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

Sparapani, Rodney r@p@r@p@ @end|ng |rom mcw@edu
Sat Dec 2 18:59:10 CET 2023 

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).

--
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<mailto:mailman-bounces using stat.ethz.ch>> on behalf of Robert Lerche <rlerche using pacificbiosciences.com<mailto:rlerche using pacificbiosciences.com>>
Date: Saturday, December 2, 2023 at 11:04 AM
To: Tomas Kalibera <tomas.kalibera using gmail.com<mailto:tomas.kalibera using gmail.com>>, ess-bugs using r-project.org<mailto:ess-bugs using r-project.org> <ess-bugs using r-project.org<mailto:ess-bugs using r-project.org>>
Cc: ess-bugs-owner using r-project.org<mailto:ess-bugs-owner using r-project.org> <ess-bugs-owner using r-project.org<mailto:ess-bugs-owner using r-project.org>>, R-windows using R-project.org<mailto:R-windows using R-project.org> <R-windows using R-project.org<mailto: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<mailto: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<mailto:ess-bugs-bounces using r-project.org>> On Behalf Of ess-bugs-owner using r-project.org<mailto:ess-bugs-owner using r-project.org>
Sent: Saturday, December 2, 2023 8:13 AM
To: Robert Lerche <rlerche using pacificbiosciences.com<mailto:rlerche using pacificbiosciences.com>>
Subject: RE: [R-win] Difficulty installing R packages under Windows 11 / Cygwin

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