Re: R as on Ubuntu and Fedora

[George N. White III]

On 27 February 2018 at 06:34, José Abílio Matos  wrote:

> On Wednesday, 21 February 2018 03.10.31 WET Max Pyziur wrote:
>
> > ggplot2, tibble, tidyr dplyr. They seem to be popular and becoming more
>
> > integral to R.
>
> >
>
> > As for the point about 435 on Ubuntu vs the ~140 on Fedora: I assume
> those
>
> > 435 are reflective of popularity, frequency of usage, and maintenance. It
>
> > would be ridiculous to put all 6,000 CRAN packages into the Fedora eco
>
> > system.
>
> >
>
> > But consider perl and the number of packages that have been rpm'd, even
>
> > though some are close to stale. The benefit of having a package is that
> it
>
> > is built with the whole distro in mind.
>
>
>
This has pros and cons.  Pro is that you can install packages without
having to find and install supporting libraries.  Con is that newer
packages may require versions of supporting packages that are
newer than the version in the distro.

> If you install packages local to a user, then they might not/probably are
>
> > not available to other users (but to engage in self argument: how many
>
> > other "users" have access to your own systems - desktop & laptop?)
>
>
>
At work we have an operational system with multiple users.  The current
version uses a bare C++ library, but the same library is wrapped by
an R package which is far easier to use than a system where every
change needs a C++ compiler.  The operational system uses a
number of very large 3rd party applications, including R, each expecting
specific versions of libraries.   Getting all these applications to play
nicely is difficult.  A few years ago, many of the potential conflicts
were avoided by static linking.  The recent trend in which every application
"calls home"  combined with transitions to https has caused many
developers to abandon static linking, so there are more now more
conflicts than ever before.   The conflicts are not just differing versions
of libraries, there are many libraries (e.g., the proj4 projections) that
provide data files.  Some applications provide non-standard versions of
these
data files, and expect users to set an environment variable that
instructs the library to the "special" versions of the data files.  This
breaks all the applications that were developed to work with the
standard data files.

There are people looking to address some of these issues using
lightweight virtualization, but at present those techniques are
limited to ad-hoc projects and testing.



> > Sure, there is little challenge to installing R packages using
>
> > install.packages("SomePackageName"); my concern is more for the sake of
>
> > consistency: if perl, python, php, etc., have their modules/function
>
> > libraries built for Fedora, why not R?
>
> >
>
> > Curious, not kvetching,
>
> >
>
> > MP
>
>
>
> BTW I think that CRAN now is over 10 000 packages so even 435 is less than
> 5%.
>
>
>
> I maintain some of those packages in Fedora, and from practical experience
> I
>
can tell you that one of the problems when packaging a new R package into
>
Fedora is that every time you start you have to unravel all the
> dependencies.
>
Sometimes you need to go 5 levels deeps, with a net result of ~40/50 new
>
packages that need to be added before adding the package you interested in.
>
>
>

How often does a new R package require a version or configuration
of a library that differs from what the distro provides?  Libraries like
hdf5 and gdal
have many configuration options.  In my experience, distro versions often
omit
options needed for my work (remote sensing).  Too often you can easily
install
an R package, only to discover that it fails for your "use case" and has to
be
rebuilt using non-distro libraries.


> Recently some of the packages required to have the packages you referred
> above
>
are starting to show in Fedora. But that is a process that takes time and
> requires energy.
>
>
>
> I presented a talk in useR 2008:
>
> https://jamatos.fedorapeople.org/talk-user2008.pdf
>
>
>
> FWIW this problem is not specific to R the same happens for python. There
> are
>
packages where unraveling new dependencies is also a problem.
>

The talk mentions some of the issues with "suggested" packages.  Of course,
the first question is whether all the "suggested" packages can be built
using
R install.packages().  Creating distro packages is labor intensive.
Packages that
are very widely used should be in distro packages, but so should packages
that are less widely used but still popular and which require extra steps to
build (e.g., rely on 3rd party libraries so need dev packages outside the
normal "build-essential" lists , or which don't reliable detect installed
distro
packages).  It would be nice to have such  packages identified on CRAN so
package developers can work on the issues.

Many large organizations provide managed platforms for large
applications.
These platforms get distro packages, are are generally expected to have a
5-year
lifetime.  

Re: R as on Ubuntu and Fedora

[José Abílio Matos]

On Wednesday, 21 February 2018 03.10.31 WET Max Pyziur wrote:
> ggplot2, tibble, tidyr dplyr. They seem to be popular and becoming more
> integral to R.
> 
> As for the point about 435 on Ubuntu vs the ~140 on Fedora: I assume those
> 435 are reflective of popularity, frequency of usage, and maintenance. It
> would be ridiculous to put all 6,000 CRAN packages into the Fedora eco
> system.
> 
> But consider perl and the number of packages that have been rpm'd, even
> though some are close to stale. The benefit of having a package is that it
> is built with the whole distro in mind.
> 
> If you install packages local to a user, then they might not/probably are
> not available to other users (but to engage in self argument: how many
> other "users" have access to your own systems - desktop & laptop?)
> 
> Sure, there is little challenge to installing R packages using
> install.packages("SomePackageName"); my concern is more for the sake of
> consistency: if perl, python, php, etc., have their modules/function
> libraries built for Fedora, why not R?
> 
> Curious, not kvetching,
> 
> MP

BTW I think that CRAN now is over 10 000 packages so even 435 is less than 5%.

I maintain some of those packages in Fedora, and from practical experience I 
can tell you that 
one of the problems when packaging a new R package into Fedora is that every 
time you start 
you have to unravel all the dependencies. Sometimes you need to go 5 levels 
deeps, with a net 
result of ~40/50 new packages that need to be added before adding the package 
you interested 
in.

Recently some of the packages required to have the packages you referred above 
are starting 
to show in Fedora. But that is a process that takes time and requires energy.

I presented a talk in useR 2008:
https://jamatos.fedorapeople.org/talk-user2008.pdf

FWIW this problem is not specific to R the same happens for python. There are 
packages where 
unraveling new dependencies is also a problem.

Regards,
-- 
José Matos
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Re: R as on Ubuntu and Fedora

[Heinz Diehl]

On 21.02.2018, Max Pyziur wrote: 

> I've noticed that Ubuntu has considerably greater support for R than Fedora
> (more R deb packages than R rpm packages).

See https://cran.r-project.org/web/packages/available_packages_by_name.html
There's a plethora of different packages. You can either install them
with the "install.packages()" function or directly from R-studio,
which is what I'm using.

https://www.rstudio.com/products/rstudio/download/#download
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Re: [Off-topic] Re: R as on Ubuntu and Fedora

[Ed Greshko]

On 02/21/18 11:14, Max Pyziur wrote:
> On Tue, 20 Feb 2018, Todd Zullinger wrote:
>
> [...]
>>
>> # Non-R packages:
>> fonts-KOI8-R.noarch
>> fonts-KOI8-R-100dpi.noarch
>> fonts-KOI8-R-75dpi.noarch
>
> Wow! Does someone still use KOI8-R in a universe of UTF8 and Unicode?
>
>

That might be like asking "Does anyone use big5 or GB2312 in the UTF8 and 
Unicode
world?"  And the answer would be Yes.

The Taiwan Government still uses big5 in some cases.  Some sites in Taiwan 
still use
big5.  And in the PRC the Government there still uses GB2312.


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[Off-topic] Re: R as on Ubuntu and Fedora

[Max Pyziur]

On Tue, 20 Feb 2018, Todd Zullinger wrote:

[...]


# Non-R packages:
fonts-KOI8-R.noarch
fonts-KOI8-R-100dpi.noarch
fonts-KOI8-R-75dpi.noarch


Wow! Does someone still use KOI8-R in a universe of UTF8 and Unicode?



perl-Tree-R.noarch

There's an R SIG for Fedora, which looks like it's been
quiet since October.  Perhaps some folks interested in R
packaging would be welcome there?

   https://stat.ethz.ch/mailman/listinfo/r-sig-fedora





MP
p...@brama.com
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Re: R as on Ubuntu and Fedora

[Max Pyziur]

On Tue, 20 Feb 2018, Matthew Miller wrote:


On Tue, Feb 20, 2018 at 06:28:57PM -0500, Max Pyziur wrote:

Greetings,
I've been learning R on both Fedora and Ubuntu.
I've noticed that Ubuntu has considerably greater support for R than
Fedora (more R deb packages than R rpm packages).
Is there a rationale for this?


I'm not sure about R in specific, but generally the rationale is "no
one did it". Are there particular packages that you're interested in?


ggplot2, tibble, tidyr dplyr. They seem to be popular and becoming more 
integral to R.


As for the point about 435 on Ubuntu vs the ~140 on Fedora: I assume those 
435 are reflective of popularity, frequency of usage, and maintenance. It 
would be ridiculous to put all 6,000 CRAN packages into the Fedora eco 
system.


But consider perl and the number of packages that have been rpm'd, even 
though some are close to stale. The benefit of having a package is that it 
is built with the whole distro in mind.


If you install packages local to a user, then they might not/probably are 
not available to other users (but to engage in self argument: how many 
other "users" have access to your own systems - desktop & laptop?)


Sure, there is little challenge to installing R packages using 
install.packages("SomePackageName"); my concern is more for the sake of 
consistency: if perl, python, php, etc., have their modules/function 
libraries built for Fedora, why not R?


Curious, not kvetching,

MP

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Re: R as on Ubuntu and Fedora

[Ranjan Maitra]

I have used R since 1997 (version 0.4) and Fedora since Fedora 1 (2003). Ubuntu 
which my wife used for 10-12 years (before she saw the light, as it were) can 
not even begin to match Fedora's support and user community.

With regard to R: I prefer installing the packages using install.packages() 
inside R and update them using update.packages(). I feel that that is a better 
option for me.

HTH,

Best wishes,
Ranjan


On Tue, 20 Feb 2018 19:21:40 -0500 Matthew Miller <mat...@fedoraproject.org> 
wrote:

> On Tue, Feb 20, 2018 at 06:28:57PM -0500, Max Pyziur wrote:
> > Greetings,
> > I've been learning R on both Fedora and Ubuntu.
> > I've noticed that Ubuntu has considerably greater support for R than
> > Fedora (more R deb packages than R rpm packages).
> > Is there a rationale for this?
> 
> I'm not sure about R in specific, but generally the rationale is "no
> one did it". Are there particular packages that you're interested in?
> 
> -- 
> Matthew Miller
> <mat...@fedoraproject.org>
> Fedora Project Leader
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Re: R as on Ubuntu and Fedora

[George N. White III]

On 20 February 2018 at 19:28, Max Pyziur <p...@brama.com> wrote:

>
> Greetings,
>
> I've been learning R on both Fedora and Ubuntu.
>
> I've noticed that Ubuntu has considerably greater support for R than
> Fedora (more R deb packages than R rpm packages).
>
> Is there a rationale for this?
>

Counting the number of packages isn't worth the effort.  R is used by many
different communities, e.g., pharma, academia, etc.  Within these
communities, linux users tend to gravitate to the same platform and
packages used in that community will get attention on that platform.  Many
R packages use external libraries, so user communities will insist that
these libraries are packaged and usable.  Ubuntu is a very popular
distribution, so can be expected to have a wider range of user communities.
You may, however, find that key libraries and R packages for your subject
area are not current or have unreported bugs (because they are not heavily
used).

While you are learning R, any distro should provide basic packages.   If
your ultimate interest is in a specialized subject area, you need to look
at the packages and support libraries being used in that field and check
for packages of current versions.   For advanced R users, the biggest issue
is not R packages, but the presence of workable support libraries.  If you
suitable supporting libraries, it is generally very simple to install
current R packages from the sources on CRAN.

My work is in remote sensing and uses spatial statistics and images.  A
"mission critical" package from a national space agency was developed on
Ubuntu, so I use Ubuntu but have often had to build some supporting
libraries (gdal, hdf5, netcdf4) because the distro packages for these
libraries were outdated or built with stripped own options that make them
unusable for my work.  This situation has improved over time, but just when
I think the distro has caught up with my needs a new feature is introduced
and I end up having to build support libraries from sources all over
again.   Building support libraries often gets into nitty gritty
distro-specific details figuring out how to ensure that your R packages use
the locally compiled libraires without creating conflicts with the
distro-supplied versions of the packages.

-- 
George N. White III
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Re: R as on Ubuntu and Fedora

[Todd Zullinger]

Max Pyziur wrote:
> On Wed, 21 Feb 2018, Ed Greshko wrote:
>> On 02/21/18 07:28, Max Pyziur wrote:
>>> I've been learning R on both Fedora and Ubuntu.
>>>
>>> I've noticed that Ubuntu has considerably greater
>>> support for R than Fedora (more R deb packages than R
>>> rpm packages).
>>>
>>> Is there a rationale for this?

I'd presume that it's mostly that less folks have
contributed R-based packages to Fedora.  The only way to
change that is for more folks interested in R to maintain
packages in Fedora. :)

>> I don't use R or Ubuntu.  But I wonder if counting the number of packages is 
>> actually
>> reflective of the level of support.  Is there a one-to-one correspondence 
>> between deb
>> and rpm packages and the distributions?
>>
>> I count 140 rpm's (R-*) packages on Fedora.  This excludes the devel 
>> packages.  How
>> many more does Ubuntu have and what functionality do they provide that is 
>> missing
>> from Fedora?
>>
>> With that info, I would think one could write a BZ against R requesting the 
>> missing
>> pieces.  Probably would get a better, more definitive answer that way.

I'm not an R user either, so I could be wildly wrong here.
But I believe that most of the different packages are
extensions/modules/additional data files rather than than
missing pieces of the core R software.  Similar to CPAN for
Perl modules, R has CRAN for R packages.

(That's probably nothing new to either of you, but might be
useful to someone casually following this thread.)

There are 12,173 packages listed at
https://cloud.r-project.org/web/packages/available_packages_by_name.html

So I guess no distribution has much of it covered. ;)

> I count about 435 on Ubuntu.

To be fair, Ubuntu gets to build on top of the substantial
work of Debian.

For grins, I poked at the latest docker images from Debian,
Ubuntu, and Fedora and came up with these numbers:

# debian (docker.io/debian:latest)
$ apt-get update
$ apt-cache pkgnames | grep -ciw r
292

# ubuntu (docker.io/ubuntu:latest)
$ apt-get update
$ apt-cache pkgnames | grep -ciw r
365

# fedora (registry.fedoraproject.org/fedora:rawhide)
# (There are 42 '-devel' packages and 4 matches which are
# not R packages.)
$ dnf list available | grep -iw r | grep -cv -- -devel
167

# Non-R packages:
fonts-KOI8-R.noarch
fonts-KOI8-R-100dpi.noarch
fonts-KOI8-R-75dpi.noarch
perl-Tree-R.noarch

There's an R SIG for Fedora, which looks like it's been
quiet since October.  Perhaps some folks interested in R
packaging would be welcome there?

https://stat.ethz.ch/mailman/listinfo/r-sig-fedora

-- 
Todd
~~
Most of one's life is one prolonged effort to prevent oneself
thinking.
-- Aldous Huxley



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Re: [EXT] Re: R as on Ubuntu and Fedora

[Weiner, Michael]

On Wed, 21 Feb 2018, Max Pyziur wrote:

I count about 435 on Ubuntu.

fyi,

MP
--
Out of over 6000 packages available from CRAN alone, 435 is nothing. I dont 
believe the number of packages available from a distribution's repository is 
reflective of the level of support. R makes it extremely easy to install 
packages. Who needs all of CRAN to be available in a repository? It is simple 
enough to do a 'install.packages("BLAH"). What is important is R core and devel 
support, and to that point, both OSs are basically the same
===


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Re: R as on Ubuntu and Fedora

[Matthew Miller]

On Tue, Feb 20, 2018 at 06:28:57PM -0500, Max Pyziur wrote:
> Greetings,
> I've been learning R on both Fedora and Ubuntu.
> I've noticed that Ubuntu has considerably greater support for R than
> Fedora (more R deb packages than R rpm packages).
> Is there a rationale for this?

I'm not sure about R in specific, but generally the rationale is "no
one did it". Are there particular packages that you're interested in?

-- 
Matthew Miller
<mat...@fedoraproject.org>
Fedora Project Leader
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Re: R as on Ubuntu and Fedora

[Max Pyziur]

On Wed, 21 Feb 2018, Ed Greshko wrote:


On 02/21/18 07:28, Max Pyziur wrote:

I've been learning R on both Fedora and Ubuntu.

I've noticed that Ubuntu has considerably greater support for R than Fedora 
(more R
deb packages than R rpm packages).

Is there a rationale for this?



I don't use R or Ubuntu.  But I wonder if counting the number of packages is 
actually
reflective of the level of support.  Is there a one-to-one correspondence 
between deb
and rpm packages and the distributions?

I count 140 rpm's (R-*) packages on Fedora.  This excludes the devel packages.  
How
many more does Ubuntu have and what functionality do they provide that is 
missing
from Fedora?

With that info, I would think one could write a BZ against R requesting the 
missing
pieces.  Probably would get a better, more definitive answer that way.


I count about 435 on Ubuntu.

fyi,

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Re: R as on Ubuntu and Fedora

[Ed Greshko]

On 02/21/18 07:28, Max Pyziur wrote:
> I've been learning R on both Fedora and Ubuntu.
>
> I've noticed that Ubuntu has considerably greater support for R than Fedora 
> (more R
> deb packages than R rpm packages).
>
> Is there a rationale for this? 


I don't use R or Ubuntu.  But I wonder if counting the number of packages is 
actually
reflective of the level of support.  Is there a one-to-one correspondence 
between deb
and rpm packages and the distributions?

I count 140 rpm's (R-*) packages on Fedora.  This excludes the devel packages.  
How
many more does Ubuntu have and what functionality do they provide that is 
missing
from Fedora?

With that info, I would think one could write a BZ against R requesting the 
missing
pieces.  Probably would get a better, more definitive answer that way.

-- 
A motto of mine is: When in doubt, try it out



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R as on Ubuntu and Fedora

[Max Pyziur]

Greetings,

I've been learning R on both Fedora and Ubuntu.

I've noticed that Ubuntu has considerably greater support for R than 
Fedora (more R deb packages than R rpm packages).


Is there a rationale for this?

Much thanks,

Max Pyziur
p...@brama.com
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