CentOS - Apr 2018 - Semi-OT: install python package in userspace

CentOS 7 box. As there's no package in any of the repos, we're trying to
install scikit-learn in the user's space. It refuses. My late try was,
after d/l a .whl from last year, hoping that would work with the numpy
package in the regular repos, I did a pip install --user scikit-learn...,
and it still seems to want to write to system space: OSError: [Errno 13]
Permission denied:
'/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info

Anyone got any pointers?

       mark

On Fri, April 6, 2018 11:25 am, m.roth at 5-cent.us
wrote:
> CentOS 7 box. As there's no package in any of the repos, we're
trying to
> install scikit-learn in the user's space. It refuses. My late try was,
> after d/l a .whl from last year, hoping that would work with the numpy
> package in the regular repos, I did a pip install --user scikit-learn...,
> and it still seems to want to write to system space: OSError: [Errno 13]
> Permission denied:
> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>
> Anyone got any pointers?
I would take a look at the dependencies it is trying to install and will
install them first one at a time into userspace. It looks that --user flag
is not being passed to the installation of dependencies.

Valeri
>
>        mark
>
> _______________________________________________
> CentOS mailing list
> CentOS at centos.org
> https://lists.centos.org/mailman/listinfo/centos
>

++++++++++++++++++++++++++++++++++++++++
Valeri Galtsev
Sr System Administrator
Department of Astronomy and Astrophysics
Kavli Institute for Cosmological Physics
University of Chicago
Phone: 773-702-4247
++++++++++++++++++++++++++++++++++++++++

Just sudo it

On Fri, 6 Apr 2018 17:25 , <m.roth at 5-cent.us> wrote:
> CentOS 7 box. As there's no package in any of the repos, we're
trying to
> install scikit-learn in the user's space. It refuses. My late try was,
> after d/l a .whl from last year, hoping that would work with the numpy
> package in the regular repos, I did a pip install --user scikit-learn...,
> and it still seems to want to write to system space: OSError: [Errno 13]
> Permission denied:
> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>
> Anyone got any pointers?
>
>        mark
>
> _______________________________________________
> CentOS mailing list
> CentOS at centos.org
> https://lists.centos.org/mailman/listinfo/centos
>

On Fri, April 6, 2018 11:42 am, Richard Demeny wrote:
> Just sudo it
This is exactly why I have big reservation in giving users sudo
permissions. If they need sudo on UNIX or Linux for small thing like this,
then they have no idea what they are doing and can easily screw the system
up. Not to mention regular user should not hahe these permissions on
multi-user system. If they know enough to not screw system up, they do not
need almighty permissions and are able to install what they need into
userspace. The last is the goal of the OP.

Valeri
>
> On Fri, 6 Apr 2018 17:25 , <m.roth at 5-cent.us> wrote:
>
>> CentOS 7 box. As there's no package in any of the repos, we're
trying to
>> install scikit-learn in the user's space. It refuses. My late try
was,
>> after d/l a .whl from last year, hoping that would work with the numpy
>> package in the regular repos, I did a pip install --user
>> scikit-learn...,
>> and it still seems to want to write to system space: OSError: [Errno
13]
>> Permission denied:
>> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>>
>> Anyone got any pointers?
>>
>>        mark
>>
>> _______________________________________________
>> CentOS mailing list
>> CentOS at centos.org
>> https://lists.centos.org/mailman/listinfo/centos
>>
> _______________________________________________
> CentOS mailing list
> CentOS at centos.org
> https://lists.centos.org/mailman/listinfo/centos
>

++++++++++++++++++++++++++++++++++++++++
Valeri Galtsev
Sr System Administrator
Department of Astronomy and Astrophysics
Kavli Institute for Cosmological Physics
University of Chicago
Phone: 773-702-4247
++++++++++++++++++++++++++++++++++++++++

Richard Demeny wrote:
> Just sudo it
>
> On Fri, 6 Apr 2018 17:25 , <m.roth at 5-cent.us> wrote:
>
>> CentOS 7 box. As there's no package in any of the repos, we're
trying to
>> install scikit-learn in the user's space. It refuses. My late try
was,
>> after d/l a .whl from last year, hoping that would work with the numpy
>> package in the regular repos, I did a pip install --user
>> scikit-learn...,
>> and it still seems to want to write to system space: OSError: [Errno
13]
>> Permission denied:
>> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>>
>> Anyone got any pointers?
>>
First, this is a mailing list, not Outlook. Please don't top post.

Second, No. You do not appear to understand the issues.

I am *NOT* installing it as root. This is my manager's approach, and I
agree with it. As it's not a package, in a std. repo, it would not be
updated for bugfixes, and, far more critically, security fixes, when we do
that every month. That's why we want it installed in the user's space.

These are servers, used by many researchers, not someone's home Linux box.
And even at home, I wouldn't install it that way.

And I want him to use the system numpy, not install a newer one, that
would also have the same update issues. Btw, numpy in the std. repos
hasn't been seen a package update since 2015, which is why I'm trying to
install a scikit-learn from last year....

       mark

--On Friday, April 06, 2018 1:25 PM -0400 m.roth at 5-cent.us wrote:
> Anyone got any pointers?
Not a Python programmer but a quick google turned up some likely-looking 
resources:

<https://github.com/pypa/pip/issues/1668>

<https://bugzilla.redhat.com/show_bug.cgi?id=662034#c10>

My google search: python pip user writes to site-packages

On 06.04.2018 18:25, m.roth at 5-cent.us wrote:
> CentOS 7 box. As there's no package in any of the repos, we're
trying to
> install scikit-learn in the user's space. It refuses. My late try was,
> after d/l a .whl from last year, hoping that would work with the numpy
> package in the regular repos, I did a pip install --user scikit-learn...,
> and it still seems to want to write to system space: OSError: [Errno 13]
> Permission denied:
> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
can't reproduce your issue:

[ulf at centos7-x1 ~]$ pip install --user scikit-learn
Collecting scikit-learn
  Downloading scikit_learn-0.19.1-cp27-cp27mu-manylinux1_x86_64.whl (12.2MB)
    100% |????????????????????????????????| 12.2MB 101kB/s
Installing collected packages: scikit-learn
Successfully installed scikit-learn-0.19.1
You are using pip version 8.1.2, however version 9.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip'
command.

But on my testbox, i'm not sucessful to use the system numpy and scipy
packages. i had to install them using pip.

best regards
Ulf

On 04/06/18 13:51, Ulf Volmer wrote:
> On 06.04.2018 18:25, m.roth at 5-cent.us wrote:
>> CentOS 7 box. As there's no package in any of the repos, we're
trying to
>> install scikit-learn in the user's space. It refuses. My late try
was,
>> after d/l a .whl from last year, hoping that would work with the numpy
>> package in the regular repos, I did a pip install --user
scikit-learn...,
>> and it still seems to want to write to system space: OSError: [Errno
13]
>> Permission denied:
>> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
> 
> can't reproduce your issue:
> 
> [ulf at centos7-x1 ~]$ pip install --user scikit-learn
> Collecting scikit-learn
>    Downloading scikit_learn-0.19.1-cp27-cp27mu-manylinux1_x86_64.whl
(12.2MB)
>      100% |????????????????????????????????| 12.2MB 101kB/s
> Installing collected packages: scikit-learn
> Successfully installed scikit-learn-0.19.1
> You are using pip version 8.1.2, however version 9.0.3 is available.
> You should consider upgrading via the 'pip install --upgrade pip'
command.
> 
> But on my testbox, i'm not sucessful to use the system numpy and scipy
> packages. i had to install them using pip.
Python is a  "sneaky snake" ;-)

Valeri
> 
> best regards
> Ulf
> _______________________________________________
> CentOS mailing list
> CentOS at centos.org
> https://lists.centos.org/mailman/listinfo/centos
> 
-- 
++++++++++++++++++++++++++++++++++++++++
Valeri Galtsev
Sr System Administrator
Department of Astronomy and Astrophysics
Kavli Institute for Cosmological Physics
University of Chicago
Phone: 773-702-4247
++++++++++++++++++++++++++++++++++++++++

I created the epypel (Extra Extra Python Packages for Enterprise
Linux) yum repo for exactly this reason:
https://harbottle.gitlab.io/epypel/

There are a bunch of additional Python 2 and Python 3 packages there
and if you want any added, please put in a request here:
https://gitlab.com/harbottle/epypel/issues/new

The repo does not upgrade any packages in base or EPEL, so should be
safe to use on most CentOS 7 systems.

On Fri, Apr 6, 2018 at 5:25 PM,  <m.roth at 5-cent.us>
wrote:
> CentOS 7 box. As there's no package in any of the repos, we're
trying to
> install scikit-learn in the user's space. It refuses. My late try was,
> after d/l a .whl from last year, hoping that would work with the numpy
> package in the regular repos, I did a pip install --user scikit-learn...,
> and it still seems to want to write to system space: OSError: [Errno 13]
> Permission denied:
> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>
> Anyone got any pointers?
>
>        mark
>
> _______________________________________________
> CentOS mailing list
> CentOS at centos.org
> https://lists.centos.org/mailman/listinfo/centos

Just had a look at scikit-learn.  An issue you have with the current
version of this package is that is depends on NumPy (>= 1.8.2).  The
version of NumPy in CentOS 7 base is 1.7.1. You may need to look at
building a Python virtual environment.  You can google that ;)

On Tue, Apr 10, 2018 at 9:43 AM, Richard Grainger <grainger at gmail.com>
wrote:
> I created the epypel (Extra Extra Python Packages for Enterprise
> Linux) yum repo for exactly this reason:
> https://harbottle.gitlab.io/epypel/
>
> There are a bunch of additional Python 2 and Python 3 packages there
> and if you want any added, please put in a request here:
> https://gitlab.com/harbottle/epypel/issues/new
>
> The repo does not upgrade any packages in base or EPEL, so should be
> safe to use on most CentOS 7 systems.
>
> On Fri, Apr 6, 2018 at 5:25 PM,  <m.roth at 5-cent.us> wrote:
>> CentOS 7 box. As there's no package in any of the repos, we're
trying to
>> install scikit-learn in the user's space. It refuses. My late try
was,
>> after d/l a .whl from last year, hoping that would work with the numpy
>> package in the regular repos, I did a pip install --user
scikit-learn...,
>> and it still seems to want to write to system space: OSError: [Errno
13]
>> Permission denied:
>> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>>
>> Anyone got any pointers?
>>
>>        mark
>>
>> _______________________________________________
>> CentOS mailing list
>> CentOS at centos.org
>> https://lists.centos.org/mailman/listinfo/centos