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

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forthwith withdrawn from texlive-collection-mathscience, because of its 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

Hello! I'm confused as to what the actual problem with includeRnw is? Is the
problem

that it relies on R-knitr? Before it would be withdrawn, may I be given an
opportunity

to fix said problem?


includeRnw only invokes the already existing R installation, and should not
affect

any other global settings or affect the installation in any way. If this is the
case,

it's a bug and I'd like more details so I could fix said bug.


I agree that for larger projects using includeRnw easily would be redundant as

R is invoked on a per-file basis and not by it's own including syntax.
However,

one might like files properly separated and executed individually. I myself

find it a fairly nice workflow for many of my projects.

________________________________
From: Roger Bivand <Roger.Bivand at nhh.no>
Sent: Saturday, November 10, 2018 6:35:05 PM
To: I?aki Ucar
Cc: r-sig-fedora at r-project.org; Andreas Storvik Strauman
Subject: Re: [R-sig-Fedora] Fedora 29 upgrade: texlive-scheme-medium may depend
on R (texlive-includernw)

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

	[[alternative HTML version deleted]]

On Sat, 10 Nov 2018, Andreas Storvik Strauman wrote:
> Hello! I'm confused as to what the actual problem with includeRnw is?
Is
> the problem that it relies on R-knitr? Before it would be withdrawn, may 
> I be given an opportunity to fix said problem?
Yes, the problem is that it expesses an external dependence on anything 
outside texlive. On packaging systems (for me Fedora), this explicitly 
pulls in all of R and all R-knitr's other package dependencies. If an 
existing R installation is not found by the package manager, the user gets 
an unnecessary install of R which will mask the existing and intended R 
installation, with different package libraries, etc.
>
> includeRnw only invokes the already existing R installation, and should 
> not affect any other global settings or affect the installation in any 
> way. If this is the case, it's a bug and I'd like more details so I
> could fix said bug.
My point exactly. It should only run R RHOME to check for the existence of 
R (if this is what it does) at run time, not at install time. If it then, 
at run time, does not find R, or having found R does not find knitr 
(though Sweave is part of utils, so knitr is only needed by those using 
knitr to weave Rnw documents, or to convert from Rmd), it should issue 
helpful error messages to tell the user to install R, or to install knitr 
within R. By requiring to see R when being run by root/admin at install 
time, it is making invasive assumptions about the user environment.

It could be that the texlive-includernw package itself does not require 
install time dependency fulfillment, and that this is something only the 
Fedora texlive packager has mis-understood.
>
> I agree that for larger projects using includeRnw easily would be 
> redundant as R is invoked on a per-file basis and not by it's own 
> including syntax. However, one might like files properly separated and 
> executed individually. I myself find it a fairly nice workflow for many 
> of my projects.
R is a pretty large install just for one texlive package.

Roger
>
> ________________________________
> From: Roger Bivand <Roger.Bivand at nhh.no>
> Sent: Saturday, November 10, 2018 6:35:05 PM
> To: I?aki Ucar
> Cc: r-sig-fedora at r-project.org; Andreas Storvik Strauman
> Subject: Re: [R-sig-Fedora] Fedora 29 upgrade: texlive-scheme-medium may
depend on R (texlive-includernw)
>
> 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
>
-- 
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