R devel - Jan 2020 - as-cran issue ==> set _R_CHECK_LENGTH_1_* settings!

>>>>> Avraham Adler 
>>>>>     on Mon, 13 Jan 2020 14:38:12 -0500 writes:
    > Those of us stuck on Windows but who attempt to develop properly are
    > wounded to the quick, sir!

    > :)

    > Avi

Indeed, you had a ' :) ' , but others have perceived this as an insult.
I'm really really sorry for that and do want to apologize to all
of you affected.

Indeed, on one hand, not everybody has a choice, and even then,
I'm (and 100s of 1000s of others) are very grateful to those
among you who develop and test R (and other free software, say,
Emacs, or Rstudio) on Windows. 

I do want to entice people to have a long look beyond closed
source OS into the world of Free Software where not only R is
FOSS (Free and Open Source Software) but (all / almost) all the
tools you use are of that same spirit.

Best,
Martin



    > On Mon, Jan 13, 2020 at 12:24 PM Martin Maechler <maechler at
stat.math.ethz.ch>
    > wrote:

    >> >>>>> Ben Bolker
    >> >>>>>     on Mon, 13 Jan 2020 11:49:09 -0500 writes:
    >> 
    >> > From R NEWS (changes in 3.6.0)
    >> > Experimentally, setting environment variable
    >> _R_CHECK_LENGTH_1_LOGIC2_
    >> > will lead to warnings (or errors if the variable is set to a
?true?
    >> > value) when && or || encounter and use arguments of
length more than
    >> one.
    >> 
    >> Indeed,  thank you, Ben.
    >> 
    >> Note (Dirk) this is not just something
    >> "by Henrik (..) as he tried to convince us all to use it
more"
    >> 
    >> I've activated this (and the other
    >> _R_CHECK_LENGTH_1_CONDITION_ ! )
    >> for years (maybe not many years, it just feels like it), and *EVERY
TIME*
    >> it triggers, it's been revealing a programmeR's thinko /
bug / ..,
    >> something where the code was clearly suboptimal and should've
been
    >> improved.
    >> (Unfortunately, the bug has often been in packages, and sometimes I
had to
    >> disable the setting when I wanted that "buggy" package to
work ..)
    >> 
    >> Occasionally being puristic, let me state this:
    >> __________________________________________________________________
    >>
/------------------------------------------------------------------\
    >> |                                                                 
|
    >> | Every careful R programmer should use (something like
"true",    |
    >> | "verbose", or even package=... )                       
|
    >> |                                                                 
|
    >> | export _R_CHECK_LENGTH_1_CONDITION_=true                        
|
    >> | export _R_CHECK_LENGTH_1_LOGIC2_=verbose                        
|
    >> |                                                                 
|
    >> | in her/his ~/.profile equivalent (*)                            
|
    >>
\__________________________________________________________________/
    >> 
    >> 
    >> *) well assuming a careful R programmer would never develop on
    >> Windows anyway (where you need different means to set such
    >> environment variables).
    >> 
    >> 
    >> 
    >> > On 2020-01-13 11:46 a.m., Therneau, Terry M., Ph.D. via
R-devel
    >> wrote:
    >> >> Thanks for the feedback Dirk.   I sent my follow-up before
I saw it.
    >> >>
    >> >> Looking at the source code, it appears that there is no
options()
    >> call
    >> >> to turn this on. Nor does "R --help" reveal a
command line option.
    >> >> How then does a user turn this on outside of the R CMD
check
    >> >> envirionment, so as to chase things like this down?
    >> >>
    >> >> The fact that 1. renaming my function makes the error go
away, 2. my
    >> >> function is just a wrapper to inherits(), and 3. its a new
error in
    >> code
    >> >> that hasn't changed, all point me towards some oddity
with the check
    >> >> function.
    >> >>
    >> >> Terry
    >> >>
    >> >>
    >> >> On 1/13/20 10:22 AM, Dirk Eddelbuettel wrote:
    >> >>>
    >> >>> On 13 January 2020 at 10:02, Therneau, Terry M., Ph.D.
via R-devel
    >> wrote:
    >> >>> | Where can I find out (and replicate) what options
as-cran turns
    >> on?
    >> >>>
    >> >>> See the file src/library/tools/R/check.R in the R
sources, and
    >> grep for
    >> >>> as_cran which is the internal variable controlled by
the --as-cran
    >> option
    >> >>>
    >> >>> [...]
    >> >>>
    >> >>> | The check log contains multiple instances of the
lines below:
    >> >>> |
    >> >>> | < Warning message:
    >> >>> | < In if (ismat(kmat)) { :
    >> >>> | <   the condition has length > 1 and only the
first element will
    >> be
    >> >>> used
    >> >>> |
    >> >>> | I don't see how the error could arise, but if I
know what
    >> as-cran is
    >> >>> doing perhaps I can
    >> >>> | replicate it.
    >> >>>
    >> >>> This was widely discussed on this list and should also
be in the
    >> NEWS
    >> >>> file.
    >> >>>
    >> >>> The change is about what the message says: the if ()
tests a scalar
    >> >>> logical,
    >> >>> it appears that ismat(kmat) returns more than a
scalar.
    >> >>>
    >> >>> There has always been an opt-in for this to error --
cf many
    >> messages
    >> >>> by Henrik
    >> >>> over the years as he tried to convince us all to use
it more.
    >> >>>
    >> >>>
    >> >>> Dirk
    >> >>>
    >> >>
    >> >> ______________________________________________
    >> >> R-devel at r-project.org mailing list
    >> >> https://stat.ethz.ch/mailman/listinfo/r-devel
    >> 
    >> > ______________________________________________
    >> > R-devel at r-project.org mailing list
    >> > https://stat.ethz.ch/mailman/listinfo/r-devel
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel
    >> 
    > -- 
    > Sent from Gmail Mobile

    > [[alternative HTML version deleted]]

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

> I do want to entice people to have a long look beyond closed
> source OS into the world of Free Software where not only R is
> FOSS (Free and Open Source Software) but (all / almost) all the
> tools you use are of that same spirit.
And while everyone is talking about operating systems...

Recently, I tried to install R on Fedora.
However, it only gave me the option of downloading and installing R
3.6.1, when the current release is/was R 3.6.2.
I decided to wait, and may try again later, over the next week.

Is it possible for things to be free *and* simple?

On 15 January 2020 at 09:29, Abby Spurdle wrote:
| Recently, I tried to install R on Fedora.
| However, it only gave me the option of downloading and installing R
| 3.6.1, when the current release is/was R 3.6.2.
| I decided to wait, and may try again later, over the next week.
| 
| Is it possible for things to be free *and* simple?

Sure.

Look at the Dockerfile (== "recipe", like shell) for the r-base
container.

  https://github.com/rocker-org/rocker/blob/master/r-base/Dockerfile

Starts from vanilla Debian testing, and installs R. Takes no time, is fully
automated and has been running that way for years.  You can build up from
there, my blog has examples, as have many many other sites by other people.


One other recent-ish example is the r-apt Rocker image. Sets the repo for
current R (based on builds that Michael Rutter looks after based on my
official Debian package), then adds info for the PPAs Michael looks after and
you got over 4,000 CRAN packages ready to install as binaries -- just like
that.  The link is for 'disco' aka 19.04, we have the others too (but I
need
to add 19.10 now).

  https://github.com/rocker-org/rocker/blob/master/r-apt/disco/Dockerfile

Both meet free *and* simple. And you don't have to build either. Just
'docker
pull'. There is more at the Rocker Project for you.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

> On Jan 14, 2020, at 3:29 PM, Abby Spurdle <spurdle.a at gmail.com>
wrote:
> 
>> I do want to entice people to have a long look beyond closed
>> source OS into the world of Free Software where not only R is
>> FOSS (Free and Open Source Software) but (all / almost) all the
>> tools you use are of that same spirit.
> 
> And while everyone is talking about operating systems...
> 
> Recently, I tried to install R on Fedora.
> However, it only gave me the option of downloading and installing R
> 3.6.1, when the current release is/was R 3.6.2.
> I decided to wait, and may try again later, over the next week.
> 
> Is it possible for things to be free *and* simple?
Abby,

Which version of Fedora are you on?

The Fedora RPM build system for R:

  https://koji.fedoraproject.org/koji/packageinfo?packageID=1230

would seem to suggest that R 3.6.2 may not be available for Fedora 29 or
earlier, which is not a surprise, given the rapid update cycle used on Fedora.

R 3.6.2 is available for Fedora 30, 31 and 32 per the above page.

If you are on Fedora >=30, you might check your yum repo to see if it has
been properly updated.

Otherwise, if you are on Fedora <=29, you should think about updating your
Fedora installation.

You may or may not be aware that there is a dedicated list for R on Fedora/RHEL
and derivatives:

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

Tom Callaway, who is the RH/Fedora maintainer for R is on that list, so you can
pose queries to him via that list for any issues with R on Fedora.

Regards,

Marc Schwartz

> I do want to entice people to have a long look beyond closed
> source OS into the world of Free Software where not only R is
> FOSS (Free and Open Source Software) but (all / almost) all the
> tools you use are of that same spirit.
>
> Best,
> Martin
I've reconsidered.
You're 100% correct.

I'm planning to try ReactOS.
(Hope it works...)

Thanks Martin, great advice...

>>>>> Abby Spurdle 
>>>>>     on Tue, 21 Jan 2020 09:15:39 +1300 writes:
    >> I do want to entice people to have a long look beyond closed
    >> source OS into the world of Free Software where not only R is
    >> FOSS (Free and Open Source Software) but (all / almost) all the
    >> tools you use are of that same spirit.
    >> 
    >> Best,
    >> Martin

    > I've reconsidered.
    > You're 100% correct.

Thank you.

    > I'm planning to try ReactOS.
    > (Hope it works...)

    > Thanks Martin, great advice...

Well, to choose ReactOS ()
instead of a version of Linux (there
have some Linux distributions that have aimed for being close to
Windows in their "look and feel") is  much braver and more
risky, but then, your learning experience, including possibly being the
first one to run R there (?) ((possibly even learning how to
*build* R there from the sources ??)),  will feel more
frontier-like and self determined than just following the Linux
crowd ;-) ;-) :-)

Martin