fgsea not downloading due to new r version. Is there a way around this?
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amir.khan • 0
@3bc9e0e8
Last seen 3 months ago
United Kingdom

Running into an error of not being able to install or run fgsea in R Version 1.4.1106.

# library(fgsea)
Error: package or namespace load failed for ‘fgsea’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘fastmatch’
In addition: Warning message:
package ‘fgsea’ was built under R version 4.1.1
#install.packages("fgsea", repos="http://cran.rstudio.com/", dependencies=TRUE)
Warning in install.packages :
  package ‘fgsea’ is not available for this version of R 
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

Is there a way around this??

sessionInfo( )
r fgsea • 362 views
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ATpoint ★ 1.2k
@atpoint-13662
Last seen 9 hours ago
Germany

fgsea is a Bioconductor and not a CRAN package. Use:

BiocManager::install("fgsea")

...and not install.packages().

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Seems to have done the trick and worked. thanks!

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@james-w-macdonald-5106
Last seen 6 hours ago
United States

That's probably just a blip in your connection or something. The fgsea package is definitely available, so I would just try again. You might also specify a different repo.

> library(fgsea)
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

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

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

other attached packages:
[1] fgsea_1.20.0        BiocManager_1.30.16

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7          magrittr_2.0.1      tidyselect_1.1.1   
 [4] munsell_0.5.0       BiocParallel_1.28.3 lattice_0.20-45    
 [7] colorspace_2.0-2    R6_2.5.1            rlang_0.4.12       
[10] fastmatch_1.1-3     fansi_0.5.0         dplyr_1.0.7        
[13] tools_4.1.2         parallel_4.1.2      grid_4.1.2         
[16] data.table_1.14.2   gtable_0.3.0        utf8_1.2.2         
[19] DBI_1.1.1           ellipsis_0.3.2      assertthat_0.2.1   
[22] tibble_3.1.6        lifecycle_1.0.1     crayon_1.4.2       
[25] Matrix_1.4-0        gridExtra_2.3       purrr_0.3.4        
[28] ggplot2_3.3.5       vctrs_0.3.8         glue_1.5.1         
[31] compiler_4.1.2      pillar_1.6.4        generics_0.1.1     
[34] scales_1.1.1        pkgconfig_2.0.3

Note that fastmatch is also installed.

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