Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
Chris Evans writes: Just one thing that may chime with the ongoing discussion that my post seems to have seeded: I wouldn't know how to handle "You'll need new versions of poly-R (updated 29 September 2021) and markdown-mode (updated 6 January 2021)" and I never got my head around what melpa is. The end of that section includes the line: "As in previous tutorials, we can install all three of these packages from [MELPA](https://melpa.org/#/)." The previous tutorial is available on my blog: https://plantarum.ca/2020/12/30/emacs-tutorial-03/ And on youtube: https://www.youtube.com/watch?v=So1LYzSk9o0 I've updated the post to point directly to these locations. You'll find explicit instructions on how to install packages from Melpa at either location. Best, Tyler __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
This looks really helpful Tyler: many thanks. I'm buried in a bunch of non-work stresses and the usual work overload and I got the answer to what I was doing wrong with knitr/Rstudio in terms of the block cacheing. I'd love to have ESS as a fallback in the future but I can see I'm not going to get to this in the near future. Just one thing that may chime with the ongoing discussion that my post seems to have seeded: I wouldn't know how to handle "You'll need new versions of poly-R (updated 29 September 2021) and markdown-mode (updated 6 January 2021)" and I never got my head around what melpa is. Of course, that's an indictment of my choices and particularly my time management choices but perhaps I represent a large group of users or potential users (or ex-users?) of ESS: there was a point at which I simply didn't make the time to keep up with these things. It happened to coincide with my discovering Rstudio and Rmarkdown (yes, I know that was coincidence that it happened around the same time, but I didn't really see the appeal of Rstudio until I discovered Rmarkdown) and I just slid from using ESS for most of my R work to using Emacs for most of my server text file work but hardly using ESS at all. Having tried, admittedly without allocating much time to it, to follow the discussion here, I think there are three some for me: 1) when I started with Emacs and ESS (20 years ago?) I was younger and had more time to learn things (oh to wind back time!!!, but perhaps this means ESS will still get many new users, just that they'll be young!) 2) there was a big book for Emacs and ESS was a pretty simple bold onto Emacs so there wasn't much else I needed to learn for ESS 3) despite the fact that I never learned any pertinent lisp it just worked and when I needed to install it on Windoze I could just pull Vincent Goulet's package of everything I needed and that just worked too! 4) I think Rmarkdown is brilliant but it's complicated particularly if you have to cache it (and I do have to) and it's clearly a challenge to support 5) so you (ESS genii) are where you are, still doing miracles unpaid and I'm both incredibly grateful and in awe but I've dropped off the learning curve. I don't know if this any help at all but it's mostly appreciation of your help Tyler and of everything so many people do for ESS (and FLOSS generally) and an apology for not doing more! Very best, Chris - Original Message - > From: "Tyler Smith" > To: "Chris Evans" > Cc: "ess-help" > Sent: Friday, 1 October, 2021 16:40:50 > Subject: Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files > Hello Chris, > > Here is the Rmd tutorial I've been working on: > https://github.com/ess-intro/presentation-rmarkdown/blob/master/presentation-rmarkdown.Rmd > > I've just updated it to incorporate some simplifications in > configuration that I've been working on with the Polymode > developer Vitalie Spinu. You'll need new versions of poly-R > (updated 29 September 2021) and markdown-mode (updated 6 January > 2021) to use this as-is. With those completed, there's no further > reason to procrastinate on turning this into a video, so I guess > that's coming soon now too! > > Best, > > Tyler > > Chris Evans via ESS-help writes: > >> I am having problems with long Rmd files (and large data, long >> processing times) in Rstudio. (Sorry, yes, I use Emacs for >> things and >> ESS when I'm working with R (but rarely Rmd files) on a server, >> but I use Rstudio routinely "at home".) This has made me decide >> it's >> >> http://johnstantongeddes.org/open%20science/2014/03/26/Rmd-polymode.html >> >> looked pretty straightforward but I thought I should ask here if >> any changes since 2014 might make that too historical, perhaps >> not >> as I couldn't find much that was recent on the topic of ESS and >> Rmd. However, before I mess with an Emacs/ESS that works just >> fine >> currently, I thought I'd ask here. >> >> I'm running on Ubuntu 20.04 "at home" and Debian (4.19.152-1 >> (2020-10-18) in case it matters) on the server (and might as >> well >> set things up on both if it's easy). >> >> Any advice will be gratefully received (and, who knows, might >> even tempt me back to Emacs/ESS for much more of what I'm >> doing!) >> >> TIA, >> >> Chris > > -- > Tyler Smith > plantarum.ca -- Chris Evans (he/him) Visiting Professor, University of Sheffield and UDLA, Quito, Ecuador I do some consultation work for the University of Roehampton and other places but remains my main Email address. I have a work web site at: https://www.psyctc.org/psyctc/ and a site I manage for CORE and CORE system trust at: http://www.coresystemtrust.org.uk/ I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/ If you want an Emeeting, I am trying to keep
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
Hello Chris, Here is the Rmd tutorial I've been working on: https://github.com/ess-intro/presentation-rmarkdown/blob/master/presentation-rmarkdown.Rmd I've just updated it to incorporate some simplifications in configuration that I've been working on with the Polymode developer Vitalie Spinu. You'll need new versions of poly-R (updated 29 September 2021) and markdown-mode (updated 6 January 2021) to use this as-is. With those completed, there's no further reason to procrastinate on turning this into a video, so I guess that's coming soon now too! Best, Tyler Chris Evans via ESS-help writes: I am having problems with long Rmd files (and large data, long processing times) in Rstudio. (Sorry, yes, I use Emacs for things and ESS when I'm working with R (but rarely Rmd files) on a server, but I use Rstudio routinely "at home".) This has made me decide it's http://johnstantongeddes.org/open%20science/2014/03/26/Rmd-polymode.html looked pretty straightforward but I thought I should ask here if any changes since 2014 might make that too historical, perhaps not as I couldn't find much that was recent on the topic of ESS and Rmd. However, before I mess with an Emacs/ESS that works just fine currently, I thought I'd ask here. I'm running on Ubuntu 20.04 "at home" and Debian (4.19.152-1 (2020-10-18) in case it matters) on the server (and might as well set things up on both if it's easy). Any advice will be gratefully received (and, who knows, might even tempt me back to Emacs/ESS for much more of what I'm doing!) TIA, Chris -- Tyler Smith plantarum.ca __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
Are the bugs something that could be helped if there was small funding for a student internship? If potentially useful, any of the ESS developers can contact me directly. On Thu, Sep 23, 2021 at 3:53 AM Martin Maechler via ESS-help < ess-help@r-project.org> wrote: > > Lionel Henry via ESS-help > > on Wed, 22 Sep 2021 15:15:42 +0200 writes: > > > We'd love to do a release but ESS is not in a good place > > right now. > > Definitely. The reason is that there have been too many bugs > introduced with the new features, so we could/should not > release. > > This has been the real reason for not releasing formally. > > In addition, another important goal for the release has been to > create an ESS+ "package" (not mainly an ELPA package, but also a > traditional tarball / zip file) which will contain > ESS plus relevant parts of polymode even though the latter is > only maintained by one of us; the use of both *and* correct > interplay between polymode and ESS is really crucial for parts > modern R using ESS, notably as we had decided to declare the ess > noweb-mode (for editing *.Rnw, i.e., Sweave & (tex-based) knitr) > as obsolete. > > > Recent versions of Emacs interrupt background > > commands (essential to completion and contextual help like > > eldoc) when the user starts typing, which causes hard to > > solve problems. > > > The dev branch is mostly working but not 100% > > correctly. Unfortunately none of us seem to have the time > > to work on ESS at the moment. > > > That said, while Martin, Vitalie and I notice issues here > > and there, we haven't had serious bug reports in a while, > > despite the dev branch being used by many Melpa users. So > > maybe releasing in the current state is better than nothing. > > Well... > It would be the first ESS release with serious (for some / in > some use case situaitons) known bugs .. > > > Best, Lionel > > > > On 9/22/21, Dirk Eddelbuettel via ESS-help > > wrote: > >> > >> On 20 September 2021 at 13:59, Sparapani, Rodney via > >> ESS-help wrote: | Generally, this stuff should just work > >> out-of-the-box. > >> > >> Understood. > >> > >> | And we are not a company like RStudio so this FOSS > >> setup works for us as | developers and hopefully it still > >> serves the users well. > >> > >> But legal structure has nothing to with 'calling a > >> release'. Which is done by authors (who should know the > >> code better than users) saying "yep what we have at HEAD > >> right now is good" and then cut a tarball. That is a > >> _marker_. Which some less-informed people like me can > >> take (and then ship downstream to Debian, and with that > >> Ubuntu etc). > >> > >> Without a marker, no shipment. Less ideal to me and > >> others. > >> > >> So pretty-please if someone would: could a release one of > >> these moons. It does not have to be frequent or regularly > >> schedule or anything. But maybe more often than once > >> every few years? Maybe when you sync with upstream Emacs > >> (assuming you do now)? > >> > >> Dirk > >> > >> -- > >> https://dirk.eddelbuettel.com | @eddelbuettel | > >> e...@debian.org > >> > >> __ > >> ESS-help@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/ess-help > >> > > > __ > > ESS-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/ess-help > > __ > ESS-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/ess-help > [[alternative HTML version deleted]] __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
> Lionel Henry via ESS-help > on Wed, 22 Sep 2021 15:15:42 +0200 writes: > We'd love to do a release but ESS is not in a good place > right now. Definitely. The reason is that there have been too many bugs introduced with the new features, so we could/should not release. This has been the real reason for not releasing formally. In addition, another important goal for the release has been to create an ESS+ "package" (not mainly an ELPA package, but also a traditional tarball / zip file) which will contain ESS plus relevant parts of polymode even though the latter is only maintained by one of us; the use of both *and* correct interplay between polymode and ESS is really crucial for parts modern R using ESS, notably as we had decided to declare the ess noweb-mode (for editing *.Rnw, i.e., Sweave & (tex-based) knitr) as obsolete. > Recent versions of Emacs interrupt background > commands (essential to completion and contextual help like > eldoc) when the user starts typing, which causes hard to > solve problems. > The dev branch is mostly working but not 100% > correctly. Unfortunately none of us seem to have the time > to work on ESS at the moment. > That said, while Martin, Vitalie and I notice issues here > and there, we haven't had serious bug reports in a while, > despite the dev branch being used by many Melpa users. So > maybe releasing in the current state is better than nothing. Well... It would be the first ESS release with serious (for some / in some use case situaitons) known bugs .. > Best, Lionel > On 9/22/21, Dirk Eddelbuettel via ESS-help > wrote: >> >> On 20 September 2021 at 13:59, Sparapani, Rodney via >> ESS-help wrote: | Generally, this stuff should just work >> out-of-the-box. >> >> Understood. >> >> | And we are not a company like RStudio so this FOSS >> setup works for us as | developers and hopefully it still >> serves the users well. >> >> But legal structure has nothing to with 'calling a >> release'. Which is done by authors (who should know the >> code better than users) saying "yep what we have at HEAD >> right now is good" and then cut a tarball. That is a >> _marker_. Which some less-informed people like me can >> take (and then ship downstream to Debian, and with that >> Ubuntu etc). >> >> Without a marker, no shipment. Less ideal to me and >> others. >> >> So pretty-please if someone would: could a release one of >> these moons. It does not have to be frequent or regularly >> schedule or anything. But maybe more often than once >> every few years? Maybe when you sync with upstream Emacs >> (assuming you do now)? >> >> Dirk >> >> -- >> https://dirk.eddelbuettel.com | @eddelbuettel | >> e...@debian.org >> >> __ >> ESS-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/ess-help >> > __ > ESS-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/ess-help __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
On 22 September 2021 at 15:15, Lionel Henry wrote: | We'd love to do a release but ESS is not in a good place right now. | Recent versions of Emacs interrupt background commands (essential to | completion and contextual help like eldoc) when the user starts | typing, which causes hard to solve problems. Yes :-/ I guess that was the state of affairs last time this came up. | The dev branch is mostly working but not 100% correctly. Unfortunately | none of us seem to have the time to work on ESS at the moment. | | That said, while Martin, Vitalie and I notice issues here and there, | we haven't had serious bug reports in a while, despite the dev branch | being used by many Melpa users. So maybe releasing in the current | state is better than nothing. Noted. It's a trade-off. Nobody wants unhappy users from not-quite-baked code but the staleness is also an issue. And I trust you all to make the right call. It will, as always, sort itself out eventually. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
We'd love to do a release but ESS is not in a good place right now. Recent versions of Emacs interrupt background commands (essential to completion and contextual help like eldoc) when the user starts typing, which causes hard to solve problems. The dev branch is mostly working but not 100% correctly. Unfortunately none of us seem to have the time to work on ESS at the moment. That said, while Martin, Vitalie and I notice issues here and there, we haven't had serious bug reports in a while, despite the dev branch being used by many Melpa users. So maybe releasing in the current state is better than nothing. Best, Lionel On 9/22/21, Dirk Eddelbuettel via ESS-help wrote: > > On 20 September 2021 at 13:59, Sparapani, Rodney via ESS-help wrote: > | Generally, this stuff should just work out-of-the-box. > > Understood. > > | And we are not a company like RStudio so this FOSS setup works for us as > | developers and hopefully it still serves the users well. > > But legal structure has nothing to with 'calling a release'. Which is done > by > authors (who should know the code better than users) saying "yep what we > have > at HEAD right now is good" and then cut a tarball. That is a _marker_. > Which some less-informed people like me can take (and then ship downstream > to > Debian, and with that Ubuntu etc). > > Without a marker, no shipment. Less ideal to me and others. > > So pretty-please if someone would: could a release one of these moons. It > does not have to be frequent or regularly schedule or anything. But maybe > more often than once every few years? Maybe when you sync with upstream > Emacs (assuming you do now)? > > Dirk > > -- > https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > __ > ESS-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/ess-help > __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
On 20 September 2021 at 13:59, Sparapani, Rodney via ESS-help wrote: | Generally, this stuff should just work out-of-the-box. Understood. | And we are not a company like RStudio so this FOSS setup works for us as | developers and hopefully it still serves the users well. But legal structure has nothing to with 'calling a release'. Which is done by authors (who should know the code better than users) saying "yep what we have at HEAD right now is good" and then cut a tarball. That is a _marker_. Which some less-informed people like me can take (and then ship downstream to Debian, and with that Ubuntu etc). Without a marker, no shipment. Less ideal to me and others. So pretty-please if someone would: could a release one of these moons. It does not have to be frequent or regularly schedule or anything. But maybe more often than once every few years? Maybe when you sync with upstream Emacs (assuming you do now)? Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
hi, Rodney,
thanks for this message, which i found very informative.
i wonder about a few things.
i'm installing ESS via straight.el. the recipe is
> (ess :type git :flavor melpa :files ("*.el" "lisp/*.el" "doc/ess.texi"
> ("etc" "etc/*") ("obsolete" "lisp/obsolete/*") (:exclude "etc/other")
> "ess-pkg.el") :host github :repo "emacs-ess/ESS")
the info pages say:
> 1.2 New features in ESS
> ===
>
> Changes and New Features in 19.04 (unreleased):
given your message, should this maybe be changed to list "what has
changed recently"? or a log of changes? or, some such?
also, =ess-version= reports
> ess-version: 18.10.3snapshot [] (loaded from
> /home/minshall/.emacs.d/straight/build/ess/)
and, i always wonder to what extent i'm running more 18.10.3, to what
extent i'm running "19.04-delta". i'm not sure what one might do if one
is basically following the tip of the git repo (especially via something
like straight.el?). but, something might be nice?
thanks much for the package. it's a great help.
cheers, Greg
__
ESS-help@r-project.org mailing list
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Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
On 20 September 2021 at 13:59, Sparapani, Rodney via ESS-help wrote: | Over the last few years, we have moved away from having to set up features | with .emacs/etc. as much as possible. Generally, this stuff should just | work out-of-the-box. I completely concur and _love it_. I mostly just have an old .emacs because well over the years I put some toggles or preferences there. But stuff does work. (Every now and then defaults change in ways some of us don't like. I for one prefer older indentations over the newer clang-format / R's lintr or styler default which I find unreadable. Luckly I have a snippet I added in 1997 or so straight from the manual and all is good for me. [ I did have to holler once or twice whem the lintr was autoenabled with bad defaults to boot. ]) Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
Hi Gang: I’m not directly answering the question because I don’t use Rmd (but I do use Rnw all of the time). And, just to react to a few of Dirk’s and Tyler’s comments. Over the last few years, we have moved away from having to set up features with .emacs/etc. as much as possible. Generally, this stuff should just work out-of-the-box. For example, there was a time where I was struggling with Rnw and couldn’t figure out what was wrong by changing settings/debugging/etc. But, after an upgrade, everything just worked. If you think you have really identified a bug, then please make a reproducible example and posted on git as an issue. In my view, this last post is related to our new release model. This model has not been communicated to my recollection but is de facto. We had planned to release 1:2 times per year. However, that largely stopped about 2018. Now, it is pretty much just grabbing from git where most of these issues have been worked out, i.e., the repo is supposed to be in a continual working state (although there may be occasional mishaps just like anything else). Part of the reason for moving to git (unintentionally) is that our copyrights have mostly been attributed to the FSF. However, there are a few pieces that are inconveniently absent. Similarly, there are a few key pieces that oldsters like me still want that are found in obsolete. Not directly related, but a similar concern is that there is still the issue of polymode being needed but not part of ESS which you have to get from git (don’t get me stared julia-mode!). So, lots of excuses, pick your favorite. But the upshot is that git is as convenient as it gets. And we are not a company like RStudio so this FOSS setup works for us as developers and hopefully it still serves the users well. I hope that helps from a philosophical point of view. My students are unconvinced and use RStudio but I am not allowed to fail them for their merely youthful indiscretions ;o) -- Rodney Sparapani, Associate Professor of Biostatistics Chair ISBA Section on Biostatistics and Pharmaceutical Statistics Institute for Health and Equity, Division of Biostatistics Medical College of Wisconsin, Milwaukee Campus [[alternative HTML version deleted]] __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
Hi, Polymode went through a major overhaul which I think was after 2014, so that blog post may be outdated. The overhaul made polymode much easier to use, such that there's very little config needed to get it set up. I wrote a tutorial describing my Rmd workflow in the past year for Dirk's ESS Intro series which you might find useful. Unfortunately I can't find the link just now, as I'm at the cottage with very sporadic network connection. Best, Tyler -- plantarum.ca On Sun, Sep 19, 2021, at 2:33 AM, Chris Evans via ESS-help wrote: > I am having problems with long Rmd files (and large data, long > processing times) in Rstudio. (Sorry, yes, I use Emacs for things and > ESS when I'm working with R (but rarely Rmd files) on a server, but I > use Rstudio routinely "at home".) This has made me decide it's > > http://johnstantongeddes.org/open%20science/2014/03/26/Rmd-polymode.html > > looked pretty straightforward but I thought I should ask here if any > changes since 2014 might make that too historical, perhaps not > as I couldn't find much that was recent on the topic of ESS and Rmd. > However, before I mess with an Emacs/ESS that works just fine > currently, I thought I'd ask here. > > I'm running on Ubuntu 20.04 "at home" and Debian (4.19.152-1 > (2020-10-18) in case it matters) on the server (and might as well > set things up on both if it's easy). > > Any advice will be gratefully received (and, who knows, might even > tempt me back to Emacs/ESS for much more of what I'm doing!) > > TIA, > > Chris > > -- > Chris Evans (he/him) Visiting Professor, University > of Sheffield and UDLA, Quito, Ecuador > I do some consultation work for the University of Roehampton > and other places > but remains my main Email address. I have a work > web site at: >https://www.psyctc.org/psyctc/ > and a site I manage for CORE and CORE system trust at: >http://www.coresystemtrust.org.uk/ > I have "semigrated" to France, see: >https://www.psyctc.org/pelerinage2016/semigrating-to-france/ > > https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/ > > If you want an Emeeting, I am trying to keep them to Thursdays and my > diary is at: >https://www.psyctc.org/pelerinage2016/ceworkdiary/ > Beware: French time, generally an hour ahead of UK. > > __ > ESS-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/ess-help > __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files
Chris, I don't have great advice. I have been doing this in Emacs with ESS (and friends like polymode) 'for years' and it mostly worked. So thumbs up -- it worth doing and I prefer doing it in Emacs. Polymode is actually rather cool. The world being what it is these days, the predictable six-month cycle of ESS updates stopped at some point with "much bigger, much better" next release "right around the corner". And then that never happened (yet). So sometimes I tried updating via the Emacs package manager, but once or twice something odd happened so I reverted to the content of the deb package I look after -- it is still at 18.10 (even though it is now, just like other Debian ELPA packages, mostly a shim around the (versioned) ELPA package). Long story short, 'apt install elpa-ess' should work. As emails I have 25-ish years of cruft in .emacs but not too too much relative to ESS and RMarkdown. It generally just works and it is fun to use. I really do live in it for just about everything I write these days. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
