Re: [R-sig-Debian] R-SIG-Debian Digest, Vol 152, Issue 4

2018-05-13 Thread Bill Harris 
On Sun, May 13, 2018 at 9:27 AM, Johannes Ranke 
wrote:

> Hi,
>
> I wonder if you have read the notes on R 3.5.0 on stretch on
>
> https://cran.r-project.org/bin/linux/debian/
>
> I think this should answer your questions. If not, please let us know.
>
>
Johannes,

I think I have--I think that's how I got the last line in my
sources.list--but I missed it this morning in my hurry.

Do I understand correctly that I should be able to replace the last line of
my sources.list (in my reply to Dirk) with

deb http:///bin/linux/debian stretch-cran35/


and then use

update.packages(lib.loc="/usr/local/lib/R/site-library", ask=FALSE,
checkBuilt=TRUE)


to update all my packages (all packages--or just those that use Rcpp?)?
That seems to suggest I /not/ let aptitude safe-upgrade touch anything in
R, right?  I'm guessing / hoping I can use that to update all my CRAN R
packages.  Do I need to do anything to keep any of the r-cran-... Debian
packages from updating?

Figuring out which packages used Rcpp and which didn't seems tedious; am I
right?

Thanks,

Bill

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Re: [R-sig-Debian] R-SIG-Debian Digest, Vol 152, Issue 4

2018-05-13 Thread Bill Harris 
On Sun, May 13, 2018 at 9:30 AM, Dirk Eddelbuettel <e...@debian.org> wrote:

>
> On 13 May 2018 at 09:03, Bill Harris wrote:
> |
> | safest way to go.  Does something like this make sense:
> |
> |
> |1. aptitude safe-upgrade should be safe: there won't be any 3.5.0
> Debian
> |packages coming through until the environment is ready for them to
> come
> |through (which most likely means that base R and other Stretch R
> packages
> |are upgraded to 3.5.0?)..
>
> Unsure.
>
> You did not specify if you look only at Debian distro repositories, or if
> you
> include the backports managed by Johannes (which should be safe he plays
> along with the r-api-3.5 tag).
>

Here is my complete sources.list:

#

# deb cdrom:[Official Debian GNU/Linux Live 9.1.0 gnome 2017-07-23T04:21]/
stretch main

#deb cdrom:[Official Debian GNU/Linux Live 9.1.0 gnome 2017-07-23T04:21]/
stretch main

deb http://ftp.us.debian.org/debian/ stretch main non-free contrib
deb-src http://ftp.us.debian.org/debian/ stretch main non-free contrib

deb http://security.debian.org/debian-security stretch/updates main contrib
non-free
deb-src http://security.debian.org/debian-security stretch/updates main
contrib non-free

# stretch-updates, previously known as 'volatile'
deb http://ftp.us.debian.org/debian/ stretch-updates main contrib non-free
deb-src http://ftp.us.debian.org/debian/ stretch-updates main contrib
non-free

## R https://cran.r-project.org/
## deb https://cran.cnr.berkeley.edu/bin/linux/debian stretch-cran34/
deb http://cran.wustl.edu/bin/linux/debian stretch-cran34/

I'll be glad to take advice.


>
> |2. update.packages() inside R is /not/ safe, because it could pick up
> |problematic packages from CRAN that aren't under your control.
>
> I actually take the opposite view.
>
> I am comfortable compiling from source, so this mode happens to be my
> default. I use the littler scripts install.r and update.r _all the time_ to
> install / update.
>
>
I think I reasoned through to that once, and then I forgot.  so
install.packages() and update.packages() is safe; aptitude  safe-upgrade
may or may not be safe, depending upon what you see in my sources-list.
Right?


> |3. install.packages() inside R is /not/ safe, for the same reason.
>
> That seems to be the same as 2. so ...
>
> |4. A prominent note will be posted here, when these two restrictions
> are
> |removed.
> |
> | Are those true statements?  Would steps 2 and 3 work if the packages
> don't
> | require compiled C++ code?  If so, is there a way to tell which packages
> | are at risk without memorizing what seems like a very long list?
> |
> | If we (think we) need a new package we don't currently have installed,
> are
> | we out of luck until 3.5.0 is officially released in Stretch?
>
> Again, "pure Debian" or "Debian plus CRAN repos" ?
>

In addition to what you see in my sources.list, I've also installed a few
packages from github or similat (hydromad comes to mind).  Perhaps the CRAN
package that might test all this the most is rstan.

I'm okay if a small number of github packages--or any packages, for that
matter--fail; I just would rather not do something that makes a /lot/ of
extra work if I could avoid it.

>
> | Is there a place where an official summary of the state of the R system
> on
> | Stretch is maintained?
> |
> | I've tried to scan this list, but I may well have missed the answers to
> my
> | questions about Stretch.
>
> We're volunteers so something may always fall short somewhere.
> Documentation
> is always a good candidate.  Contributions are always welcome.
>
> I'll keep that in mind.
>

Thanks,

Bill

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Re: [R-sig-Debian] R-SIG-Debian Digest, Vol 152, Issue 4

2018-05-13 Thread Bill Harris 
>
> Date: Sat, 5 May 2018 18:02:12 -0500
> From: Dirk Eddelbuettel 
> To: Matthieu S 
> Cc: r-sig-debian@r-project.org
> Subject: Re: [R-sig-Debian] Ubuntu 18.04 bionic: availability of R
> Ubuntu packages/ppa?
> Message-ID: <23278.14324.913149.453...@rob.eddelbuettel.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Thanks, we try. Not too much infrastructure that we have built so these
> transitions can be slow.  On my side, Debian has one schedules but not yet
> started.


Dirk, all,

I can't say enough about my appreciation of the work you folks do in
keeping R going so well on Debian.

In these interesting times, I think you're saying that things will resolve
themselves at some point, but we're in a transition.  I see a number of
postings on Ubuntu, but I'm on Debian Stretch, trying to figure out the
safest way to go.  Does something like this make sense:


   1. aptitude safe-upgrade should be safe: there won't be any 3.5.0 Debian
   packages coming through until the environment is ready for them to come
   through (which most likely means that base R and other Stretch R packages
   are upgraded to 3.5.0?)..
   2. update.packages() inside R is /not/ safe, because it could pick up
   problematic packages from CRAN that aren't under your control.
   3. install.packages() inside R is /not/ safe, for the same reason.
   4. A prominent note will be posted here, when these two restrictions are
   removed.

Are those true statements?  Would steps 2 and 3 work if the packages don't
require compiled C++ code?  If so, is there a way to tell which packages
are at risk without memorizing what seems like a very long list?

If we (think we) need a new package we don't currently have installed, are
we out of luck until 3.5.0 is officially released in Stretch?

Is there a place where an official summary of the state of the R system on
Stretch is maintained?

I've tried to scan this list, but I may well have missed the answers to my
questions about Stretch.

Thank you,

Bill

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Re: [R-sig-Debian] Debian backport on Stretch?

2017-11-18 Thread Bill Harris 
Incidentally, you can see a bit more complete description at
https://unix.stackexchange.com/questions/402560/how-do-i-install-r-on-debian-stretch-given-the-r-api-3-issue
.

On Sat, Nov 18, 2017 at 3:17 PM, Bill Harris <
bill_har...@facilitatedsystems.com> wrote:

> I got a new laptop in September and installed Stretch (I had been using
> Jessie), and I tried to follow the instructions on
> https://cran.r-project.org/bin/linux/debian/, as I had multiple times in
> the past: I added
>
> deb http://cran.wustl.edu/bin/linux/debian stretch-cran34/
>
> to the end of sources.list, I followed the rest of the above directions as
> of early September, as best I recall, and I only got a partial
> installation.  3.4.2 is installed, but I'm limited in what packages I can
> load using aptitude (I haven't tried install.packages()).  From my reading,
> this has to do with r-api-3 problems. If my problem isn't obvious, I'll be
> glad to provide more details.
>
> My question is there a successful and not too difficult way to install
> 3.4.2, or is deleting this R, deleting the wustl.edu backport entry, and
> reinstalling R and its packages  from the standard Stretch repo the best
> approach at this time?
>
> If I should go back to the standard Stretch install, does that mean I need
> to be especially cautious about installing packages with install.packages()
> inside R, because that would get me a package that depended on r-api-34?  I
> use a few packages like rstan, rstanarm, and brms that I don't see when I
> do aptitude search, and I'm not sure what that means I should do.
>
> Thanks,
>
> Bill
>
>

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Re: [R-sig-Debian] Upgrading 2.15.3 to 3.0.x on Debian Squeeze?

2013-12-13 Thread Bill Harris 
Johannes Ranke jra...@uni-bremen.de writes:

 - http://cran.us.r-project.org/bin/linux/debian/ says I should run
   `dpkg -get-selections | grep r-cran` and compare with the list of
   packages supported below.  I've done that, but I don't know what to
   do with that knowledge: do I `aptitude remove` all of those packages
   /not/ listed below or do something else?

 Well these are the packages that will not work after the upgrade to R
 3.0.x. You can leave them on your system, but I would recommend to
 remove them and install them from within R using install.packages() 
 after the upgrade. But just to be clear: you do not need to remove those
 that are in the list of supported packages in the README as these will
 be upgraded together with base R.

I used synaptic to tell me which Debian packages came from r-cran, and I
tried deleting them in synaptic.  I did not delete those that also
wanted to delete r-base, but I forgot to pay attention to the list of
packages that are available in the Debian cran3 archive.  

Then I updated the sources list and did a safe-upgrade.  I think that
process may have left most or all of the packages in place that the
safe-upgrade could fix, but it won't seem to matter.

 - http://www.r-bloggers.com/upgrading-r-and-packages/ suggests a script
   that updates installed packages.  I've used that on minor upgrades on
   XP successfully.  I don't see documentation that suggests it's needed
   for major upgrades or perhaps on Linux.

 I do not think that this is helpful, unless the number of R packages
 installed stemming from Debian squeeze is large.

Are the instructions the same for Windows?

 Is this a fairly foolproof upgrade?  Minor upgrades have certainly
 seemed simple on both Linux and Windows.

 I have upgraded painlessly using this approach, but it would be nice to 
 hear about your experiences.

It seems to have worked well.  I wonder if you could also say Delete
any packages using synaptic or aptitude /except/ for those which want to
delete r-base, as well?

Bill
-- 
Bill Harris  
Facilitated Systems
http://makingsense.facilitatedsystems.com/

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Re: [R-sig-Debian] Upgrading 2.15.3 to 3.0.x on Debian Squeeze?

2013-12-09 Thread Bill Harris 
Johannes Ranke jra...@uni-bremen.de writes:

 On Mon, Dec 09, 2013 at 09:27:11PM -0800, Bill Harris wrote:
 I'm running Debian Squeeze on an amd64 machine and currently have R
 2.15.3.  Some packages have been installed with aptitude and some with
 install.packages().  Now I'd like to update R to 3.0.2 (I upgraded arm
 to a version that requires 3.0 :-( ), and I'm a confused.

 The only critical point is that R packages that belong to Debian squeeze
 will not work with the new R. So the question is wether you rely on any
 such packages.

Yes, for better or worse.  I once thought Dirk recommended that; I now
see that he seems more ambivalent than I recall.

 - http://cran.us.r-project.org/bin/linux/debian/ seems to say I just
   change the sources list to point to '...cran3' instead of to '...cran'
   and then update / upgrade.  Yet

 Correct.

Great.  That's easy enough.

 - http://cran.us.r-project.org/bin/linux/debian/ says I should run
   `dpkg -get-selections | grep r-cran` and compare with the list of
   packages supported below.  I've done that, but I don't know what to
   do with that knowledge: do I `aptitude remove` all of those packages
   /not/ listed below or do something else?

 Well these are the packages that will not work after the upgrade to R
 3.0.x. You can leave them on your system, but I would recommend to
 remove them and install them from within R using install.packages() 
 after the upgrade. But just to be clear: you do not need to remove those
 that are in the list of supported packages in the README as these will
 be upgraded together with base R.

`dpkg -get-selections | grep r-cran | wc -l` shows 100 such packages,
but synaptic shows 25 packages installed from squeeze-cran/main.  So I
have 25 packages to remove (easy) and 100 to reinstall later (a bit more
of a chore :-) ).

 - http://www.r-bloggers.com/upgrading-r-and-packages/ suggests a script
   that updates installed packages.  I've used that on minor upgrades on
   XP successfully.  I don't see documentation that suggests it's needed
   for major upgrades or perhaps on Linux.

 I do not think that this is helpful, unless the number of R packages
 installed stemming from Debian squeeze is large.
 
I'm going to ignore it.

   http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
   seems to suggest that running `update.packages(checkBuilt=TRUE)` is
   sufficient (except perhaps for what aptitude has to do).  What is the
   right thing to do?

 Yes, this should be enough, except for the packages from Debian squeeze
 mentioned above, that need special care.

Again, easy enough.

 If the answers to those three questions aren't simple, are there
 explicit, step-by-step instructions somewhere?  I've looked
 unsuccessfully.

 Feel free to make suggestions to improve the Debian README on CRAN. I
 tried to make it as clear as possible, but needless to say it could be
 improved.

The two things I didn't understand were

- what to do when I identified packages that were installed in Debian (I
  guessed right, but I didn't have the guts to try it and see)

- what to do when I read seemingly contradictory instructions, even if
  they were potentially for different platforms

You helped. 

 I have upgraded painlessly using this approach, but it would be nice to 
 hear about your experiences.

I'll check back in.

Vielen Dank!

Bill
-- 
Bill Harris  
Facilitated Systems
http://makingsense.facilitatedsystems.com/

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