Re: [CentOS] Semi-OT: install python package in userspace

[Keith Keller]

On 2018-04-10, Richard Grainger  wrote:
> If you can use python3 rather than python2, it looks like the
> dependencies in the standard repos are new enough.

SCL might be an option for providing a more recent python.  I'm not sure
if scikit is in SCL too, but I'm pretty sure numpy is, and scikit can be
installed into a smaller virtualenv.

--keith


-- 
kkel...@wombat.san-francisco.ca.us


___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[David C. Miller]

David Miller.

- Original Message -
> From: "m roth" <m.r...@5-cent.us>
> To: "CentOS mailing list" <centos@centos.org>
> Sent: Friday, April 6, 2018 12:04:43 PM
> Subject: Re: [CentOS] Semi-OT: install python package in userspace

> Valeri Galtsev wrote:
> 
>>>> On Fri, 6 Apr 2018 17:25 , <m.r...@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, 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.
> 
> 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

Mark,

You might also want to look at conda for managing a self contained python and 
all the crazy external dependencies. Being in a research environment means 
these people will probably come back with lots of requests for other modules 
and external dependencies like tensorflow, qt5, hdf5, etc.  Conda handles 
building the snowflake versions for all that junk.

David.
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Richard Grainger]

If you can use python3 rather than python2, it looks like the
dependencies in the standard repos are new enough.  Do you want me to
have a go at packaging scikit-learn for python3 and adding it to the
repo?

On Tue, Apr 10, 2018 at 9:51 AM, Richard Grainger  wrote:
> 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  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,   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@centos.org
>>> https://lists.centos.org/mailman/listinfo/centos
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Richard Grainger]

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  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,   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@centos.org
>> https://lists.centos.org/mailman/listinfo/centos
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Richard Grainger]

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,   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@centos.org
> https://lists.centos.org/mailman/listinfo/centos
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Pete Biggs]

On Mon, 2018-04-09 at 09:15 -0700, Paul Heinlein wrote:
> On Sat, 7 Apr 2018, Pete Biggs wrote:
> 
> > > Does CentOS changed the package management? :-)
> > 
> > Quite.
> > 
> > This is not an Ubuntu dig, but when I challenge some of the users 
> > about the more dangerous sudo's they try, inevitably they say they 
> > got the command from the net, and by that they usually mean Ubuntu 
> > forums.
> 
> Whether the instructions come from the Ubuntu forums or not, we 
> regularly experience the same thing: users unthinkingly following 
> instructions in a REAME or posted on a web page. My experience 
> suggests these folks are just on autopilot. We don't even follow up 
> any more on most of the alerts; they'll ask us if it's important. So 
> we rarely give out sudo on shared systems and when we do there's some 
> "extreme vetting" going on.

I very rarely follow up as well - it's just when they do something 
blatantly dangerous or when they do something multiple times.

> 
> Also, Python has such a mature virtual-environment setup that more 
> publicly posted instructions are using that route anyway.
> 

I've stopped installing random python modules - if it's not in the
standard repositories the users are told to install it in their $HOME.
If nothing else it's a good learning experience to do it.

P.


___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Liam O'Toole]

On 2018-04-09, Valeri Galtsev
 wrote:
>
>
> On 04/09/18 11:15, Paul Heinlein wrote:
>> On Sat, 7 Apr 2018, Pete Biggs wrote:
>> 
 Does CentOS changed the package management? :-)
>>>
>>> Quite.
>>>
>>> This is not an Ubuntu dig, but when I challenge some of the users
>>> about the more dangerous sudo's they try, inevitably they say they
>>> got the command from the net, and by that they usually mean Ubuntu
>>> forums.
>> 
>> Whether the instructions come from the Ubuntu forums or not, we
>> regularly experience the same thing: users unthinkingly following
>> instructions in a REAME or posted on a web page. My experience
>> suggests these folks are just on autopilot.
>
> Sadly, people became zombies. The ability to categorize (hence use the
> menu) is wiped completely. Even the majority of "modern" Desktop
> Environment interfaces expect you to search for what you need instead
> of giving the menu: everything arranged by category. That's why I
> switched to MATE quite a while ago. I guess, I didn't blend in into
> iPad generation...

[...]

Both GNOME and KDE Plasma offer you a menu of applications by category,
if that is what you want. I don't see the problem.

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Valeri Galtsev]

On 04/09/18 11:15, Paul Heinlein wrote:

On Sat, 7 Apr 2018, Pete Biggs wrote:


Does CentOS changed the package management? :-)


Quite.

This is not an Ubuntu dig, but when I challenge some of the users 
about the more dangerous sudo's they try, inevitably they say they got 
the command from the net, and by that they usually mean Ubuntu forums.


Whether the instructions come from the Ubuntu forums or not, we 
regularly experience the same thing: users unthinkingly following 
instructions in a REAME or posted on a web page. My experience suggests 
these folks are just on autopilot.


Sadly, people became zombies. The ability to categorize (hence use the 
menu) is wiped completely. Even the majority of "modern" Desktop 
Environment interfaces expect you to search for what you need instead of 
giving the menu: everything arranged by category. That's why I switched 
to MATE quite a while ago. I guess, I didn't blend in into iPad 
generation...


Soon we will ask google how much money we have in our wallet ;-)

Valeri

We don't even follow up any more on 
most of the alerts; they'll ask us if it's important. So we rarely give 
out sudo on shared systems and when we do there's some "extreme vetting" 
going on.


Also, Python has such a mature virtual-environment setup that more 
publicly posted instructions are using that route anyway.




--

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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Paul Heinlein]

On Sat, 7 Apr 2018, Pete Biggs wrote:


Does CentOS changed the package management? :-)


Quite.

This is not an Ubuntu dig, but when I challenge some of the users 
about the more dangerous sudo's they try, inevitably they say they 
got the command from the net, and by that they usually mean Ubuntu 
forums.


Whether the instructions come from the Ubuntu forums or not, we 
regularly experience the same thing: users unthinkingly following 
instructions in a REAME or posted on a web page. My experience 
suggests these folks are just on autopilot. We don't even follow up 
any more on most of the alerts; they'll ask us if it's important. So 
we rarely give out sudo on shared systems and when we do there's some 
"extreme vetting" going on.


Also, Python has such a mature virtual-environment setup that more 
publicly posted instructions are using that route anyway.


--
Paul Heinlein
heinl...@madboa.com
45°38' N, 122°6' W
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Pete Biggs]

On Sat, 2018-04-07 at 12:23 +0200, Leon Fauster wrote:
> > Am 07.04.2018 um 01:41 schrieb Pete Biggs :
> > 
> > On Fri, 2018-04-06 at 11:50 -0500, Valeri Galtsev wrote:
> > > 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.
> > > 
> > 
> > +100
> > 
> > Nobody has sudo permissions on my systems. The most common report of a
> > sudo attempt on my CentOS systems is 'sudo apt-get update', although I
> > have had 'sudo passwd root' (they got a bollocking).
> 
> Does CentOS changed the package management? :-)
> 
Quite.

This is not an Ubuntu dig, but when I challenge some of the users about
the more dangerous sudo's they try, inevitably they say they got the
command from the net, and by that they usually mean Ubuntu forums.

P.
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Leon Fauster]

> Am 07.04.2018 um 01:41 schrieb Pete Biggs :
> 
> On Fri, 2018-04-06 at 11:50 -0500, Valeri Galtsev wrote:
>> 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.
>> 
> +100
> 
> Nobody has sudo permissions on my systems. The most common report of a
> sudo attempt on my CentOS systems is 'sudo apt-get update', although I
> have had 'sudo passwd root' (they got a bollocking).

Does CentOS changed the package management? :-)

--
LF


___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Pete Biggs]

On Fri, 2018-04-06 at 11:50 -0500, Valeri Galtsev wrote:
> 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.
> 
+100

Nobody has sudo permissions on my systems. The most common report of a
sudo attempt on my CentOS systems is 'sudo apt-get update', although I
have had 'sudo passwd root' (they got a bollocking).

P.

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Ulf Volmer]

On 06.04.2018 21:04, m.r...@5-cent.us wrote:

> So, I'm working on trying to install scipy in the virtenv... and for
> unknown reasons, it simply can't find the system libs.

try to run 'pip install --upgrade pip' in your virtualenv. Fix the issue
for me.

best regards
Ulf
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Valeri Galtsev]

On 04/06/18 13:58, Richard Demeny wrote:

python has nothing to do with snakes. it was named after a television show..


As one comedian said: sense of humor is a money: either you have it or 
don't ;-) No offense intended, just trying to make Friday brighter...


Valeri

PS And Jupyter has nothing to with planetary system and misspelling. 
Just a crapy way to call a project IMHO. Probably almost as bad as 
"MacOS X". Did you try to search for the last one any time during the 
first year if its existence? Then you know what I mean. Yes, people with 
the brain finally switched to using numbers: "10"...




On Fri, Apr 6, 2018 at 7:53 PM, Valeri Galtsev 
wrote:




On 04/06/18 13:51, Ulf Volmer wrote:


On 06.04.2018 18:25, m.r...@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@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@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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos


___
CentOS mailing list
CentOS@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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Ulf Volmer]

On 06.04.2018 20:53, Valeri Galtsev wrote:
> On 04/06/18 13:51, Ulf Volmer wrote:

>> 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" ;-)

i will not doubt that.

BTW: for Marc: if you often have to deal with python and different
modules to use, give virtualenv a try. This will give you (as user) the
option to use different python environment with different modules.

best regards
Ulf
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[m . roth]

Valeri Galtsev wrote:

>>> On Fri, 6 Apr 2018 17:25 ,  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, 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.

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


___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Richard Demeny]

python has nothing to do with snakes. it was named after a television show..

On Fri, Apr 6, 2018 at 7:53 PM, Valeri Galtsev 
wrote:

>
>
> On 04/06/18 13:51, Ulf Volmer wrote:
>
>> On 06.04.2018 18:25, m.r...@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@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@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
> 
> ___
> CentOS mailing list
> CentOS@centos.org
> https://lists.centos.org/mailman/listinfo/centos
>
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Valeri Galtsev]

On 04/06/18 13:51, Ulf Volmer wrote:

On 06.04.2018 18:25, m.r...@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@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@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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Ulf Volmer]

On 06.04.2018 18:25, m.r...@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@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
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Valeri Galtsev]

On 04/06/18 11:53, m.r...@5-cent.us wrote:

Richard Demeny wrote:

Just sudo it

On Fri, 6 Apr 2018 17:25 ,  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@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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Kenneth Porter]

--On Friday, April 06, 2018 1:25 PM -0400 m.r...@5-cent.us wrote:


Anyone got any pointers?


Not a Python programmer but a quick google turned up some likely-looking 
resources:






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


___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[m . roth]

Richard Demeny wrote:
> Just sudo it
>
> On Fri, 6 Apr 2018 17:25 ,  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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Valeri Galtsev]

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 ,  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@centos.org
>> https://lists.centos.org/mailman/listinfo/centos
>>
> ___
> CentOS mailing list
> CentOS@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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Richard Demeny]

Just sudo it

On Fri, 6 Apr 2018 17:25 ,  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@centos.org
> https://lists.centos.org/mailman/listinfo/centos
>
___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos

Re: [CentOS] Semi-OT: install python package in userspace

[Valeri Galtsev]

On Fri, April 6, 2018 11:25 am, m.r...@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@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

___
CentOS mailing list
CentOS@centos.org
https://lists.centos.org/mailman/listinfo/centos