Unable to download R package
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Entering edit mode
5 months ago
Kira • 0

I've changed a new laptop and wanted to download a package name 'TCGAbiolinks' back again, but it keeps on showing

   Error in loadNamespace(name) : there is no package called ‘BiocManager’

There is a BiocManager package, it shows

   The downloaded source packages are in
‘C:\Users\User\AppData\Local\Temp\Rtmp8SLPIg\downloaded_packages’

but I can't load the package using

   library('BiocManager')

Can somebody please help me? Thank you

BiocManager • 439 views
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Entering edit mode
5 months ago
GenoMax 108k

Use directions in this answer to install BiocManager : BiocLite installation issues in R version 4.0.5

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   if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
 BiocManager::install(version = "3.12")

I've tried this a dozen times, still the same problem, the whole thing shows like this:

 Installing package into ‘C:/Users/User/Documents/R/win-library/4.0’
 (as ‘lib’ is unspecified)

 There is a binary version available but the source version is later:
         binary  source needs_compilation
 BiocManager 1.30.12 1.30.15             FALSE

 installing the source package ‘BiocManager’

 trying URL 'https://cran.rstudio.com/src/contrib/BiocManager_1.30.15.tar.gz'
 Content type 'application/x-gzip' length 262210 bytes (256 KB)
 downloaded 256 KB

usage: gdc-client.exe [-h] [--version] {download,upload,settings} ...

The Genomic Data Commons Command Line Client

optional arguments:
 -h, --help            show this help message and exit
--version             show program's version number and exit

commands:
{download,upload,settings}
                    for more information, specify -h after a command
download            download data from the GDC
upload              upload data to the GDC
settings            display default settings

gdc-client error: argument command: invalid choice: '/c' (choose from 'download', 'upload', 'settings')
Warning in install.packages :
installation of package ‘BiocManager’ had non-zero exit status

 The downloaded source packages are in
‘C:\Users\User\AppData\Local\Temp\RtmpasGEa5\downloaded_packages’
 > BiocManager::install(version = "3.12")
  Error in loadNamespace(name) : there is no package called ‘BiocManager’
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Entering edit mode

This does not appear to be a problem with BiocManager now. Why are you getting an error about gdc-client? Is that what you are trying to use/install?

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Erm........, so how can I solve this gdc-client error?

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Thank you very much for your help, problem solved. I deleted gdc-client .exe and download TCGAbiolinks again, it works XD !!

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