Install R package fgsea: Error in download.file
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6 weeks ago
yueli7 ▴ 210

IHello,

I want to install R package. Every time it comes out: "Error in download.file(url, destfile, method, mode = "wb", ...) ". I have no idea of that.

Any suggestion?

Thanks in advance for any help!

Best,

Yue

> BiocManager::install("fgsea")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.6 (BiocManager 1.30.15), R 3.4.4 (2018-03-15)
Installing package(s) 'BiocVersion', 'fgsea'
also installing the dependencies ‘formatR’, ‘lambda.r’, ‘futile.options’, ‘futile.logger’, ‘snow’, ‘BiocParallel’

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  参数没有用(checkBuilt = FALSE)

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8    
 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8    LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.15 compiler_3.4.4      tools_3.4.4  
bioconductor R package fgsea • 348 views
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You posted the same question 4 times!! please remove the other questions if they contain the same information.
install R package
install R package
install R package

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5 weeks ago
yueli7 ▴ 210
sudo gedit /etc/apt/sources.list

change all the codename to "focal" which corresponding to Ubuntu 20.04.1 codename.

sudo apt-get update
sudo apt-get upgrade
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5 weeks ago
simplitia ▴ 50

you could also just look through the archive for the version that supports your R version. From there you can download and compile locally and install. this would work but its tedious since it does not install all the dependencies.

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