R SIG Fedora - Nov 2018 - Fedora 29 upgrade: texlive-scheme-medium may depend on R

On upgrading my F28 to F29, I've found that R-core and a number of R 
packages:

R-evaluate R-glue R-highr R-knitr R-magrittr R-markdown R-mime R-stringi 
R-stringr R-yaml

are installed, although I only ever install R from source and always keep 
my Rs locally. So I don't use Fedora R rpms, but these were installed 
without my command.

Something in texlive is doing this. A remedy is to yse rpm -r --nodeps <> 
to get rid of them, because dnf remove R-core takes out texlive too. I do 
use the RStudio rpm, but by command-line install, so it isn't the culprit. 
However, the choice of packages points to an injudicious editing of an rpm 
dependency list in some texlive package related to rmarkdown or similar.

I'm reporting this here in case other Fedora users are puzzled to see 
another R (or an rpm R) appearing on their systems if they also use 
texlive.

If anyone has any ideas about resolving this properly, I'd be grateful (it 
isn't the best way to spread the use of R among Fedora texlive users IMO). 
Unfortunately, DNF/RPM and likely other packaging systems have issues 
detecting user-installed programs like R, so trying "R RHOME"
isn't going
to work when say ~/bin is where R lives. Almost certainly, the texlive 
component should not be included in any scheme groups.

I would CC RStudio, but support does not expose an email, so I'm CC-ing 
the rmarkown maintainer.

Roger

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

On Sat, 10 Nov 2018 at 15:17, Roger Bivand <Roger.Bivand at nhh.no>
wrote:
>
> On upgrading my F28 to F29, I've found that R-core and a number of R
> packages:
>
> R-evaluate R-glue R-highr R-knitr R-magrittr R-markdown R-mime R-stringi
> R-stringr R-yaml
>
> are installed, although I only ever install R from source and always keep
> my Rs locally. So I don't use Fedora R rpms, but these were installed
> without my command.
>
> Something in texlive is doing this. A remedy is to yse rpm -r --nodeps
<>
> to get rid of them, because dnf remove R-core takes out texlive too. I do
> use the RStudio rpm, but by command-line install, so it isn't the
culprit.
> However, the choice of packages points to an injudicious editing of an rpm
> dependency list in some texlive package related to rmarkdown or similar.
$ dnf repoquery --tree --whatrequires R-knitr

texlive-scheme-medium installs texlive-collection-mathscience, which
installs texlive-includernw, which necessarily depends on R-knitr.

The solution is not to depend on texlive collections. Install
texlive-scheme-basic instead, plus additional packages as you need
them.

I?aki
> I'm reporting this here in case other Fedora users are puzzled to see
> another R (or an rpm R) appearing on their systems if they also use
> texlive.
>
> If anyone has any ideas about resolving this properly, I'd be grateful
(it
> isn't the best way to spread the use of R among Fedora texlive users
IMO).
> Unfortunately, DNF/RPM and likely other packaging systems have issues
> detecting user-installed programs like R, so trying "R RHOME"
isn't going
> to work when say ~/bin is where R lives. Almost certainly, the texlive
> component should not be included in any scheme groups.
>
> I would CC RStudio, but support does not expose an email, so I'm CC-ing
> the rmarkown maintainer.
>
> Roger
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
> http://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>
> _______________________________________________
> R-SIG-Fedora mailing list
> R-SIG-Fedora at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora


-- 
I?aki ?car

On Sat, 10 Nov 2018, I?aki Ucar wrote:
> On Sat, 10 Nov 2018 at 15:17, Roger Bivand <Roger.Bivand at nhh.no>
wrote:
>>
>> On upgrading my F28 to F29, I've found that R-core and a number of
R
>> packages:
>>
>> R-evaluate R-glue R-highr R-knitr R-magrittr R-markdown R-mime
R-stringi
>> R-stringr R-yaml
>>
>> are installed, although I only ever install R from source and always
keep
>> my Rs locally. So I don't use Fedora R rpms, but these were
installed
>> without my command.
>>
>> Something in texlive is doing this. A remedy is to yse rpm -r --nodeps
<>
>> to get rid of them, because dnf remove R-core takes out texlive too. I
do
>> use the RStudio rpm, but by command-line install, so it isn't the
culprit.
>> However, the choice of packages points to an injudicious editing of an
rpm
>> dependency list in some texlive package related to rmarkdown or
similar.
>
> $ dnf repoquery --tree --whatrequires R-knitr
>
> texlive-scheme-medium installs texlive-collection-mathscience, which
> installs texlive-includernw, which necessarily depends on R-knitr.
Thanks for the analysis. I do not see that any other latex package in 
texlive-sceme-medium involves creating such havoc drawing in non-texlive 
packages.

I appeal to Andreas Storvik Strauman to ensure that texlive-includernw is 
forthwith withdrawn from texlive-collection-mathscience, because of its 
side-effects.

It may be useful, but actually Rnw files would only need R anyway, and 
bringinging such a payload is really very bad for everybody not exposed to 
this behaviour previously. I wasted a lot of time trying to see why Rcpp 
could not find R.h in a previously totally dependable workflow.
>
> The solution is not to depend on texlive collections. Install
> texlive-scheme-basic instead, plus additional packages as you need
> them.
Not an option. Installing texlive-scheme-* should not have non-texlive 
side effects.

Roger
>
> I?aki
>
>> I'm reporting this here in case other Fedora users are puzzled to
see
>> another R (or an rpm R) appearing on their systems if they also use
>> texlive.
>>
>> If anyone has any ideas about resolving this properly, I'd be
grateful (it
>> isn't the best way to spread the use of R among Fedora texlive
users IMO).
>> Unfortunately, DNF/RPM and likely other packaging systems have issues
>> detecting user-installed programs like R, so trying "R RHOME"
isn't going
>> to work when say ~/bin is where R lives. Almost certainly, the texlive
>> component should not be included in any scheme groups.
>>
>> I would CC RStudio, but support does not expose an email, so I'm
CC-ing
>> the rmarkown maintainer.
>>
>> Roger
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>> _______________________________________________
>> R-SIG-Fedora mailing list
>> R-SIG-Fedora at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>
>
>
>
-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en