Bioconductor installation error
1
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Entering edit mode
Cody ▴ 10
@1121d46e
Last seen 23 months ago
United States

Just installed R version 4.2 on my MacBook Pro M1 and trying to install Bioconductor. Used the basic command as suggested

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")


# error message is as follows: 
There is a binary version available but the source version
  is later:

installing the source package ‘BiocManager’

trying URL 'https://cran.rstudio.com/src/contrib/BiocManager_1.30.17.tar.gz'
Content type 'application/x-gzip' length 287948 bytes (281 KB)
==================================================
downloaded 281 KB

* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘BiocManager’:
 .onAttach failed in attachNamespace() for 'BiocManager', details:
  call: if (is.na(version)) version <- .VERSION_UNKNOWN
  error: argument is of length zero
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocManager’
Warning in install.packages :
  installation of package ‘BiocManager’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/_j/kkz0_r715b74r1fj1fl35c440000gn/T/Rtmp2qO20T/downloaded_packages’

#Please advise! (Sorry for having such a basic issue but I cannot figure it out just from google searching...)
Install • 1.2k views
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Entering edit mode

Had exactly the same issue here, in both Mac and Windows

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Same here, but I wonder if it is due to using highSierra Mac? I have most recent R, but for HIghSierra not Monterey ... I think these are different versions, and Bioconductor may only work with R 4.2 running later Mac systems?

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shepherl 3.8k
@lshep
Last seen 19 minutes ago
United States

There is an open issue on BiocManager but we think this is intermittent from updating configuration files for the release today. https://github.com/Bioconductor/BiocManager/issues/131
It should resolve shortly.

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