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tjbutler003 avatar tjbutler003 commented on June 14, 2024

@giovp what version of R are you using? I had trouble with xbioc when I was using 3.6.1 I think, but when I went back to 3.5.x I was able to download it fine. However, now I am using MuSiC with 3.6.2 and that has been working for me after a fresh install.

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giovp avatar giovp commented on June 14, 2024

I have R 3.6.2,
I can't indeed install xbioc

emotes::install_github("renozao/xbioc")
Downloading GitHub repo renozao/xbioc@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                       
2: CRAN packages only                        
3: None                                      
4: pkgmaker (0.31.1 -> ac95c24f3...) [GitHub]

Enter one or more numbers, or an empty line to skip updates:
1
pkgmaker (0.31.1 -> ac95c24f3...) [GitHub]
Downloading GitHub repo renozao/pkgmaker@developchecking for file/private/var/folders/3t/lc9m5zv966934dq4d6gf6l60g_dj6h/T/Rtmp1OVDRI/remotes85b01bf24d5a/renozao-pkgmaker-ac95c24/DESCRIPTION...preparingpkgmaker:checking DESCRIPTION meta-information ...checking for LF line-endings in source and make files and shell scriptschecking for empty or unneeded directories
   Removed empty directorypkgmaker/vignettes’
─  buildingpkgmaker_0.31.tar.gzWarning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'
   
* installing *source* packagepkgmaker...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Setting package specific options: package:pkgmaker:logger (1 default option(s))
Creating meta registry in package 'pkgmaker' ... OK
Creating registry 'extra_handler' in package 'pkgmaker' ... OK
Creating registry 'extra_action' in package 'pkgmaker' ... OK
Registering extra handler 'install.packages' [function] ... OK
** help
*** installing help indices
** 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 (pkgmaker)
✓  checking for file/private/var/folders/3t/lc9m5zv966934dq4d6gf6l60g_dj6h/T/Rtmp1OVDRI/remotes85b02152fc04/renozao-xbioc-b4f512c/DESCRIPTION...preparingxbioc:checking DESCRIPTION meta-information ...checking for LF line-endings in source and make files and shell scriptschecking for empty or unneeded directorieslooking to see if adata/datalistfile should be addedbuildingxbioc_0.1.18.tar.gzWarning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'
   
* installing *source* packagexbioc...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: (converted from warning) packageS4Vectorswas built under R version 3.6.3
Execution halted
ERROR: lazy loading failed for packagexbioc* removing/Library/Frameworks/R.framework/Versions/3.6/Resources/library/xbiocError: Failed to install 'xbioc' from GitHub:
  (converted from warning) installation of package/var/folders/3t/lc9m5zv966934dq4d6gf6l60g_dj6h/T//Rtmp1OVDRI/file85b0807a8d7/xbioc_0.1.18.tar.gzhad non-zero exit status

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giovp avatar giovp commented on June 14, 2024

You said I should revert to 3.5 and then move back again to 3.6.2?
@xuranw is there a way to install on 3.6.2? I am also happy to update to 4.0 if it helps

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tjbutler003 avatar tjbutler003 commented on June 14, 2024

I tried a reinstall of everything a few months ago, which might have been 3.6.0, and was unable to get that to work. I think I went back to 3.5.3 at that time, and did not have a problem with installing 'xbioc'. Then when I got a new computer, IT did an automatic install of R at that time which looks like it was 3.6.2, and I did the install of bioconductor packages as the default. Since that new change, it seems to be working.

Maybe try installing xbioc, but choose option 3 for update 'none' and see if it can install a less recent version? Or message renozao to see what issues there are with installing xbioc? I do think xbioc was necessary for running MuSiC, and seemed to really trip me up last time.

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GuoYu-Peng avatar GuoYu-Peng commented on June 14, 2024

Can't install but different problem.

Downloading GitHub repo xuranw/MuSiC@master  
xuranw-MuSiC-01e51ba/vignettes/benchmark.jpeg: truncated gzip input  
tar.exe: Error exit delayed from previous errors.  
Error: Failed to install 'MuSiC' from GitHub:  
  Does not appear to be an R package (no DESCRIPTION)  
In addition: Warning messages:  
1: In utils::untar(tarfile, ...) :  
  ‘tar.exe -xf "C:\Users\m\AppData\Local\Temp\Rtmpq8g5YY\file16c860152486.tar.gz" -C  
 "C:/Users/m/AppData/Local/Temp/Rtmpq8g5YY/remotes16c83f8c2845"’ returned error code 1  
2: In system(cmd, intern = TRUE) :  
  running command 'tar.exe -tf  
 "C:\Users\m\AppData\Local\Temp\Rtmpq8g5YY\file16c860152486.tar.gz"' had status 1```

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liu-ying-jun avatar liu-ying-jun commented on June 14, 2024

You could try to first install "xbioc" separately, then install "MuSiC". I just succeeded installing "MuSiC" on R 4.0 with this approach. To install "xbioc", try this code:
devtools::install_github("renozao/xbioc")

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giovp avatar giovp commented on June 14, 2024

I also managed with R 4.0, thank you!

@MatthewP-Newbee try upgrading to 4.0

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giovp avatar giovp commented on June 14, 2024

Closing this, @xuranw maybe good to make this explicit in the installation info of the REAME file?

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