Question

Cant update old packages

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Entering edit mode

bs14ab • 0

@bs14ab-23532

Last seen 4.4 years ago

Hi, I keep trying to update my Bioconductor in R studio, on Windows 10 and It won't update old packages. I have tried running RStudio as an administrator, and think that I have edited the permissions to use the R folder for full control (but not completely sure if this is correct). Please see my error code below and Session info.

> BiocManager::install()
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1
  (2020-06-06)
Old packages: 'backports', 'rlang'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source
  versions are later:
          binary source needs_compilation
backports  1.1.7  1.1.8              TRUE
rlang      0.4.6  0.4.7              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.1.7.zip'
Content type 'application/zip' length 81641 bytes (79 KB)
downloaded 79 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_0.4.6.zip'
Content type 'application/zip' length 1117248 bytes (1.1 MB)
downloaded 1.1 MB

package ‘backports’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\abbie\AppData\Local\Temp\Rtmpg7ESQ3\downloaded_packages
> BiocManager::valid()

* sessionInfo()

R version 4.0.1 (2020-06-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.1      tools_4.0.1        
[4] yaml_2.2.1          tinytex_0.24        xfun_0.15          

Bioconductor version '3.11'

  * 2 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "backports", "rlang"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
2 packages out-of-date; 0 packages too new 

> sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.1      tools_4.0.1        
[4] yaml_2.2.1          tinytex_0.24        xfun_0.15

software error packages update • 1.6k views

ADD COMMENT • link updated 4.4 years ago by James W. MacDonald 67k • written 4.4 years ago by bs14ab • 0

0

Entering edit mode

I have updated to R 4.0.2 which i thought fixed it but now the error is:

Warning messages:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying D:\Program Files\R-4.0.2\library\00LOCK\bit64\libs\x64\bit64.dll to D:\Program Files\R-4.0.2\library\bit64\libs\x64\bit64.dll: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying D:\Program Files\R-4.0.2\library\00LOCK\rlang\libs\x64\rlang.dll to D:\Program Files\R-4.0.2\library\rlang\libs\x64\rlang.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying D:\Program Files\R-4.0.2\library\00LOCK\vctrs\libs\x64\vctrs.dll to D:\Program Files\R-4.0.2\library\vctrs\libs\x64\vctrs.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying D:\Program Files\R-4.0.2\library\00LOCK\bit64\libs\x64\bit64.dll to D:\Program Files\R-4.0.2\library\bit64\libs\x64\bit64.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying D:\Program Files\R-4.0.2\library\00LOCK\rlang\libs\x64\rlang.dll to D:\Program Files\R-4.0.2\library\rlang\libs\x64\rlang.dll: Permission denied
6: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying D:\Program Files\R-4.0.2\library\00LOCK\vctrs\libs\x64\vctrs.dll to D:\Program Files\R-4.0.2\library\vctrs\libs\x64\vctrs.dll: Permission denied

I have been through many stack overflow posts and other forums to change my permissions, but it still isnt working. Sorry if it is obvious but I am still new to bioconductor and learning! Also now have windows as opposed to a Mac.

Thanks

ADD REPLY • link updated 4.4 years ago by shepherl 4.1k • written 4.4 years ago by bs14ab • 0

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Entering edit mode

Can you go and delete any 00LOCK that are present and try again.

ADD REPLY • link 4.4 years ago shepherl 4.1k