Closed giovp closed 4 years ago
tjbutler003
commented
4 years ago @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.
giovp
commented
4 years ago 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@develop
✓ checking for file ‘/private/var/folders/3t/lc9m5zv966934dq4d6gf6l60g_dj6h/T/Rtmp1OVDRI/remotes85b01bf24d5a/renozao-pkgmaker-ac95c24/DESCRIPTION’ ...
─ preparing ‘pkgmaker’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory ‘pkgmaker/vignettes’
─ building ‘pkgmaker_0.31.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘pkgmaker’ ...
** 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’ ...
─ preparing ‘xbioc’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘xbioc_0.1.18.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘xbioc’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package ‘S4Vectors’ was built under R version 3.6.3
Execution halted
ERROR: lazy loading failed for package ‘xbioc’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/xbioc’
Error: 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.gz’ had non-zero exit statusYou 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
tjbutler003
commented
4 years ago 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.
dodoflyy
commented
4 years ago 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```
liu-ying-jun
commented
4 years ago 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")
giovp
commented
4 years ago I also managed with R 4.0, thank you!
@MatthewP-Newbee try upgrading to 4.0
giovp
commented
4 years ago Closing this, @xuranw maybe good to make this explicit in the installation info of the REAME file?
Hi,
I can't install the package. Error: