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 Before it would be withdrawn, may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 <[email protected]>
Sent: Saturday, November 10, 2018 6:35:05 PM
To: Iñaki Ucar
Cc: [email protected]; 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, Iñaki Ucar wrote:
On Sat, 10 Nov 2018 at 15:17, Roger Bivand <[email protected]> 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
Iñaki
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: [email protected]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [email protected]
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: [email protected]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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