Getting error in installing GenomeInfoDb

[beginner984]

Hello

I am not able to install GenomeInfoDb

Can you help me please?

> remotes::install_github("Bioconductor/GenomeInfoDb")
Downloading GitHub repo Bioconductor/GenomeInfoDb@HEAD
✓  checking for file ‘/tmp/Rtmp4he3Nm/remotese273c245ce2/Bioconductor-GenomeInfoDb-d4604b1/DESCRIPTION’ ...
─  preparing ‘GenomeInfoDb’:
  ✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘GenomeInfoDb_1.31.1.tar.gz’

Installing package into ‘/opt/R/4.0.5/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘GenomeInfoDb’ ...
mv: cannot move '/opt/R/4.0.5/lib/R/site-library/GenomeInfoDb' to '/opt/R/4.0.5/lib/R/site-library/00LOCK-GenomeInfoDb/GenomeInfoDb': Permission denied
ERROR: cannot remove earlier installation, is it in use?
  * removing ‘/opt/R/4.0.5/lib/R/site-library/GenomeInfoDb’
Warning message:
  In i.p(...) :
  installation of package ‘/tmp/Rtmp4he3Nm/filee27222dfe53/GenomeInfoDb_1.31.1.tar.gz’ had non-zero exit status
> 

> version
_                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          0.5                         
year           2021                        
month          03                          
day            31                          
svn rev        80133                       
language       R                           
version.string R version 4.0.5 (2021-03-31)
nickname       Shake and Throw             
> 

[hpages]

Hi,

1. Always use BiocManager::install() which is the only safe way to install Bioconductor packages. In particular you should never install Bioconductor packages from GitHub.
2. You're using R 4.0.5. You need to use the latest R version (4.1.2) to use the latest version of Bioconductor (3.14).
3. Always use R and install packages from your regular user account.

H.

[hpages]

And also:

4. Always show your sessionInfo().

Thanks, H.

[beginner984]

Thank you

I failed to install that

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.16

loaded via a namespace (and not attached):
 [1] ps_1.6.0          prettyunits_1.1.1 crayon_1.4.2      withr_2.4.2       rprojroot_2.0.2  
 [6] R6_2.5.1          cli_3.1.0         curl_4.3.2        remotes_2.4.1     rstudioapi_0.13  
[11] callr_3.7.0       tools_4.1.2       compiler_4.1.2    processx_3.5.2    pkgbuild_1.2.0   
> 

[hpages]

I failed to install that

It's not clear to me what "that" is. Can you clarify what you failed to install, how you tried to install it, and what error message you got?

You've apparently managed to switch to the current version of R (4.1.2) and to install BiocManager but have you tried to install GenomeInfoDb again with BiocManager::install("GenomeInfoDb")?

Please don't assume that people will spend time trying to guess what you've been doing.