Problem running bss_run.py -h script

Forums Forums BrainSuite Statistics toolbox (BSS) Problem running bss_run.py -h script

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    • #340
      zafarneyaz
      Participant

      Hi,
      I installed BSS in ubuntu 16 LTS (xenial). But on running bss_run.py -h, this message comes on terminal

      Error: /usr/share/brainsuite/lib/libreadline.so.6: undefined symbol: PC

      Something went wrong. Please send this error message to the developers.
      Unexpected error: <type ‘exceptions.SystemExit’>
      Traceback (most recent call last):
      File “/usr/share/brainsuite/bin/bss_run.py”, line 61, in <module>
      print traceback.print_exc(file=sys.stdout)
      NameError: name ‘traceback’ is not defined

    • #347
      shjoshi
      Moderator

      Hi Dr. Neyaz,

      We have now made the installation process on Linux/Mac much simpler.
      The new instructions are located at
      http://brainsuite.org/bss/bss-download/

      Essentially you just have to download the install.sh script and run it as:

      bash install.sh <full path to the bss installation directory>

      The above problem will have been fixed in this version.

      Thanks,
      Shantanu

    • #361
      zafarneyaz
      Participant

      I tried with the new installation file, but the following message came.

      An unexpected error has occurred, please consider sending the
      following traceback to the conda GitHub issue tracker at:

      https://github.com/conda/conda/issues

      Include the output of the command ‘conda info’ in your report.

    • #393
      shjoshi
      Moderator

      Hmm. is it possible to paste the entire error including the output on the screen when you run the installation command?

      Thanks,
      Shantanu

    • #547
      zafarneyaz
      Participant

      zafar@zafar-Lenovo-ideapad-300-15ISK:~/Desktop$ sudo bash install.sh /usr/share/bss
      This will install the BrainSuite Statistics toolbox.
      This will also install a mini version of anaconda python, R, rpy2, and statsmodels.
      % Total % Received % Xferd Average Speed Time Time Time Current
      Dload Upload Total Spent Left Speed
      100 26.5M 100 26.5M 0 0 20679 0 0:22:23 0:22:23 –:–:– 20071
      PREFIX=/usr/share/bss
      installing: python-2.7.12-1 …
      installing: conda-env-2.6.0-0 …
      installing: enum34-1.1.6-py27_0 …
      installing: openssl-1.0.2j-0 …
      installing: pycosat-0.6.1-py27_1 …
      installing: readline-6.2-2 …
      installing: requests-2.11.1-py27_0 …
      installing: ruamel_yaml-0.11.14-py27_0 …
      installing: sqlite-3.13.0-0 …
      installing: tk-8.5.18-0 …
      installing: yaml-0.1.6-0 …
      installing: zlib-1.2.8-3 …
      installing: conda-4.2.11-py27_0 …
      installing: pycrypto-2.6.1-py27_4 …
      installing: pip-8.1.2-py27_0 …
      installing: wheel-0.29.0-py27_0 …
      installing: setuptools-27.2.0-py27_0 …
      Python 2.7.12 :: Continuum Analytics, Inc.
      creating default environment…
      using -f (force) option
      installation finished.
      Installing BrainSuite statistical toolbox…This may take a few minutes…Fetching package metadata ………….
      Solving package specifications: ……….

      Package plan for installation in environment /usr/share/bss:

      The following packages will be downloaded:

      package | build
      —————————|—————–
      gettext-0.19.7 | 1 5.6 MB conda-forge
      gmp-6.1.1 | 0 727 KB conda-forge
      icu-56.1 | 4 21.9 MB conda-forge
      jpeg-9b | 0 918 KB conda-forge
      libffi-3.2.1 | 2 47 KB conda-forge
      libgcc-4.8.5 | 1 922 KB r
      libgfortran-3.0.0 | 1 281 KB
      libiconv-1.14 | 3 2.0 MB conda-forge
      libpng-1.6.17 | 0 214 KB
      libsodium-1.0.10 | 0 1.5 MB conda-forge
      mkl-11.3.3 | 0 122.1 MB
      ncurses-5.9 | 9 954 KB conda-forge
      pcre-8.38 | 1 631 KB conda-forge
      pixman-0.32.6 | 0 3.7 MB conda-forge
      xz-5.2.2 | 0 853 KB conda-forge
      freetype-2.5.5 | 1 2.5 MB
      glib-2.48.0 | 4 4.7 MB conda-forge
      hdf5-1.8.15.1 | 3 1.9 MB
      libtiff-4.0.6 | 6 507 KB conda-forge
      libxml2-2.9.4 | 2 4.9 MB conda-forge
      pandoc-1.17.2 | 0 17.3 MB conda-forge
      zeromq-4.1.5 | 0 5.0 MB conda-forge
      backports.shutil_get_terminal_size-1.0.0| py27_0 5 KB conda-forge
      backports_abc-0.4 | py27_0 5 KB conda-forge
      certifi-2016.8.31 | py27_0 219 KB conda-forge
      conda-env-2.5.2 | py27_0 26 KB conda-forge
      configparser-3.5.0 | py27_0 31 KB conda-forge
      decorator-4.0.10 | py27_0 12 KB conda-forge
      fontconfig-2.11.1 | 6 405 KB
      functools32-3.2.3.2 | py27_1 16 KB conda-forge
      ipython_genutils-0.1.0 | py27_0 33 KB conda-forge
      markupsafe-0.23 | py27_0 31 KB conda-forge
      mistune-0.7.3 | py27_0 22 KB conda-forge
      numpy-1.9.3 | py27_3 5.7 MB
      ptyprocess-0.5.1 | py27_0 19 KB conda-forge
      pyparsing-2.0.3 | py27_0 63 KB
      pytz-2016.7 | py27_0 161 KB conda-forge
      pyyaml-3.11 | py27_0 339 KB conda-forge
      pyzmq-16.0.0 | py27_0 806 KB conda-forge
      simplegeneric-0.8.1 | py27_0 6 KB conda-forge
      sip-4.18 | py27_0 263 KB conda-forge
      six-1.10.0 | py27_1 18 KB conda-forge
      ssl_match_hostname-3.5.0.1 | py27_0 6 KB conda-forge
      traits-4.4.0 | py27_0 421 KB
      vtk-5.10.1 | py27_1 92.2 MB
      wcwidth-0.1.7 | py27_0 22 KB conda-forge
      cairo-1.12.18 | 6 594 KB
      conda-4.1.12 | py27_0 200 KB conda-forge
      configobj-5.0.6 | py27_0 50 KB
      entrypoints-0.2.2 | py27_0 6 KB conda-forge
      h5py-2.5.0 | np19py27_3 2.3 MB
      jinja2-2.8 | py27_1 282 KB conda-forge
      jsonschema-2.5.1 | py27_0 70 KB conda-forge
      pathlib2-2.1.0 | py27_0 26 KB conda-forge
      pexpect-4.2.1 | py27_0 65 KB conda-forge
      pydicom-0.9.9 | py27_0 598 KB conda-forge
      pyface-4.4.0 | py27_0 694 KB
      pygments-2.1.3 | py27_1 1.2 MB conda-forge
      python-dateutil-2.5.3 | py27_0 236 KB conda-forge
      scipy-0.17.1 | np19py27_1 30.0 MB
      singledispatch-3.4.0.3 | py27_0 12 KB conda-forge
      traitlets-4.3.1 | py27_0 121 KB conda-forge
      harfbuzz-0.9.35 | 6 1.1 MB r
      jupyter_core-4.2.0 | py27_0 56 KB conda-forge
      nibabel-2.1.0 | py27_0 2.6 MB conda-forge
      pandas-0.17.1 | np19py27_0 12.2 MB
      patsy-0.4.1 | py27_0 291 KB conda-forge
      pickleshare-0.7.3 | py27_0 8 KB conda-forge
      prompt_toolkit-1.0.8 | py27_0 311 KB conda-forge
      py2cairo-1.10.0 | py27_2 36 KB
      tornado-4.4.2 | py27_0 569 KB conda-forge
      traitsui-4.4.0 | py27_0 837 KB
      apptools-4.2.1 | py27_0 282 KB
      ipython-5.1.0 | py27_1 980 KB conda-forge
      jupyter_client-4.4.0 | py27_0 101 KB conda-forge
      nbformat-4.1.0 | py27_0 120 KB conda-forge
      pango-1.36.8 | 3 796 KB r
      statsmodels-0.6.1 | np19py27_0 5.0 MB
      terminado-0.6 | py27_0 18 KB conda-forge
      envisage-4.4.0 | py27_1 267 KB
      ipykernel-4.5.0 | py27_0 128 KB conda-forge
      nbconvert-4.2.0 | py27_0 310 KB conda-forge
      qt-4.8.7 | 4 32.7 MB
      r-base-3.2.2 | 0 20.6 MB r
      jupyter_console-5.0.0 | py27_0 28 KB conda-forge
      notebook-4.2.3 | py27_0 5.4 MB conda-forge
      pyqt-4.11.4 | py27_1 3.5 MB conda-forge
      matplotlib-1.4.3 | np19py27_2 44.5 MB
      mayavi-4.4.0 | np19py27_0 10.3 MB
      qtconsole-4.2.1 | py27_0 132 KB conda-forge
      widgetsnbextension-1.2.6 | py27_3 1.1 MB conda-forge
      ipywidgets-5.2.2 | py27_2 61 KB conda-forge
      jupyter-1.0.0 | py27_3 3 KB
      r-3.2.2 | 0 2 KB r
      r-bitops-1.0_6 | r3.2.2_1a 22 KB r
      r-boot-1.3_17 | r3.2.2_0a 575 KB r
      r-chron-2.3_47 | r3.2.2_0a 98 KB r
      r-cluster-2.0.3 | r3.2.2_0a 466 KB r
      r-codetools-0.2_14 | r3.2.2_0a 45 KB r
      r-digest-0.6.8 | r3.2.2_2a 93 KB r
      r-foreign-0.8_66 | r3.2.2_0a 220 KB r
      r-formatr-1.2.1 | r3.2.2_0a 45 KB r
      r-highr-0.5.1 | r3.2.2_0a 30 KB r
      r-kernsmooth-2.23_15 | r3.2.2_0a 83 KB r
      r-lattice-0.20_33 | r3.2.2_0a 697 KB r
      r-magrittr-1.5 | r3.2.2_1a 154 KB r
      r-mass-7.3_45 | r3.2.2_0a 1.0 MB r
      r-mime-0.4 | r3.2.2_0a 26 KB r
      r-nnet-7.3_11 | r3.2.2_0a 99 KB r
      r-rpart-4.1_10 | r3.2.2_0a 861 KB r
      r-spatial-7.3_11 | r3.2.2_0a 122 KB r
      r-stringi-1.0_1 | r3.2.2_0a 10.7 MB r
      r-survival-2.38_3 | r3.2.2_0a 4.4 MB r
      r-yaml-2.1.13 | r3.2.2_1a 80 KB r
      rpy2-2.7.0 | py27r3.2.2_0 357 KB r
      r-catools-1.17.1 | r3.2.2_2a 157 KB r
      r-class-7.3_14 | r3.2.2_0a 81 KB r
      r-data.table-1.9.6 | r3.2.2_0a 1.5 MB r
      r-htmltools-0.2.6 | r3.2.2_2a 83 KB r
      r-markdown-0.7.7 | r3.2.2_1a 104 KB r
      r-matrix-1.2_2 | r3.2.2_0a 3.1 MB r
      r-nlme-3.1_122 | r3.2.2_0a 2.0 MB r
      r-stringr-1.0.0 | r3.2.2_0a 78 KB r
      r-evaluate-0.8 | r3.2.2_0a 39 KB r
      r-mgcv-1.8_9 | r3.2.2_0a 1.8 MB r
      r-knitr-1.11 | r3.2.2_0a 550 KB r
      r-recommended-3.2.2 | r3.2.2_0 707 B r
      r-rmarkdown-0.8.1 | r3.2.2_0a 1.1 MB r
      bss-v2016f.4 | r3.2.2_0 96 KB bss
      ————————————————————
      Total: 511.1 MB

      The following NEW packages will be INSTALLED:

      apptools: 4.2.1-py27_0
      backports.shutil_get_terminal_size: 1.0.0-py27_0 conda-forge
      backports_abc: 0.4-py27_0 conda-forge
      bss: v2016f.4-r3.2.2_0 bss
      cairo: 1.12.18-6
      certifi: 2016.8.31-py27_0 conda-forge
      configobj: 5.0.6-py27_0
      configparser: 3.5.0-py27_0 conda-forge
      decorator: 4.0.10-py27_0 conda-forge
      entrypoints: 0.2.2-py27_0 conda-forge
      envisage: 4.4.0-py27_1
      fontconfig: 2.11.1-6
      freetype: 2.5.5-1
      functools32: 3.2.3.2-py27_1 conda-forge
      gettext: 0.19.7-1 conda-forge
      glib: 2.48.0-4 conda-forge
      gmp: 6.1.1-0 conda-forge
      h5py: 2.5.0-np19py27_3
      harfbuzz: 0.9.35-6 r
      hdf5: 1.8.15.1-3
      icu: 56.1-4 conda-forge
      ipykernel: 4.5.0-py27_0 conda-forge
      ipython: 5.1.0-py27_1 conda-forge
      ipython_genutils: 0.1.0-py27_0 conda-forge
      ipywidgets: 5.2.2-py27_2 conda-forge
      jinja2: 2.8-py27_1 conda-forge
      jpeg: 9b-0 conda-forge
      jsonschema: 2.5.1-py27_0 conda-forge
      jupyter: 1.0.0-py27_3
      jupyter_client: 4.4.0-py27_0 conda-forge
      jupyter_console: 5.0.0-py27_0 conda-forge
      jupyter_core: 4.2.0-py27_0 conda-forge
      libffi: 3.2.1-2 conda-forge
      libgcc: 4.8.5-1 r
      libgfortran: 3.0.0-1
      libiconv: 1.14-3 conda-forge
      libpng: 1.6.17-0
      libsodium: 1.0.10-0 conda-forge
      libtiff: 4.0.6-6 conda-forge
      libxml2: 2.9.4-2 conda-forge
      markupsafe: 0.23-py27_0 conda-forge
      matplotlib: 1.4.3-np19py27_2
      mayavi: 4.4.0-np19py27_0
      mistune: 0.7.3-py27_0 conda-forge
      mkl: 11.3.3-0
      nbconvert: 4.2.0-py27_0 conda-forge
      nbformat: 4.1.0-py27_0 conda-forge
      ncurses: 5.9-9 conda-forge
      nibabel: 2.1.0-py27_0 conda-forge
      notebook: 4.2.3-py27_0 conda-forge
      numpy: 1.9.3-py27_3
      pandas: 0.17.1-np19py27_0
      pandoc: 1.17.2-0 conda-forge
      pango: 1.36.8-3 r
      pathlib2: 2.1.0-py27_0 conda-forge
      patsy: 0.4.1-py27_0 conda-forge
      pcre: 8.38-1 conda-forge
      pexpect: 4.2.1-py27_0 conda-forge
      pickleshare: 0.7.3-py27_0 conda-forge
      pixman: 0.32.6-0 conda-forge
      prompt_toolkit: 1.0.8-py27_0 conda-forge
      ptyprocess: 0.5.1-py27_0 conda-forge
      py2cairo: 1.10.0-py27_2
      pydicom: 0.9.9-py27_0 conda-forge
      pyface: 4.4.0-py27_0
      pygments: 2.1.3-py27_1 conda-forge
      pyparsing: 2.0.3-py27_0
      pyqt: 4.11.4-py27_1 conda-forge
      python-dateutil: 2.5.3-py27_0 conda-forge
      pytz: 2016.7-py27_0 conda-forge
      pyyaml: 3.11-py27_0 conda-forge
      pyzmq: 16.0.0-py27_0 conda-forge
      qt: 4.8.7-4
      qtconsole: 4.2.1-py27_0 conda-forge
      r: 3.2.2-0 r
      r-base: 3.2.2-0 r
      r-bitops: 1.0_6-r3.2.2_1a r
      r-boot: 1.3_17-r3.2.2_0a r
      r-catools: 1.17.1-r3.2.2_2a r
      r-chron: 2.3_47-r3.2.2_0a r
      r-class: 7.3_14-r3.2.2_0a r
      r-cluster: 2.0.3-r3.2.2_0a r
      r-codetools: 0.2_14-r3.2.2_0a r
      r-data.table: 1.9.6-r3.2.2_0a r
      r-digest: 0.6.8-r3.2.2_2a r
      r-evaluate: 0.8-r3.2.2_0a r
      r-foreign: 0.8_66-r3.2.2_0a r
      r-formatr: 1.2.1-r3.2.2_0a r
      r-highr: 0.5.1-r3.2.2_0a r
      r-htmltools: 0.2.6-r3.2.2_2a r
      r-kernsmooth: 2.23_15-r3.2.2_0a r
      r-knitr: 1.11-r3.2.2_0a r
      r-lattice: 0.20_33-r3.2.2_0a r
      r-magrittr: 1.5-r3.2.2_1a r
      r-markdown: 0.7.7-r3.2.2_1a r
      r-mass: 7.3_45-r3.2.2_0a r
      r-matrix: 1.2_2-r3.2.2_0a r
      r-mgcv: 1.8_9-r3.2.2_0a r
      r-mime: 0.4-r3.2.2_0a r
      r-nlme: 3.1_122-r3.2.2_0a r
      r-nnet: 7.3_11-r3.2.2_0a r
      r-recommended: 3.2.2-r3.2.2_0 r
      r-rmarkdown: 0.8.1-r3.2.2_0a r
      r-rpart: 4.1_10-r3.2.2_0a r
      r-spatial: 7.3_11-r3.2.2_0a r
      r-stringi: 1.0_1-r3.2.2_0a r
      r-stringr: 1.0.0-r3.2.2_0a r
      r-survival: 2.38_3-r3.2.2_0a r
      r-yaml: 2.1.13-r3.2.2_1a r
      rpy2: 2.7.0-py27r3.2.2_0 r
      scipy: 0.17.1-np19py27_1
      simplegeneric: 0.8.1-py27_0 conda-forge
      singledispatch: 3.4.0.3-py27_0 conda-forge
      sip: 4.18-py27_0 conda-forge
      six: 1.10.0-py27_1 conda-forge
      ssl_match_hostname: 3.5.0.1-py27_0 conda-forge
      statsmodels: 0.6.1-np19py27_0
      terminado: 0.6-py27_0 conda-forge
      tornado: 4.4.2-py27_0 conda-forge
      traitlets: 4.3.1-py27_0 conda-forge
      traits: 4.4.0-py27_0
      traitsui: 4.4.0-py27_0
      vtk: 5.10.1-py27_1
      wcwidth: 0.1.7-py27_0 conda-forge
      widgetsnbextension: 1.2.6-py27_3 conda-forge
      xz: 5.2.2-0 conda-forge
      zeromq: 4.1.5-0 conda-forge

      The following packages will be SUPERCEDED by a higher-priority channel:

      conda: 4.2.11-py27_0 –> 4.1.12-py27_0 conda-forge
      conda-env: 2.6.0-0 –> 2.5.2-py27_0 conda-forge

      Fetching packages …
      gettext-0.19.7 100% |###############################| Time: 0:05:38 17.42 kB/s
      gmp-6.1.1-0.ta 100% |###############################| Time: 0:00:49 15.13 kB/s
      icu-56.1-4.tar 100% |###############################| Time: 0:23:19 16.41 kB/s
      jpeg-9b-0.tar. 100% |###############################| Time: 0:01:05 14.35 kB/s
      libffi-3.2.1-2 100% |###############################| Time: 0:00:01 29.80 kB/s
      libgcc-4.8.5-1 100% |###############################| Time: 0:00:59 15.74 kB/s
      libgfortran-3. 100% |###############################| Time: 0:00:13 20.99 kB/s
      libiconv-1.14- 34% |########## | Time: 0:00:49 14.59 kAn unexpected error has occurred.
      Please consider posting the following information to the
      conda GitHub issue tracker at:

      https://github.com/conda/conda/issues

      Current conda install:

      platform : linux-64
      conda version : 4.2.11
      conda is private : False
      conda-env version : 4.2.11
      conda-build version : not installed
      python version : 2.7.12.final.0
      requests version : 2.11.1
      root environment : /usr/share/bss (writable)
      default environment : /usr/share/bss
      envs directories : /usr/share/bss/envs
      package cache : /usr/share/bss/pkgs
      channel URLs : https://conda.anaconda.org/conda-forge/linux-64
      https://conda.anaconda.org/conda-forge/noarch
      https://conda.anaconda.org/bss/linux-64
      https://conda.anaconda.org/bss/noarch
      https://conda.anaconda.org/r/linux-64
      https://conda.anaconda.org/r/noarch
      https://repo.continuum.io/pkgs/free/linux-64
      https://repo.continuum.io/pkgs/free/noarch
      https://repo.continuum.io/pkgs/pro/linux-64
      https://repo.continuum.io/pkgs/pro/noarch
      config file : /home/zafar/.condarc
      offline mode : False

      $ /usr/share/bss/bin/conda install bss -y

      Traceback (most recent call last):
      File “/usr/share/bss/lib/python2.7/site-packages/conda/exceptions.py”, line 479, in conda_exception_handler
      return_value = func(*args, **kwargs)
      File “/usr/share/bss/lib/python2.7/site-packages/conda/cli/main.py”, line 145, in _main
      exit_code = args.func(args, p)
      File “/usr/share/bss/lib/python2.7/site-packages/conda/cli/main_install.py”, line 80, in execute
      install(args, parser, ‘install’)
      File “/usr/share/bss/lib/python2.7/site-packages/conda/cli/install.py”, line 420, in install
      raise CondaRuntimeError(‘RuntimeError: %s’ % e)
      CondaRuntimeError: Runtime error: RuntimeError: Runtime error: Could not open u’/usr/share/bss/pkgs/libiconv-1.14-3.tar.bz2.part’ for writing (HTTPSConnectionPool(host=’binstar-cio-packages-prod.s3.amazonaws.com’, port=443): Read timed out.).

      install.sh: line 67: /usr/share/bss/bin/R: No such file or directory 16.29 kB/s
      export PATH=/usr/share/bss/bin/:${PATH}
      BrainSuite statistical toolbox was installed successfully.
      Cleaning up temporary files…rm: cannot remove ‘/usr/share/bss/tmp/Miniconda2—x86_64.sh’: No such file or directory
      Done.

      Try running
      /usr/share/bss/bin/bss_run.py -h
      It should display help and then exit.

      zafar@zafar-Lenovo-ideapad-300-15ISK:~/Desktop$

      there is no file bss_run.py -h in bin

    • #560
      shjoshi
      Moderator

      Hello,

      It seems even if you invoked install.sh with sudo, some of the installation files were not written to /usr/share.

      Can you actually try installing bss in your user or home directory, where you don’t need sudo?

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