Hello,
Does re-running as sudo change the error?

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 5 May 2018, at 02:18, Wang Lei <[log in to unmask]> wrote:

Dear experts,
It's been a week since my last mail. Is There anyone solved this problem? 
I have tried fresh install FSL 5.0.11 on 3 PC in ubuntu 16.04, all 3 have this issue.




Wang Lei <[log in to unmask]> 于 2018年4月28日周六 15:41写道：
Hi, Matthew,
 I have just tried the cmd you gave me. After downloaded a few packages, it reported an error, the complete output message is below:

Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.1

Please update conda by running

    $ conda update -n base conda



Downloading and Extracting Packages
jsoncpp 1.8.3: ######################################################### | 100% 
sqlite 3.23.1: ######################################################### | 100% 
graphite2 1.3.11: ###################################################### | 100% 
pylint 1.8.2: ########################################################## | 100% 
xz 5.2.3: ############################################################## | 100% 
libxcb 1.13: ########################################################### | 100% 
tornado 5.0.2: ######################################################### | 100% 
psutil 5.4.5: ########################################################## | 100% 
sortedcontainers 1.5.10: ############################################### | 100% 
certifi 2018.4.16: ##################################################### | 100% 
vtk 8.1.0: ############################################################# | 100% 
pytz 2018.4: ########################################################### | 100% 
pcre 8.42: ############################################################# | 100% 
pexpect 4.5.0: ######################################################### | 100% 
cytoolz 0.9.0.1: ####################################################### | 100% 
decorator 4.3.0: ####################################################### | 100% 
mkl 2018.0.2: ########################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda/exceptions.py", line 789, in __call__
        return func(*args, **kwargs)
      File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda_env/cli/main.py", line 74, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda_env/cli/main_create.py", line 108, in execute
        installer.install(prefix, pkg_specs, args, env)
      File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda_env/installers/pip.py", line 36, in _pip_install_via_requirements
        delete=False)
      File "/usr/local/fsl/fslpython/lib/python3.6/tempfile.py", line 549, in NamedTemporaryFile
        (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags, output_type)
      File "/usr/local/fsl/fslpython/lib/python3.6/tempfile.py", line 260, in _mkstemp_inner
        fd = _os.open(file, flags, 0o600)
    PermissionError: [Errno 13] Permission denied: '/usr/local/fsl/etc/fslconf/condaenv.bfuezlq6.requirements.txt'

`$ /usr/local/fsl/fslpython/bin/conda-env create -f /usr/local/fsl/etc/fslconf/fslpython_environment.yml`

  environment variables:
                 ANTSPATH=/home/user/bin/ants/bin
                 CIO_TEST=<not set>
                CLASSPATH=.:/usr/local/Java/jdk1.8.0_144/lib:/usr/local/Java/jdk1.8.0_144/jre/li
                          b
               CONDA_ROOT=/usr/local/fsl/fslpython
            DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
          LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64:
           MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
                     PATH=/home/user/anaconda3/bin:/usr/local/fsl/bin:/usr/local/Java/jdk1.8.0_144/bin:/usr/local/cuda-8
                          .0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/u
                          sr/games:/usr/local/games:/snap/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
            XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
         XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0

     active environment : None
       user config file : /home/user/.condarc
 populated config files : /home/user/.condarc
          conda version : 4.4.10
    conda-build version : not installed
         python version : 3.6.4.final.0
       base environment : /usr/local/fsl/fslpython  (read only)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
          package cache : /usr/local/fsl/fslpython/pkgs
                          /home/user/.conda/pkgs
       envs directories : /home/user/.conda/envs
                          /usr/local/fsl/fslpython/envs
               platform : linux-64
             user-agent : conda/4.4.10 requests/2.18.4 CPython/3.6.4 Linux/4.13.0-39-generic ubuntu/16.04 glibc/2.23
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]: 
No report sent. To permanently opt-out, use

    $ conda config --set report_errors false


I think there may have permission issue, so I ran the cmd again with sudo.
But, 
CondaValueError: prefix already exists: /home/user/.conda/envs/fslpython

So, I found the "/home/user/.conda/envs/fslpython" directory, and delete the fslpython there.
I ran the cmd with sudo again. This time, program goes, with a warning says the directory '/home/user/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

Then the cmd goes on, downloaded some packages. Messages are:


Collecting SPARQLWrapper==1.7.6 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 1))
Collecting rdflib==4.2.1 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 2))
    100% |████████████████████████████████| 890kB 586kB/s 
Collecting prov==1.4.0 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))
    100% |████████████████████████████████| 245kB 768kB/s 
Collecting nidmresults<2,>=1.1.0 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))
    100% |████████████████████████████████| 235kB 642kB/s 
Collecting nidmfsl<2,>=1.1.0 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 5))
Collecting keepalive>=0.5 (from SPARQLWrapper==1.7.6->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 1))
Requirement already satisfied: isodate in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from rdflib==4.2.1->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 2))
Requirement already satisfied: pyparsing in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from rdflib==4.2.1->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 2))
Requirement already satisfied: networkx>=1.10 in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))
Requirement already satisfied: six>=1.9.0 in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))
Requirement already satisfied: lxml in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))
Requirement already satisfied: python-dateutil in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))
Requirement already satisfied: nibabel in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))
Requirement already satisfied: numpy in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))
Requirement already satisfied: future in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))
Collecting rdflib-jsonld (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))
    100% |████████████████████████████████| 61kB 1.1MB/s 
Requirement already satisfied: decorator>=3.4.0 in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from networkx>=1.10->prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))
Installing collected packages: rdflib, keepalive, SPARQLWrapper, prov, rdflib-jsonld, nidmresults, nidmfsl
  Running setup.py install for rdflib ... done
  Running setup.py install for keepalive ... done
  Running setup.py install for SPARQLWrapper ... done
  Running setup.py install for rdflib-jsonld ... done
Successfully installed SPARQLWrapper-1.7.6 keepalive-0.5 nidmfsl-1.2.1 nidmresults-1.2.1 prov-1.4.0 rdflib-4.2.1 rdflib-jsonld-0.4.0
#
# To activate this environment, use:
# > source activate fslpython
#
# To deactivate an active environment, use:
# > source deactivate
#

I assume it is OK now?
So, I check the files under $FSLDIR/bin/    BUT there still not there. Instead, I found the '$FSLDIR/fslpython/envs/' now has a new directory fslpython.
And, in '$FSLDIR/fslpython/envs/fslpython/bin/', there are many files and I finally find the files missing:

ll im*
-rwxrwxr-x 1 root root 404 4月  28 15:07 imcp*
-rwxrwxr-x 1 root root 419 4月  28 15:07 img2png*
-rwxrwxr-x 1 root root 417 4月  28 15:07 img2py*
-rwxrwxr-x 1 root root 419 4月  28 15:07 img2xpm*
-rwxrwxr-x 1 root root 408 4月  28 15:07 imglob*
-rwxrwxr-x 1 root root 404 4月  28 15:07 immv*

But, seems this '$FSLDIR/fslpython/envs/fslpython/bin/' is not in the $PATH, and the terminal still says : 'imglob : command not found'

What to do next? Should I add this directory '$FSLDIR/fslpython/envs/fslpython/bin/' to PATH, OR  should I just copy missing files to '$FSLDIR/bin/' ??


2018-04-28 0:02 GMT+08:00 Matthew Webster <[log in to unmask]>:
Hello,
 Can you try running:

$FSLDIR/fslpython/bin/conda env create -f $FSLDIR/etc/fslconf/fslpython_environment.yml

and check if imglob etc are created in $FSLDIR/bin?

Kind Regards
Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 27 Apr 2018, at 16:03, Wang Lei <[log in to unmask]> wrote:

Dear Matthew,

$FSLDIR/bin/fslpython/env is an empty directory.




签名由 网易邮箱大师 定制


在2018年04月27日 22:49，Matthew Webster 写道：
Hello,
  Can you let me know what is in the envs subdirectory?

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 27 Apr 2018, at 14:57, Wang Lei <[log in to unmask]> wrote:

Dear expert,

Yes, I have the fslpython directory under $FSLDIR. 

There are several sub-directories under fslpython: 

    bin, compiler_compact, conda-meta, envs, etc, include, lib, pkgs, share, ssl, x86_64-conda_cos6-linux-gnu

and a file, LICENSE.txt

What should I do next ?

2018-04-27 18:10 GMT+08:00 Matthew Webster <[log in to unmask]>:
Hello,
          Do you have a directory called fslpython in $FSLDIR?

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford

> On 27 Apr 2018, at 10:27, Sungoku <[log in to unmask]> wrote:
>
> Dear Experts:
> I installed FSL 5.0.11 under Ubuntu16.04 just now，using fslinstaller.py.
> Everything reported success, no errors.
> I tested a few commands and gui, works fine too.
> BUT, when I using fslvbm commands, error message showed: /usr/local/fsl/bin/imglob not found
> I checked my $FSLDIR/bin directory, and did not find the imglob file .
> Actually, I compared this bin/ directory between 5.0.11 and 5.0.10, and found three files missing :
>
> imglob, imcp, immv
>
> Are these files deleted in new version now?? But fslvbm and TBSS need imglob to run.
> Where can I get these missing files?