Installation failed at the end

SCT
1

Spinal Cord Toolbox (4.3)

Folder /home/mahdi/sct_4.3/bin has been created.
Trying URL: https://osf.io/mka78/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by ‘SSLError(SSLError(“bad handshake: SysCallError(-1, ‘Unexpected EOF’)”,),)’: /mka78/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by ‘SSLError(SSLError(“bad handshake: SysCallError(-1, ‘Unexpected EOF’)”,),)’: /mka78/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by ‘SSLError(SSLError(“bad handshake: SysCallError(-1, ‘Unexpected EOF’)”,),)’: /mka78/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host=‘osf.io’, port=443): Max retries exceeded with url: /mka78/?action=download (Caused by SSLError(SSLError(“bad handshake: SysCallError(-1, ‘Unexpected EOF’)”,),)))
Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20200420_sct_binaries_linux.tar.gz
Link download error, trying next mirror (error was: 403 Client Error: Forbidden for url: https://www.neuro.polymtl.ca/_media/downloads/sct/20200420_sct_binaries_linux.tar.gz)
Traceback (most recent call last):
File “/home/mahdi/sct_4.3/scripts/sct_download_data.py”, line 113, in
res = main()
File “/home/mahdi/sct_4.3/scripts/sct_download_data.py”, line 105, in main
install_data(url, dest_folder)
File “/home/mahdi/sct_4.3/spinalcordtoolbox/download.py”, line 117, in install_data
tmp_file = download_data(url)
File “/home/mahdi/sct_4.3/spinalcordtoolbox/download.py”, line 82, in download_data
raise Exception(‘Download error’, exceptions)
Exception: (‘Download error’, [SSLError(MaxRetryError(‘HTTPSConnectionPool(host=‘osf.io’, port=443): Max retries exceeded with url: /mka78/?action=download (Caused by SSLError(SSLError(“bad handshake: SysCallError(-1, ‘Unexpected EOF’)”,),))’,),), HTTPError(‘403 Client Error: Forbidden for url: https://www.neuro.polymtl.ca/_media/downloads/sct/20200420_sct_binaries_linux.tar.gz’,)])

ERROR: Command failed.
Installation failed!

I have this issue!

2

Hello @mahdi, thank you for reporting this issue. It looks like OSF.io is blocked on your network. We have https://www.neuro.polymtl.ca/_media/downloads/sct/20200420_sct_binaries_linux.tar.gz as a backup for that, but it doesn’t seem to be working either. Are you able to download from that link directly?

If neither is working, here is a third backup I just made: https://gist.github.com/kousu/559ddda4ec111bff4cc7d9570c6cddbc/raw/fb3ac1befe27f972bff8da67c5f04bc40e0a8fe7/20200420_sct_binaries_linux.tar.gz. Please let me know if you can download that.

If the third download does work, you’ll be able to complete the installation with:

cd spinalcordtoolbox;
curl -JLO https://gist.github.com/kousu/559ddda4ec111bff4cc7d9570c6cddbc/raw/fb3ac1befe27f972bff8da67c5f04bc40e0a8fe7/20200420_sct_binaries_linux.tar.gz && \
tar -zxvf 20200420_sct_binaries_linux.tar.gz -C bin/

(this is what the failing line does).

Please copy and paste those lines exactly, and copy the results back out for us. If you surround your results with

```
backticks like this
```

then it will be easy for us to read and help you with.
Thanks, have a good night.

3 
(base) mahdi@mpluss:~/sct_4.3/spinalcordtoolbox$ 
curl -JLO https://gist.github.com/kousu/559ddda4ec111bff4cc7d9570c6cddbc/raw/fb3ac1befe27f972bff8da67c5f04bc40e0a8fe7/20200420_sct_binaries_linux.tar.gz && \
> tar -zxvf 20200420_sct_binaries_linux.tar.gz -C bin/
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 74.6M  100 74.6M    0     0   183k      0  0:06:55  0:06:55 --:--:--  160k

tar: bin: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now

hello
thank you for your helping @nguenthe
I can download from both link directly. I followed your solution but after downloading, I got this error!

4

Thanks for showing all that. I can tell from the details that you’re missing the folder ~/sct_4.3/spinalcordtoolbox/bin. The installer should have made that already for you. Did you erase your installation and start fresh?

You should be able to get it installed by

cd spinalcordtoolbox;
./install_sct;  # this will fail at the end; but that's okay
curl -JLO https://gist.github.com/kousu/559ddda4ec111bff4cc7d9570c6cddbc/raw/fb3ac1befe27f972bff8da67c5f04bc40e0a8fe7/20200420_sct_binaries_linux.tar.gz && \
tar -zxvf 20200420_sct_binaries_linux.tar.gz -C bin/
echo 'export PATH="~/sct_4.3/spinalcordtoolbox/bin:$PATH"' >> ~/.bashrc
. ~/.bashrc
sct_check_dependencies

I want to fix this bug properly for you and other users in your situation. I am going to do a little bit of testing and then I might ask for your help trying out a fixed installation script. Would you be willing to donate some time to getting that to work with us?

5

actually, I didn’t have the bin folder and as you said I erase my installation and start fresh and then install
correctly!!

--
Spinal Cord Toolbox (4.3)

SCT info:
- version: 4.3
- path: /home/mahdi/sct_4.3
OS: linux (Linux-4.15.0-117-generic-x86_64-with-debian-buster-sid)
CPU cores: Available: 8, Used by SCT: 8
RAM: MemTotal:       16331464 kB
total        used        free      shared  buff/cache   available
Mem:          15948        2489        2039        1698       11419       11430
Swap:          2047           0        2047
Check Python executable.............................[OK]
  Using bundled python 3.6.12 |Anaconda, Inc.| (default, Sep  8 2020, 23:10:56) 
[GCC 7.3.0] at /home/mahdi/sct_4.3/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.18.5)
Check if colored is installed.......................[OK] (1.4.2)
Check if dipy is installed..........................[OK] (1.1.1)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if ivadomed (1.2.1) is installed..............[OK] (1.2.1)
Check if Keras (2.1.5) is installed.................[OK] (2.1.5)
Check if matplotlib is installed....................[OK] (3.2.1)
Check if nibabel is installed.......................[OK] (3.1.0)
Check if pandas is installed........................[OK] (1.0.4)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (5.4.3)
Check if pytest-cov is installed....................[OK] (2.9.0)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.23.0)
Check if requirements-parser is installed...........[OK] (0.2.0)
Check if scipy is installed.........................[OK] (1.4.1)
Check if scikit-image is installed..................[OK] (0.17.2)
Check if scikit-learn is installed..................[OK] (0.23.1)
Check if tensorflow (1.5.0) is installed............[OK] (1.5.0)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.46.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.25.9)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............[OK]

thank you for your helping And I am at your service for any help I can.

1 Like