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

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 04/06/18 11:53, m.roth at 5-cent.us wrote:
> 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, python is a "sneaky snake" ;-) and some modules may require 
particular version of dependencies, therefore they may ignore your 
system wide numpy (even though it may just may be compatible with them), 
and may demand latest version of numpy. Which will explain pip (or 
other) attempting to pull dependencies which allegedly are available 
system wide already.

Just speculating, your own research on your particular issue may give 
your better answer.

And yes, I second that, system administration and maintaining one's own 
laptop are ultimately different things, luckily majority of my users 
refrain from telling me what they googled up about problem they report, 
but not everybody, so I definitely have the same feelings about the 
advice someone gave you ;-)

I hope, this helps.

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
++++++++++++++++++++++++++++++++++++++++

Valeri Galtsev wrote:
<snip>
>>> 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?
<snip>
> Mark, python is a "sneaky snake" ;-) and some modules may require
> particular version of dependencies, therefore they may ignore your
> system wide numpy (even though it may just may be compatible with them),
> and may demand latest version of numpy. Which will explain pip (or
> other) attempting to pull dependencies which allegedly are available
> system wide already.
>
> Just speculating, your own research on your particular issue may give
> your better answer.
<snip>
Well, my manager came back, and he's got me using virtenv. Having read
about it, I like it.  Oh, and the issue with the system numpy in
site-packages was that, for some reason, it was *not* world-readable.
Fixed that.

So, I'm working on trying to install scipy in the virtenv... and for
unknown reasons, it simply can't find the system libs. I did this before
the last attempt to
export LAPACK=/usr/lib64/liblapack.so.3
export BLAS=/usr/lib64/libblas.so.3
and just added export LD_LIBRARY_PATH=/usr/lib64
Still can't find them.

Clues on this one?

        mark