_cocoau-3.0.0.2.0.dylib
/usr/local/phenix/phenix-installer-1.12-2829-source/base/lib/libwx_osx_cocoau-3.0.0.2.0.dylib
/usr/local/phenix/phenix-1.12-2829/base/lib/libwx_osx_cocoau-3.0.0.2.0.dylib
/usr/local/phenix/phenix-installer-1.12-2829-source/base_tmp/wxPython-src-3.0.2.0/lib/libwx_osx_cocoau-3.0.0.2.0.dylib
/usr/local/dials/dials-v1-7-2/base/lib/libwx_osx_cocoau-3.0.0.2.0.dylib

Any help to fix this problem would be highly appreciated!

Thanks,

Luca

Betty Tue, 2017-12-26 15:24

I have ran into all the error messages mentioned above.
But decided to give it another try; looked into the README file before I started and found out that it is important to point out the path of the wx-config file.
It turns out that "brew install wxMac" put wx-config into /usr/local/Cellar/wxmac/3.0.3.1_1/bin. Which differs from the path "which wx-config" gave. Once I include the correct wx-path, the package was complied without error (there were a few warnings about optimization but I just ignore them).
I did find "ctffind" and "ctffind_plot_results.sh" in /usr/local/bin. Have not checked whether ctffind works correctly or not yet, keeping my fingers crossed:-)

The syntax for configure follows:
../configure CXXFLAGS="-I/usr/local/include -L/usr/local/lib" CC=/usr/bin/gcc --with-wx-config=/usr/local/Cellar/wxmac/3.0.3.1_1/bin/wx-config
make ##complex without error
sudo make install finished instantly.