Question

Permanent error in installing GenomeInfoDb

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AZ ▴ 30

@fereshteh-15803

Last seen 20 months ago

United Kingdom

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             
>

GenomeInfoDb • 1.7k views

ADD COMMENT • link 3.1 years ago AZ ▴ 30

score 0 · Answer 1 · 2021-11-19

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 minutes ago

United States

There's two problems here. First, you are using an old version of R, and second, you are installing from the wrong place (you are trying to install a devel version of GenomeInfoDb into a version of R that shouldn't be running a devel version of anything). You need to upgrade to R-4.1.2 and the current release of Bioconductor and then do

library(BiocManager)
BiocManager::install("GenomeInfoDb")

ADD COMMENT • link 3.1 years ago James W. MacDonald 67k

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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   
>

ADD REPLY • link 3.1 years ago AZ ▴ 30

score 0 · Answer 2 · 2021-11-19

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shepherl 4.1k

@lshep

Last seen 35 minutes ago

United States

See also response on duplicated on github: https://github.com/Bioconductor/GenomeInfoDb/issues/33

ADD COMMENT • link 3.1 years ago shepherl 4.1k