Installation trouble in mac os x 10.13.3

[Hiroshi Imai]

Dear Carsten and the SPRING team

Hello. I would like to start using SPRING. I have tried to install SPRING but I have the error message in the following.
Could you please kindly let me know how to solve this problem in order to start SPRING?

I have iMac (mac os x 10.13.3).
1) I have installed X-code (version 9.3 (9E145)), +command line tools (xcode-select version 2349), and X-Quartz (version 2.7.9).
2) I have downloaded "spring-latest-MacOSX.dmg.gz" and extracted the "spring_v0-86-1661" directory.
3) I have created "/Users/sachse/tempdir/spring_build_2017c/".
4) I copied the "spring_v0-86-1661" directory under /Users/sachse/tempdir/spring_build_2017c/
5) In the "spring_v0-86-1661" directory, I typed "sh patches/binary_install_mac.sh".
6) I have edited .bashrc by adding the text in the following: export PATH="/Users/sachse/tempdir/spring_build_2017c/spring_v0-86-1661/bin:$PATH".
7) I have launched a new X-Quartz terminal, and typed in the following: spring --version && springenv python -c 'import platform; print platform.platform()'
8) Then I have seen the error message in the following.

bash-3.2$ spring --version && springenv python -c 'import platform; print platform.platform()'
Spring environment loaded.
Traceback (most recent call last):
  File "/Users/sachse/tempdir/spring_build_2017c/spring_v0-86-1661/bin/spring", line 169, in <module>
    import spring.springgui.spring_launch
ImportError: No module named spring.springgui.spring_launch



Best regards,
Hiroshi Imai

＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊
Hiroshi Imai, PhD

 

Graduate School of Science,
Osaka University,

1-1, Machikaneyama-cho, 
Toyonaka, Osaka, 560-0043, Japan

 

＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊

[Hiroshi Imai]

Dear Carsten
I found sevaral problems after a recent OS update (to macOS High Sierra such as macport etc). After solving these problems, I am going to contact you if I still have installation problems.

If you have any preference to Linux OS, which is suitable for SPRING, could you please let me know? I would like to start SPRING as soon as possible.

Best regards,
Hiroshi

Graduate School of Science, Osaka University

[Hiroshi Imai]

Dear Carsten

I have both the mac OS update issues and the SPRING installation issues.

(1) Mac OS update issues
After I have updated my mac OS from Sierra to High Sierra, the command in the following did not start at all :"$sudo port install wxwidgets-3.2 fftw-3".
By following the advice from apple, I have installed a new version of X-code, a new version of Command Line Tools, and a new version of macports.
After these installation, I have completed: "$sudo port install wxwidgets-3.2 fftw-3".

(2) SPRING installation issues
Then I excuted: "$sh build_mac.sh".
I have got the messages in the following.
==================================================================================
 ----------------------------- Running build_mac.sh ------------------------------
This script will download, build and test Spring including required components on
a Mac. Spring will be created in a new directory named spring_v(version number).
==================================================================================
----------------------------------------------------------------------------------
Unset all existing library paths to avoid confusion during compilation.
----------------------------------------------------------------------------------
----------------------------------------------------------------------------------
Get Spring source and prepare directory.
----------------------------------------------------------------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 3510k  100 3510k    0     0  1007k      0  0:00:03  0:00:03 --:--:-- 1007k
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x csachse-emspring-6ea246361ae7/README.rst
x csachse-emspring-6ea246361ae7/bootstrap.py
x csachse-emspring-6ea246361ae7/buildout_linux.cfg
x csachse-emspring-6ea246361ae7/buildout_mac.cfg
x csachse-emspring-6ea246361ae7/doc/CHANGES.rst
x csachse-emspring-6ea246361ae7/doc/Makefile
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x csachse-emspring-6ea246361ae7/doc/tutorial/tutorial.pdf
x csachse-emspring-6ea246361ae7/patches/Makefile_ctf_mp
x csachse-emspring-6ea246361ae7/patches/binary_install_linux.sh
x csachse-emspring-6ea246361ae7/patches/binary_install_mac.sh
x csachse-emspring-6ea246361ae7/patches/build_linux.sh
x csachse-emspring-6ea246361ae7/patches/build_mac.sh
x csachse-emspring-6ea246361ae7/patches/configure.patch
x csachse-emspring-6ea246361ae7/patches/ctffind4.patch
x csachse-emspring-6ea246361ae7/patches/prep_binary_linux.sh
x csachse-emspring-6ea246361ae7/patches/prep_binary_mac.sh
x csachse-emspring-6ea246361ae7/patches/virtualenv.py
mv: rename csachse-emspring-6ea246361ae7 to spring_v0-86-1661/csachse-emspring-6ea246361ae7: Directory not empty
----------------------------------------------------------------------------------
Get version number and define build spring directory.
----------------------------------------------------------------------------------
----------------------------------------------------------------------------------
Spring will be installed in spring_v0-86-1661.
Get EMAN2 source. Only the provided EMAN2 version will work with Spring.
----------------------------------------------------------------------------------
----------------------------------------------------------------------------------
Install EMAN2.
----------------------------------------------------------------------------------
mkdir: fetch: File exists
mkdir: parts: File exists
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100 98.3M  100 98.3M    0     0  1587k      0  0:01:03  0:01:03 --:--:-- 1428k
/dev/disk4              Apple_partition_scheme         
/dev/disk4s1            Apple_partition_map            
/dev/disk4s2            Apple_HFS                       /Volumes/EMAN2 daily for Mac OS X lion, built on 2013-08-05
cp: parts/EMAN2/extlib/qt4/lib/QtCore.framework/Headers/qconfig.h: Permission denied
cp: parts/EMAN2/extlib/qt4/lib/QtCore.framework/Versions/4/Headers/qconfig.h: Permission denied
cp: parts/EMAN2/extlib/qt4/lib/QtCore.framework/Versions/Current/Headers/qconfig.h: Permission denied
"/Volumes/EMAN2 daily for Mac OS X lion, built on 2013-08-05/EMAN2" unmounted successfully.
----------------------------------------------------------------------------------
1. Generate virtualenv within Spring directory.
----------------------------------------------------------------------------------
New python executable in ./bin/python
Installing setuptools..................done.
Installing pip.............done.
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100 1738k  100 1738k    0     0  5070k      0 --:--:-- --:--:-- --:--:-- 5069k
Collecting pip
  Using cached pip-9.0.3-py2.py3-none-any.whl
Installing collected packages: pip
Successfully installed pip-9.0.3
New python executable in ./bin/python
Installing setuptools..................done.
Installing pip.............done.
----------------------------------------------------------------------------------
2. Generate buildout environment for Spring.
----------------------------------------------------------------------------------

Traceback (most recent call last):

  File "bootstrap.py", line 231, in <module>
    if _final_version(distv):
  File "bootstrap.py", line 217, in _final_version
    for part in parsed_version:
TypeError: 'Version' object is not iterable
----------------------------------------------------------------------------------
3. Build all components. This step may take 1 - 2 hours depending on your hardware.
----------------------------------------------------------------------------------
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (28) Timeout was reached
patches/build_mac.sh: line 94: ./bin/buildout: No such file or directory
patches/build_mac.sh: line 110: ./bin/buildout: No such file or directory
--------------------------------------------------------------------------------
4. Install latest Python dependencies for Spring
--------------------------------------------------------------------------------
patches/build_mac.sh: line 117: ./bin/buildout: No such file or directory
----------------------------------------------------------------------------------
Install done. Check whether Spring was successfully installed by testing.
The tests will run for approx. 15 min depending on your hardware.
----------------------------------------------------------------------------------
patches/build_mac.sh: line 125: ./bin/nosetests: No such file or directory
==================================================================================
Testing done. Check in nose_results directory whether ~80 tests ran successfully.
If this is the case Spring was correctly built and installed.
==================================================================================


If the mac installation is not successful, I could use Linux PC such as CentOS6, Ubuntu etc.  I would like to start SPRING, which is very impressive according to Desfosses et al., 2014 J. Struct Biol.

Best regards,
Hiroshi

[Carsten Sachse]

Dear Hiroshi,

I have been alerted to a binary installation error on linux (see recent install thread). On the mac, the binary installer threw some confusing error messages, although in principle it seemed work fine in our environment. I have updated the installer to give less confusing messages. Please, go ahead and download the latest Spring-MacOSX binaries. You should be able to install it as we have been successful on our test systems. 

You also posted errors on build messages - the second route to install Spring. I will look into this at a later stage. For now, you should have a new functional binary installer. Let me know if it is working.

Best wishes,

Carsten 

[Hiroshi Imai]

Dear Carsten
Thank you very much for your e-mail. I am going to examine whether it would work or not for my Mac OS X.
Best wishes,
Hiroshi

[Hiroshi Imai]

Dear Carsten

The SPRING graphical user interinface has been started after typing "spring" from Xterm in my Mac OS X.
Thank you very much for your help!

I have not yet tested to run your TMV tutorial.
After completion of your TMV totorial, I am going to post you in this list.

Many thanks,
Hiroshi

[Hiroshi Imai]

Dear Carsten

It is good news.
I have completed all the tutorial of the 3D TMV reconstruction as a "beginner" mode using iMac (27-inch, Mid 2011) mac os x 10.13.4.
Therefore, the installation was successful.
 
I also installed the SPRING into a 40-CPU workstation with a CentOS7 linux.
I have come to end of the tutorial as an "intermediate" mode.

Many thanks for your help,
Hiroshi