[Bug 51605] New: R returns Cygwin warning and installation error during package installation
https://bugs.winehq.org/show_bug.cgi?id=51605
Bug ID: 51605 Summary: R returns Cygwin warning and installation error during package installation Product: Wine Version: 6.15 Hardware: x86-64 OS: Linux Status: UNCONFIRMED Severity: blocker Priority: P2 Component: -unknown Assignee: wine-bugs@winehq.org Reporter: virtualreal@gmail.com Distribution: ---
Hello,
(specific details like versions & sources can be found below)
Using R with the Devtools library I try to install a package called Catboost, with the following R script:
-- install.packages("devtools", dependencies = TRUE) library(devtools) devtools::install_url('https://github.com/catboost/catboost/releases/download/v0.26.1/catboost-R-Wi...') --
Devtools was already installed successfully, but the last command (devtools::install_url...) returns:
-- Downloading package from url: https://github.com/catboost/catboost/releases/download/v0.26.1/catboost-R-Wi... Cygwin WARNING: Couldn't compute FAST_CWD pointer. This typically occurs if you're using an older Cygwin version on a newer Windows. Please update to the latest available Cygwin version from https://cygwin.com/. If the problem persists, please see https://cygwin.com/problems.html
Error: Failed to install 'unknown package' from URL: Does not appear to be an R package (no DESCRIPTION) --
Under Windows 8 the same installation script runs fine:
-- Downloading package from url: https://github.com/catboost/catboost/releases/download/v0.26.1/catboost-R-Wi...
checking for file 'C:\Users\Admin\AppData\Local\Temp\Rtmp6tcsba\remotesd9c63bc54db\catboost/DESCRIPTION' ...
√ checking for file 'C:\Users\Admin\AppData\Local\Temp\Rtmp6tcsba\remotesd9c63bc54db\catboost/DESCRIPTION' (1.1s)
- preparing 'catboost': (2s) checking DESCRIPTION meta-information ...
√ checking DESCRIPTION meta-information
- checking for LF line-endings in source and make files and shell scripts (430ms)
- checking for empty or unneeded directories
- building 'catboost_0.26.1.tar.gz'
* installing *source* package 'catboost' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'catboost' finding HTML links ... done catboost.caret html catboost.cv html catboost.drop_unused_features html catboost.eval_metrics html catboost.get_feature_importance html catboost.get_model_params html catboost.get_object_importance html catboost.get_plain_params html catboost.load_model html catboost.load_pool html catboost.predict html catboost.restore_handle html catboost.save_model html catboost.save_pool html catboost.shrink html catboost.staged_predict html catboost.sum_models html catboost.train html catboost.virtual_ensembles_predict html dim.catboost.Pool html dimnames.catboost.Pool html head.catboost.Pool html print.catboost.Model html print.catboost.Pool html summary.catboost.Model html tail.catboost.Pool html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (catboost) Making 'packages.html' ... done
https://bugs.winehq.org/show_bug.cgi?id=51605
Fabian Maurer dark.shadow4@web.de changed:
What |Removed |Added ---------------------------------------------------------------------------- Severity|blocker |normal CC| |dark.shadow4@web.de
--- Comment #1 from Fabian Maurer dark.shadow4@web.de --- Not a blocker.
Would you mind giving simple instructions on how to reproduce from scratch? Including installation of R and using the install script.
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #2 from Jim virtualreal@gmail.com --- Hello Fabian,
I considered it as a 'blocker' since I was unable to install this R package.
As for reproducing this bug:
1.) visit https://mirror.lyrahosting.com/CRAN/ to install the Windows version of R. 2.) run Rgui.exe which can be found in the /.wine/drive_c/Program Files/R/R-4.0.5/bin/x64/ directory (sorry that I forgot to mention this!) 3.) insert the following 3 lines in this R instance:
install.packages("devtools", dependencies = TRUE) library(devtools) devtools::install_url('https://github.com/catboost/catboost/releases/download/v0.26.1/catboost-R-Wi...')
(and press Enter)
I hope this answers your question!
Jim
https://bugs.winehq.org/show_bug.cgi?id=51605
Fabian Maurer dark.shadow4@web.de changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|UNCONFIRMED |NEEDINFO Ever confirmed|0 |1
--- Comment #3 from Fabian Maurer dark.shadow4@web.de ---
I considered it as a 'blocker' since I was unable to install this R package.
Please see https://bugs.winehq.org/page.cgi?id=fields.html under Severity. Normal is applicable here.
So, the problem is this line?
installation of package ‘C:/users/fabian/Temp/Rtmp8QWGz6/file13847bf3d7e/catboost_0.26.1.tar.gz’ had non-zero exit status
I tested on Win7 and Win10, and it behaves exactly the same as Wine, so I don't see a problem here.
Where did you get the "Does not appear to be an R package (no DESCRIPTION)" and "cygwin warning" from?
Also, where does Cygwin come into play in the first place? Why do you need Cygwin?
Btw, does using "R.exe" (commandline) the same issue?
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #4 from Jim virtualreal@gmail.com --- (In reply to Fabian Maurer from comment #3)
I considered it as a 'blocker' since I was unable to install this R package.
Please see https://bugs.winehq.org/page.cgi?id=fields.html under Severity. Normal is applicable here.
So, the problem is this line?
installation of package ‘C:/users/fabian/Temp/Rtmp8QWGz6/file13847bf3d7e/catboost_0.26.1.tar.gz’ had non-zero exit status
I never saw this 'non-zero exit status' in Rgui.exe or R.exe
I tested on Win7 and Win10, and it behaves exactly the same as Wine, so I don't see a problem here.
With the 'same' you mean the same error messages or were you able to install the Catboost package successfully?
Where did you get the "Does not appear to be an R package (no DESCRIPTION)" and "cygwin warning" from?
This is the screen output from R
Also, where does Cygwin come into play in the first place? Why do you need Cygwin?
I don't need it, but that's the screen output I got from R. In an attempt to fix this issue I installed Cygwin.
Btw, does using "R.exe" (commandline) the same issue?
Yes, exactly the same. Make sure you use the 64-bit version in the .wine/drive_c/Program Files/R/R-4.0.5/bin/x64/ directory, since Catboost requires 64-bit
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #5 from Jim virtualreal@gmail.com --- Created attachment 70460 --> https://bugs.winehq.org/attachment.cgi?id=70460 R screen output
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #6 from Jim virtualreal@gmail.com --- My bad, R.exe returns a slightly different screen output, see attached file above.
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #7 from Fabian Maurer dark.shadow4@web.de --- Created attachment 70461 --> https://bugs.winehq.org/attachment.cgi?id=70461 Log when running your script
With the 'same' you mean the same error messages or were you able to install the Catboost package successfully?
I mean, even on windows it doesn't install properly. Wine behaves the same.
I still have no idea why or how you use Cygwin. Cygwin is to run Linux programs on Windows. What does that have to do with R?
So, I download https://mirror.lyrahosting.com/CRAN/bin/windows/base/old/4.0.5/R-4.0.5-win.e... Then I followed your instructions from Comment 2.
See what I got in the attachment. No idea what you're doing, but it's clearly something different.
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #8 from Jim virtualreal@gmail.com --- (In reply to Fabian Maurer from comment #7)
Created attachment 70461 [details] Log when running your script
With the 'same' you mean the same error messages or were you able to install the Catboost package successfully?
I mean, even on windows it doesn't install properly. Wine behaves the same.
So you get the exact same screen output as under Wine? That's interesting since I was able to do so (see screen output in my first message).
I still have no idea why or how you use Cygwin. Cygwin is to run Linux programs on Windows. What does that have to do with R?
Neither do I, but I installed it later in an attempt to avoid that warning message and -possibly- avoid this installation problem. Unfortunately it didn't
So, I download https://mirror.lyrahosting.com/CRAN/bin/windows/base/old/4.0.5/R-4.0.5-win. exe Then I followed your instructions from Comment 2.
See what I got in the attachment. No idea what you're doing, but it's clearly something different.
Ah, I see the message "WARNING: Rtools is required to build R packages, but is not currently installed." My apologize, I've installed the 'devtools' package a long time ago and forgot that it requires that it needs Rtools when you want to install packages from source. Please visit https://cran.r-project.org/bin/windows/Rtools/ and install rtools40v2-x86_64.exe
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #9 from Jim virtualreal@gmail.com --- typo: "My apologize, I've installed the 'devtools' package a long time ago and forgot that it needs Rtools when you want to install packages from source."
https://bugs.winehq.org/show_bug.cgi?id=51605
Fabian Maurer dark.shadow4@web.de changed:
What |Removed |Added ---------------------------------------------------------------------------- Resolution|--- |DUPLICATE Status|NEEDINFO |RESOLVED
--- Comment #10 from Fabian Maurer dark.shadow4@web.de --- Ah, so that's where Cygwin comes from. In this case, probably a dupe of https://bugs.winehq.org/show_bug.cgi?id=40528
In short, Cygwin doesn't support Wine properly. Nothing we can do, really.
*** This bug has been marked as a duplicate of bug 40528 ***
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #11 from Jim virtualreal@gmail.com --- So, assuming that the mentioned patch from Dmitry Timoshkov has been implemented in/before Wine 6.15, it didn't solved this problem? I'm asking this because Megastallman reported a similar issue and later wrote that it fixed his issue.
-- "megastallman 2020-04-07 11:13:11 CDT The same happens with Cygwin:
Running wine-5.5. Trying to run: wine .wine/drive_c/cygwin/bin/bash.exe getting: Cygwin WARNING: Couldn't compute FAST_CWD pointer. This typically occurs if you're using an older Cygwin version on a newer Windows. Please update to the latest available Cygwin version from https://cygwin.com/. If the problem persists, please see https://cygwin.com/problems.html
And nothing works. No shell, terminal hangs and needs "reset". The Cygwin version - is the latest."
-- "megastallman 2020-05-10 04:41:34 CDT Thanks Dmitry! Your patch works as well." --
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #12 from Jim virtualreal@gmail.com --- Here's this thread: https://bugs.winehq.org/show_bug.cgi?id=48891
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #13 from Fabian Maurer dark.shadow4@web.de --- That thread is about another issue, probably an older Cygwin version.
https://bugs.winehq.org/show_bug.cgi?id=51605
--- Comment #14 from Jim virtualreal@gmail.com --- (In reply to Fabian Maurer from comment #13)
That thread is about another issue, probably an older Cygwin version.
Too bad, thanks for the effort.
https://bugs.winehq.org/show_bug.cgi?id=51605
Alistair Leslie-Hughes leslie_alistair@hotmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |CLOSED
--- Comment #15 from Alistair Leslie-Hughes leslie_alistair@hotmail.com --- Closing Duplicate.
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