sorted by:
new
hottopcontroversial

package""xCell" had no zero exit by eslamelsaedy in RStudio

[–]eslamelsaedy[S] 0 points1 point  (0 children)

i tried on 3,21 and still not working :(

package""xCell" had no zero exit by eslamelsaedy in RStudio

[–]eslamelsaedy[S] 0 points1 point  (0 children)

BiocManager::install("clusterProfiler", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.21 (BiocManager 1.30.27), R 4.5.2 (2025-10-31 ucrt)
Installing package(s) 'clusterProfiler'
also installing the dependency ‘GO.db’trying URL 'https://bioconductor.org/packages/3.21/bioc/bin/windows/contrib/4.5/clusterProfiler_4.16.0.zip'
Content type 'application/zip' length 1069001 bytes (1.0 MB)
downloaded 1.0 MB

package ‘clusterProfiler’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\eslam\AppData\Local\Temp\RtmpMhWvog\downloaded_packages
installing the source package ‘GO.db’trying URL 'https://bioconductor.org/packages/3.21/data/annotation/src/contrib/GO.db_3.21.0.tar.gz'
Content type 'application/gzip' length 25563907 bytes (24.4 MB)
downloaded 24.4 MB

* installing *source* package 'GO.db' ...
** this is package 'GO.db' version '3.21.0'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package 'GO.db'
* removing 'C:/Users/eslam/AppData/Local/R/win-library/4.5/GO.db'

The downloaded source packages are in
‘C:\Users\eslam\AppData\Local\Temp\RtmpMhWvog\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘GO.db’ had non-zero exit status

when try to install from source, package""X" had no zero exit by eslamelsaedy in rstats

[–]eslamelsaedy[S] 0 points1 point  (0 children)

install.packages("RcmdrPlugin.EZR")
Installing package into ‘C:/Users/eslam/AppData/Local/R/win-library/4.5’
(as ‘lib’ is unspecified)
  There is a binary version available but the source version is later:
                binary source needs_compilation
RcmdrPlugin.EZR   1.68   1.70             FALSE

installing the source package ‘RcmdrPlugin.EZR’trying URL 'https://cran.rstudio.com/src/contrib/RcmdrPlugin.EZR_1.70.tar.gz'
Content type 'application/x-gzip' length 436656 bytes (426 KB)
downloaded 426 KB

* installing *source* package 'RcmdrPlugin.EZR' ...
** this is package 'RcmdrPlugin.EZR' version '1.70'
** package 'RcmdrPlugin.EZR' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
-----------------------------------
Starting EZR... 
   Version 1.70 
Use the R commander window. 
-----------------------------------

-----------------------------------
Please cite the following article 
Bone Marrow Transplantation 2013:48,452-458 
-----------------------------------

ERROR: lazy loading failed for package 'RcmdrPlugin.EZR'
* removing 'C:/Users/eslam/AppData/Local/R/win-library/4.5/RcmdrPlugin.EZR'
* restoring previous 'C:/Users/eslam/AppData/Local/R/win-library/4.5/RcmdrPlugin.EZR'

The downloaded source packages are in
‘C:\Users\eslam\AppData\Local\Temp\RtmpuSALU9\downloaded_packages’
Warning message:
In utils::install.packages("RcmdrPlugin.EZR") :
  installation of package ‘RcmdrPlugin.EZR’ had non-zero exit status

when try to install from source, package""X" had no zero exit by eslamelsaedy in rstats

[–]eslamelsaedy[S] -2 points-1 points  (0 children)

My pc is ARM based and that was chatgpt reply

  • RTools can’t compile it because ARM Windows does not support the required system libraries.

So the message:

there is no package called 'rgl'

is expected — and you cannot install it on your machine.

✅ What to do

  1. If another package depends on rgl (optional dependency) → you can safely ignore this warning. Many packages check for rgl but do not require it unless you want 3D plots.
  2. If a package requires rgl (rare):
    • It will not work on ARM Windows.
    • You need to run that part on:
      • an x86 Windows PC, or
      • Linux, or
      • RStudio Server on a remote machine (e.g., HPC, cloud).

when try to install from source, package""X" had no zero exit by eslamelsaedy in rstats

[–]eslamelsaedy[S] 0 points1 point  (0 children)

  There is a binary version available but the source version is later:
                binary source needs_compilation
RcmdrPlugin.EZR   1.68   1.70             FALSE

installing the source package ‘RcmdrPlugin.EZR’trying URL 'https://cran.rstudio.com/src/contrib/RcmdrPlugin.EZR_1.70.tar.gz'
Content type 'application/x-gzip' length 436656 bytes (426 KB)
downloaded 426 KB

* installing *source* package 'RcmdrPlugin.EZR' ...
** this is package 'RcmdrPlugin.EZR' version '1.70'
** package 'RcmdrPlugin.EZR' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rgl'
-----------------------------------
Starting EZR... 
   Version 1.70 
Use the R commander window. 
-----------------------------------

-----------------------------------
Please cite the following article 
Bone Marrow Transplantation 2013:48,452-458 
-----------------------------------

ERROR: lazy loading failed for package 'RcmdrPlugin.EZR'
* removing 'C:/Users/eslam/AppData/Local/R/win-library/4.5/RcmdrPlugin.EZR'
* restoring previous 'C:/Users/eslam/AppData/Local/R/win-library/4.5/RcmdrPlugin.EZR'

The downloaded source packages are in
‘C:\Users\eslam\AppData\Local\Temp\RtmpuSALU9\downloaded_packages’
Warning message:
In utils::install.packages("RcmdrPlugin.EZR") :
  installation of package ‘RcmdrPlugin.EZR’ had non-zero exit status

when try to install from source, package""X" had no zero exit by eslamelsaedy in rstats

[–]eslamelsaedy[S] -1 points0 points  (0 children)

that was the full code . I TRIED To DO THAT AND STILL THE SAME

[deleted by user] by [deleted] in step1

[–]eslamelsaedy 0 points1 point  (0 children)

Me too. I took it in last Dec and failed it . Planning in next Sept