[ESS] [R-win] Difficulty installing R packages under Windows 11 / Cygwin

[Tomas Kalibera]

On 12/2/23 18:59, Sparapani, Rodney wrote:
>
> Hi Robert:
>
> Would they allow dual-booting?  I’m not saying that you can’t get ESS
>
> to work under Cygwin.  On the contrary, it did work at one time so
>
> it certainly can be done.  However, that is not currently supported
>
> so you are on your own.  But, perhaps there are others in the same
>
> straight-jacket here on ess-help that might be willing to help?
>
> Please speak up if so!
>
> In regards to WSL, that came out after I permanently switched
>
> to macOS. But, I think it is worth a try too.  Since you will be
>
> running pure Linux binaries, then it might work out of the box.
>
> And maybe there are more people here interested in WSL than
>
> Cygwin. Also, the more recent WSL 2 (released in 2019) sounds
>
> like it is more compatible than WSL 1 (released in 2016).
>
R is not being tested under WSL. When I tried last time (which is 
several years ago), there were some issues. Maybe they are already gone 
by now, I don't know, but it is not a supported platform.

Tomas

> -- 
>
> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>
> Vice President, Wisconsin Chapter of the American Statistical Association
>
> Institute for Health and Equity, Division of Biostatistics
>
> Medical College of Wisconsin, Milwaukee Campus
>
> *From: *Robert Lerche <rlerche using pacificbiosciences.com>
> *Date: *Saturday, December 2, 2023 at 11:40 AM
> *To: *Sparapani, Rodney <rsparapa using mcw.edu>, Tomas Kalibera 
> <tomas.kalibera using gmail.com>
> *Subject: *RE: [R-win] Difficulty installing R packages under Windows 
> 11 / Cygwin
>
> ATTENTION: This email originated from a sender outside of MCW. Use 
> caution when clicking on links or opening attachments.
>
> ------------------------------------------------------------------------
>
> Thanks for your thoughtful reply.  Alas, I am using a company-provided 
> laptop.  I would much prefer to run Linux as I do on my personal 
> system but that is not in the cards.  I have plenty of access to Linux 
> servers and of course I can run things there but it’s a bit inconvenient.
>
> I thought about using WSL (Windows Subsystem for Linux). I have some 
> experience with early versions of that [which leads me to avoid it 😊].
>
> It is my fate to cope with legacy junk on projects that were late when 
> I joined. Ah well it’s a living.
>
> *From:*Sparapani, Rodney <rsparapa using mcw.edu>
> *Sent:* Saturday, December 2, 2023 9:28 AM
> *To:* Robert Lerche <rlerche using pacificbiosciences.com>; Tomas Kalibera 
> <tomas.kalibera using gmail.com>; ess-help (ess-help using r-project.org) 
> <ess-help using r-project.org>
> *Subject:* Re: [R-win] Difficulty installing R packages under Windows 
> 11 / Cygwin
>
> [EXTERNAL MESSAGE] Be mindful when clicking links or attachments
>
> Hi Robert:
>
> There was a time when we supported ESS under Cygwin.
>
> In other words, run elisp code assuming UNIX/Linux rather
>
> than Windows even though Windows is the OS.  However,
>
> that was a long time ago: at least 10 years since I last tried it.
>
> Cygwin has largely fallen out of fashion since you can now so
>
> easily install Ubuntu on typical hardware: something that
>
> has markedly improved since 2013.  Therefore, I would not
>
> expect Cygwin support to work out of the box since there
>
> has been no recent testing.  Also, Windows is not very
>
> popular with R users since there is no forking support
>
> for the parallel package.  So switching to Linux is well
>
> worth it.  I used to run Windows inside VirtualBox when
>
> I needed to do PC stuff like Office and iTunes
>
> (before switching to macOS and never looking back ;o)
>
> -- 
>
> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>
> Vice President, Wisconsin Chapter of the American Statistical Association
>
> Institute for Health and Equity, Division of Biostatistics
>
> Medical College of Wisconsin, Milwaukee Campus
>
> *From: *ESS-bugs <mailman-bounces using stat.ethz.ch> on behalf of Robert 
> Lerche <rlerche using pacificbiosciences.com>
> *Date: *Saturday, December 2, 2023 at 11:04 AM
> *To: *Tomas Kalibera <tomas.kalibera using gmail.com>, 
> ess-bugs using r-project.org <ess-bugs using r-project.org>
> *Cc: *ess-bugs-owner using r-project.org <ess-bugs-owner using r-project.org>, 
> R-windows using R-project.org <R-windows using R-project.org>
> *Subject: *RE: [R-win] Difficulty installing R packages under Windows 
> 11 / Cygwin
>
> ATTENTION: This email originated from a sender outside of MCW. Use 
> caution when clicking on links or opening attachments.
> ________________________________
>
> Let me try raw text:
>
> Tomas, my thanks for your prompt and useful response. I followed your 
> instructions and the Windows (MinGW/MSYS2) R and ggplot2 of course 
> work perfectly well launched from a Cygwin bash shell.  Alas, ESS 
> inside Cygwin Emacs 29.1 doesn't quite work, launching an R process 
> gives an error and although R is running with stdin/stdout directed to 
> the Emacs buffer there is no tab completion.
>
> [background for the benefit of ess-bugs using r-project.org]
>
> I recently received a new Windows 11 laptop from our IT department and 
> I'm trying to recreate my R environment (Cygwin/Emacs/ESS/R/ggplot2). 
> Originally I installed R 4.3.0 as packaged in Cygwin's setup.exe 
> utility (in the Math section). I was unable to add ggplot2. Tomas 
> kindly pointed me to the pre-built Windows binaries and as expected 
> installing it and ggplot2 went smoothly.
>
> I perused 
> https://urldefense.com/v3/__https://ess.r-project.org/index.php?Section=home__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKnpbUlLT$ 
> <https://urldefense.com/v3/__https:/ess.r-project.org/index.php?Section=home__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKnpbUlLT$> 
> and pulled the latest ESS via git clone. Make worked but now when I 
> try to launch R inside Emacs [with (require 'ess-r-mode) in my .emacs 
> file] an error message appears:
>
> ess-r--init-error-handler: Wrong type argument: listp, "Caused by 
> error: R error during background ESS command base::tryCatch(
>              base::local({
> base::source('/usr/share/emacs/site-lisp/ess/etc/ESSR/R/.load.R', 
> local=TRUE) #define load.ESSR
> .ess.ESSR.load('/usr/share/emacs/site-lisp/ess/etc/ESSR/R')
>              }),
>              error = function(cnd) {
>                msg <- paste0('ESSR::ERROR \"', conditionMessage(cnd), 
> '\"')
>                writeLines(msg)
>              }
>            )
> Error: cannot open the connection"
>
> Following this the buffer is live but tab completion fails.
>
> I attach the ess build log:
>
> G6WM1J3-89CBD7 ~ $ git clone 
> https://urldefense.com/v3/__https://github.com/emacs-ess/ESS.git__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKr2dFRa2$ 
> <https://urldefense.com/v3/__https:/github.com/emacs-ess/ESS.git__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKr2dFRa2$> 
> ess-latest
> Cloning into 'ess-latest'...
> remote: Enumerating objects: 44632, done.
> remote: Counting objects: 100% (1252/1252), done.
> remote: Compressing objects: 100% (424/424), done.
> remote: Total 44632 (delta 904), reused 1152 (delta 827), pack-reused 
> 43380
> Receiving objects: 100% (44632/44632), 27.28 MiB | 1.76 MiB/s, done.
> Resolving deltas: 100% (33688/33688), done.
> G6WM1J3-89CBD7 ~ $ cd ess-latest/
> G6WM1J3-89CBD7 ~/ess-latest $ make
> ********************* VERSIONS **************************
> GNU Emacs 29.1
> ESS 18.10.3snapshot
> ESSR 1.8
> *********************************************************
> make -C lisp all
> make[1]: Entering directory '/home/rlerche/ess-latest/lisp'
> which: no wget in (/cygdrive/c/Program 
> Files/R/R-4.3.2/bin:/usr/local/bin:/usr/bin:/cygdrive/c/Program Files 
> (x86)/Common 
> Files/Oracle/Java/javapath:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/System32/WindowsPowerShell/v1.0:/cygdrive/c/WINDOWS/System32/OpenSSH:/cygdrive/c/Program 
> Files/PuTTY:/cygdrive/c/Program Files 
> (x86)/GnuPG/bin:/cygdrive/c/Users/rlerche/AppData/Local/Microsoft/WindowsApps:/usr/lib/lapack)
> which: no wget in (/cygdrive/c/Program 
> Files/R/R-4.3.2/bin:/usr/local/bin:/usr/bin:/cygdrive/c/Program Files 
> (x86)/Common 
> Files/Oracle/Java/javapath:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/System32/WindowsPowerShell/v1.0:/cygdrive/c/WINDOWS/System32/OpenSSH:/cygdrive/c/Program 
> Files/PuTTY:/cygdrive/c/Program Files 
> (x86)/GnuPG/bin:/cygdrive/c/Users/rlerche/AppData/Local/Microsoft/WindowsApps:/usr/lib/lapack)
> test -f ../etc/.IS.RELEASE || /cygdrive/c/WINDOWS/system32/curl 
> https://urldefense.com/v3/__https://raw.githubusercontent.com/JuliaEditorSupport/julia-emacs/master/julia-mode.el__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKo9c7zFD$ 
> <https://urldefense.com/v3/__https:/raw.githubusercontent.com/JuliaEditorSupport/julia-emacs/master/julia-mode.el__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKo9c7zFD$> 
> > julia-mode.el
>   % Total    % Received % Xferd  Average Speed   Time    Time     
> Time  Current
>                                  Dload Upload   Total   Spent    Left  
> Speed
> 100 40906  100 40906    0     0   144k      0 --:--:-- --:--:-- 
> --:--:--  146k
> test -f ../etc/.IS.RELEASE || /cygdrive/c/WINDOWS/system32/curl 
> https://urldefense.com/v3/__https://raw.githubusercontent.com/JuliaEditorSupport/julia-emacs/master/julia-mode-latexsubs.el__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKmcNaJ6x$ 
> <https://urldefense.com/v3/__https:/raw.githubusercontent.com/JuliaEditorSupport/julia-emacs/master/julia-mode-latexsubs.el__;!!H8mHWRdzp34!7kh3oo0D5fJMElRU8O3Xz6Hmc-Y0ufB8oSgC1uqX1yvGwlD9fv0aJdrxgnpo0X7E1tfYMI0XU5Y1iNnIKmcNaJ6x$> 
> > julia-mode-latexsubs.el
>   % Total    % Received % Xferd  Average Speed   Time    Time     
> Time  Current
>                                  Dload Upload   Total   Spent    Left  
> Speed
> 100  442k  100  442k    0     0  1292k      0 --:--:-- --:--:-- 
> --:--:-- 1296k
> Computing dependencies
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-custom.el
>
> In toplevel form:
> ess-custom.el:324:2: Warning: custom-declare-variable 
> `ess-startup-directory' docstring has wrong usage of unescaped single 
> quotes (use \= or different quoting)
> ess-custom.el:1401:2: Warning: custom-declare-variable 
> `ess-post-run-hook' docstring has wrong usage of unescaped single 
> quotes (use \= or different quoting)
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-utils.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-bugs-l.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-tracebug.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-inf.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-mode.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-bugs-d.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-help.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-s-lang.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-rd.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-r-syntax.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-roxy.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-r-completion.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-r-package.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-trns.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-r-xref.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-r-mode.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-gretl.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-jags-d.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-julia.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-r-flymake.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-rdired.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-sas-a.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-sas-l.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-sas-d.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-sp6-d.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile essd-els.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-toolbar.el
> emacs -batch -Q  --directory . --directory ./obsolete -f 
> batch-byte-compile ess-site.el
> emacs -batch -Q --directory . --directory ./obsolete -f 
> batch-byte-compile julia-mode-latexsubs.el
> emacs -batch -Q --directory . --directory ./obsolete -f 
> batch-byte-compile julia-mode.el
>
> Generating ess-autoloads.el
> emacs -batch -Q --eval "(progn\
> (setq make-backup-files nil)\
> (setq generated-autoload-file (expand-file-name \"ess-autoloads.el\"))\
> (setq find-file-visit-truename t)\
> (update-directory-autoloads default-directory))"
> Package autoload is deprecated
>   INFO     Scraping files for ess-autoloads.el...
>   INFO     Scraping files for ess-autoloads.el...done
> make[1]: Leaving directory '/home/rlerche/ess-latest/lisp'
> make -C doc all
> make[1]: Entering directory '/home/rlerche/ess-latest/doc'
> making Info documentation...
> makeinfo ess.texi
> mv -f ess.info info/
> makeinfo --no-validate --plaintext --no-split -o - readme.texi \
> | perl -pe 'last if /^Concept Index/;' > ../README
> makeinfo --no-validate --plaintext --no-split -o - announc.texi \
> | perl -pe 'last if /^Concept Index/;' > ../ANNOUNCE
> makeinfo --no-validate --plaintext --no-split -o - news.texi > ../NEWS
> makeinfo --no-validate --plaintext --no-split -o - onews.texi > ../ONEWS
> make[1]: Leaving directory '/home/rlerche/ess-latest/doc'
> make -C etc all
> make[1]: Entering directory '/home/rlerche/ess-latest/etc'
> make[1]: Nothing to be done for 'all'.
> make[1]: Leaving directory '/home/rlerche/ess-latest/etc'
> cd lisp; make ess-autoloads.el
> make[1]: Entering directory '/home/rlerche/ess-latest/lisp'
> make[1]: 'ess-autoloads.el' is up to date.
> make[1]: Leaving directory '/home/rlerche/ess-latest/lisp'
> G6WM1J3-89CBD7 ~/ess-latest $ make install
> ********************* VERSIONS **************************
> GNU Emacs 29.1
> ESS 18.10.3snapshot
> ESSR 1.8
> *********************************************************
> make -C lisp all
> make[1]: Entering directory '/home/rlerche/ess-latest/lisp'
> make[1]: Nothing to be done for 'all'.
> make[1]: Leaving directory '/home/rlerche/ess-latest/lisp'
> make -C doc all
> make[1]: Entering directory '/home/rlerche/ess-latest/doc'
> make[1]: Nothing to be done for 'all'.
> make[1]: Leaving directory '/home/rlerche/ess-latest/doc'
> make -C etc all
> make[1]: Entering directory '/home/rlerche/ess-latest/etc'
> make[1]: Nothing to be done for 'all'.
> make[1]: Leaving directory '/home/rlerche/ess-latest/etc'
> cd lisp; make ess-autoloads.el
> make[1]: Entering directory '/home/rlerche/ess-latest/lisp'
> make[1]: 'ess-autoloads.el' is up to date.
> make[1]: Leaving directory '/home/rlerche/ess-latest/lisp'
> mkdir -p /usr/share/emacs/site-lisp/ess
> cp -p -R ./* /usr/share/emacs/site-lisp/ess/
> G6WM1J3-89CBD7 ~/ess-latest $ exit
>
> -----Original Message-----
> From: ESS-bugs <ess-bugs-bounces using r-project.org> On Behalf Of 
> ess-bugs-owner using r-project.org
> Sent: Saturday, December 2, 2023 8:13 AM
> To: Robert Lerche <rlerche using pacificbiosciences.com>
> Subject: RE: [R-win] Difficulty installing R packages under Windows 11 
> / Cygwin
>
> [EXTERNAL MESSAGE] Be mindful when clicking links or attachments
>
> After content filtering, the message was empty
>