Failed to install GLM3r

[TheMaskou]

Hi,

I'm simply trying to install package's GLM3r but I can't even differents ways used and tried... I'm sorry if it's seems so simple for all of you but I'm beginner and I'm blocking...

So, I'm using 4.1.1 R version and I'm tried to install the package with differents codes :

library(devtools)
install_github(repo = 'GLEON/GLM3r', force = TRUE)

library("devtools")
devtools::install_github("GLEON/GLM3r")

But a same error message is happening :

devtools::install_github("GLEON/GLM3r")
Downloading GitHub repo GLEON/GLM3r@HEAD
Error: Failed to install 'GLM3r' from GitHub:
create process 'C:/PROGRA1/R/R-411.1/bin/x64/Rcmd.exe' (system error 267, Nom de répertoire non valide.
) @win/processx.c:1040 (processx_exec)

I'm also tried to use 3.6.2 R version but 'rcmdcheck' and 'sessioninfo' dependencies are not available for package 'devtools' and it's impossible to install them too. It's globally a sames error messages for them, e.g install.packages("sessioninfo") :

install.packages("sessioninfo")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘D:/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependency ‘cli’

There are binary versions available but the source versions are later:
binary source needs_compilation
cli 2.5.0 3.1.0 TRUE
sessioninfo 1.1.1 1.2.0 FALSE

Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/cli_2.5.0.zip'
Content type 'application/zip' length 534931 bytes (522 KB)
downloaded 522 KB

package ‘cli’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Max¤µ\AppData\Local\Temp\RtmpWqE9wL\downloaded_packages
installing the source package ‘sessioninfo’

trying URL 'https://cran.rstudio.com/src/contrib/sessioninfo_1.2.0.tar.gz'
Content type 'application/x-gzip' length 171167 bytes (167 KB)
downloaded 167 KB

• installing source package 'sessioninfo' ...
  ** package 'sessioninfo' correctement décompressé et sommes MD5 vérifiées
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace 'cli' 2.5.0 is being loaded, but >= 3.1.0 is required
  Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
  Exécution arrêtée
  ERROR: lazy loading failed for package 'sessioninfo'
• removing 'D:/Documents/R/win-library/3.6/sessioninfo'
  Warning in install.packages :
  installation of package ‘sessioninfo’ had non-zero exit status

The downloaded source packages are in
‘C:\Users\Max¤µ\AppData\Local\Temp\RtmpWqE9wL\downloaded_packages’

Same complications for "Rtools" package who his version is out of bounds (necessary package for "devtools") :

install.packages("Rtools")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘D:/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘Rtools’ is not available (for R version 3.6.2)

av <- available.packages(filters=list())
av[av[, "Rtools"] == pkg, ]
Error in av[, "Rtools"] : subscript out of bounds
View(av)

Then, I even can't install devtools's package and even with that I don't know at all if it will be possible after to install from github the GLM3r package ...

If ever you can help me thank you verry verry much...

Max

[robertladwig]

Hi Max,

Thanks for the GLM3r issue report. Quick question: Did you try installing Rtools for Windows using https://cran.rstudio.com/bin/windows/Rtools/?

Cheers,
Robert

[TheMaskou]

Thank you so much for your reactivity but yes ... I've already tried to install it for windows. Under the out of codes : """

Sys.which("make")

make "C:\\rtools40\\usr\\bin\\make.exe"

install.packages("jsonlite", type = "source")

The downloaded source packages are in ‘C:\Users\Max¤µ\AppData\Local\Temp\RtmpC6YD9U\downloaded_packages’

install.packages("rtools4")

Installation du package dans ‘D:/Documents/R/win-library/4.1’ (car ‘lib’ n'est pas spécifié) Warning in install.packages : le package ‘rtools4’ n'est pas disponible for this version of R Une version de ce package pour votre version de R est peut-être disponible ailleurs, Voyez des idées à https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages """ Cheers, Max

…

________________________________ De : Robert Ladwig ***@***.***> Envoyé : lundi 1 novembre 2021 20:36 À : GLEON/GLM3r ***@***.***> Cc : TheMaskou ***@***.***>; Author ***@***.***> Objet : Re: [GLEON/GLM3r] Failed to install GLM3r (Issue #21) Hi Max, Thanks for the GLM3r issue report. Quick question: Did you try installing Rtools for Windows using https://cran.rstudio.com/bin/windows/Rtools/? Cheers, Robert — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#21 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWJVWDY5RW7IJFKUG5CGCH3UJ3T3NANCNFSM5HEREOQA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[robertladwig]

But when you try to reinstall GLM3r using

require("devtools")
devtools::install_github("GLEON/GLM3r")

you still get:

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
?

[TheMaskou]

I've problem only with 3.6.2 Rversion and with it, yes the message where Rtools is required is appearing when I want to install devtool for believe install GLM3r. But when I'm tried the process with the newest R version (4.1.1), I haven't any problem with Rtools or devtools. They are an other error message where I can't find a solution. Check the following outs. """

library(devtools)

Le chargement a nécessité le package : usethis

require("devtools") devtools::install_github("GLEON/GLM3r")

Downloading GitHub repo ***@***.*** Error: Failed to install 'GLM3r' from GitHub: create process 'C:/PROGRA~1/R/R-41~1.1/bin/x64/Rcmd.exe' (system error 267, Nom de répertoire non valide. ) @win/processx.c:1040 (processx_exec) """ Another thing, I'm trying also with 3.6.2 Rversion because I found somewhere that it was the compatible R version for "GLM3r", that'its true ? Because there is only there where I can't install "Rtools", "devtools", etc. Max

…

________________________________ De : Robert Ladwig ***@***.***> Envoyé : lundi 1 novembre 2021 21:09 À : GLEON/GLM3r ***@***.***> Cc : TheMaskou ***@***.***>; Author ***@***.***> Objet : Re: [GLEON/GLM3r] Failed to install GLM3r (Issue #21) But when you try to reinstall GLM3r using require("devtools") devtools::install_github("GLEON/GLM3r") you still get: WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding: ? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#21 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWJVWDZCFMU3TKAIEFY4XJ3UJ3XXHANCNFSM5HEREOQA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[robertladwig]

Related to your problems with R 4.1.1 and the working Rtools, it seems this problem is very Windows-specific (see https://community.rstudio.com/t/install-github-system-error-267-the-directory-name-is-invalid/107145, https://stackoverflow.com/questions/67975277/error-windows-cant-find-c-progra1-check-the-spelling-and-try-again and https://stackoverflow.com/questions/68400661/r-unable-to-install-packages-from-github-system-error-267-win-processx-c1040/68408378#68408378). I'd suggest trying the approaches outlined in the last link, i.e.

`Sys.setenv(R_REMOTES_STANDALONE="true")

remotes::install_github("GLEON/GLM3r")`

But please note that I don't currently have access to any Windows machine to try it myself, and I am unsure if changing the environmental setting is worth it (see code above).

[TheMaskou]

It working perfectly !!!

I would like to thank you warmly. Many thanks for your answers and your work. Infinitely!
I wish you a good continuation and the best. Thanks a lot for your reactivity and your skills.

Max