[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(a)winehq.org Reporter: virtualreal(a)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 -- For R, check https://mirror.lyrahosting.com/CRAN/ I'm forced to use the Windows version due to a dependency from another Windows program. I use the latest version of Cygwin: 2.909, 64-bit. I use the 64-bit version of Bunsenlabs, which is based on Debian 10. In case you need any more info, please let me know. Thanks! -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 Fabian Maurer <dark.shadow4(a)web.de> changed: What |Removed |Added ---------------------------------------------------------------------------- Severity|blocker |normal CC| |dark.shadow4(a)web.de --- Comment #1 from Fabian Maurer <dark.shadow4(a)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. -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #2 from Jim <virtualreal(a)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 -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 Fabian Maurer <dark.shadow4(a)web.de> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|UNCONFIRMED |NEEDINFO Ever confirmed|0 |1 --- Comment #3 from Fabian Maurer <dark.shadow4(a)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? -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #4 from Jim <virtualreal(a)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 -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #5 from Jim <virtualreal(a)gmail.com> --- Created attachment 70460 --> https://bugs.winehq.org/attachment.cgi?id=70460 R screen output -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #6 from Jim <virtualreal(a)gmail.com> --- My bad, R.exe returns a slightly different screen output, see attached file above. -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #7 from Fabian Maurer <dark.shadow4(a)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. -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #8 from Jim <virtualreal(a)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 -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #9 from Jim <virtualreal(a)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." -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 Fabian Maurer <dark.shadow4(a)web.de> changed: What |Removed |Added ---------------------------------------------------------------------------- Resolution|--- |DUPLICATE Status|NEEDINFO |RESOLVED --- Comment #10 from Fabian Maurer <dark.shadow4(a)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 *** -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #11 from Jim <virtualreal(a)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." -- -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #12 from Jim <virtualreal(a)gmail.com> --- Here's this thread: https://bugs.winehq.org/show_bug.cgi?id=48891 -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #13 from Fabian Maurer <dark.shadow4(a)web.de> --- That thread is about another issue, probably an older Cygwin version. -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 --- Comment #14 from Jim <virtualreal(a)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. -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
https://bugs.winehq.org/show_bug.cgi?id=51605 Alistair Leslie-Hughes <leslie_alistair(a)hotmail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |CLOSED --- Comment #15 from Alistair Leslie-Hughes <leslie_alistair(a)hotmail.com> --- Closing Duplicate. -- Do not reply to this email, post in Bugzilla using the above URL to reply. You are receiving this mail because: You are watching all bug changes.
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