BiocLite installation issues
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@patricia_slattery-24111
Last seen 12 months ago
Flinders University

Hello, I'm very much a novice when it comes to R and I have never used BiocManager and am having some issues installing some things. I've been given a script to use for some filtering and one of the steps requires me to install BiocLite (see first command). As you can see by the error it's telling me that BiocLite is not available for the version of R I'm currently using. I've tried using R 3.6.2, R 4.0.0 and R 4.0.2 and a couple of the newer versions of Bioconductor but all of them give me the same error (with different versions obviously). The error message and command, as well as session info, are pasted below.

Thank you

> BiocManager::install("http://bioconductor.org/biocLite.R")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'http://bioconductor.org/biocLite.R'
Installation path not writeable, unable to update packages: boot, class,
  foreign, KernSmooth, MASS, mgcv, nlme, nnet, spatial, survival
Warning message:
package ‘http://bioconductor.org/biocLite.R’ is not available (for R version 4.0.0) 

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

loaded via a namespace (and not attached):
 [1] crayon_1.3.4        dplyr_1.0.2         R6_2.4.1           
 [4] radiator_1.1.7      lifecycle_0.2.0     magrittr_1.5       
 [7] pillar_1.4.6        rlang_0.4.7         rstudioapi_0.11    
[10] vctrs_0.3.4         generics_0.0.2      ellipsis_0.3.1     
[13] tools_4.0.0         glue_1.4.2          purrr_0.3.4        
[16] tinytex_0.25        xfun_0.16           compiler_4.0.0     
[19] pkgconfig_2.0.3     BiocManager_1.30.10 tidyselect_1.1.0   
[22] tibble_3.0.3
BiocLite • 1.4k views
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@kevin
Last seen 11 hours ago
Republic of Ireland

Hey Patricia,

If you are following a tutorial or course whereby you are instructed to install anything via Bioclite, then the material is outdated / obsolete and needs updating.

To install any package, you can first install BiocManager via (you already seem to have this installed):

install.packages('BiocManager')

Then, you can install any other package via:

BiocManager::install('limma')
BiocManager::install('ggplot2')

To simply update all current installed Bioconductor packages, try:

BiocManager::install()

Trust that this helps.

Kevin

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Very much so, thank you!

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