- BrainSuite

October 26, 2016 at 6:31 pm #547

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:

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

Reply To: Problem running bss_run.py -h script

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