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bs14ab
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@bs14ab-23532
Last seen 4.3 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* 2 packages out-of-date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2 packages out-of-date; 0 packages too new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
I have updated to R 4.0.2 which i thought fixed it but now the error is:
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
Can you go and delete any 00LOCK that are present and try again.