Question

EBImage installation problem

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fabianalanadearaujo • 0

@233f9530

Last seen 2.5 years ago

Brazil

I'm trying to install EBImage package from Bioconductor but...

## I'm having one problem... and received this error code

 installing *source* package ‘EBImage’ ...
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘EBImage’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/EBImage’

The downloaded source packages are in
    ‘/private/var/folders/rd/n0jsjlrn7lx_1kvd5t_tpffh0000gn/T/RtmpHWIYla/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘EBImage’ had non-zero exit status

What can I do to solve this problem?

BiocManager • 1.9k views

ADD COMMENT • link updated 2.5 years ago by Vincent J. Carey, Jr. 6.7k • written 2.5 years ago by fabianalanadearaujo • 0

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This post suggest you may need to install xcode https://stackoverflow.com/questions/52522565/git-is-not-working-after-macos-update-xcrun-error-invalid-active-developer-pa

ADD REPLY • link 2.5 years ago shepherl 4.1k

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I installed Xcode and the new error message is:

Bioconductor version 3.16 (BiocManager 1.30.17), R 4.2.0 (2022-04-22)
Installing package(s) 'EBImage'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: ‘EBImage’
Do you want to attempt to install these from sources? (Yes/no/cancel) library(EBImage)
Error in askYesNo("Do you want to attempt to install these from sources?") : 
  Unrecognized response “library(EBImage)”

I don't know what I need to do to solve this problem

ADD REPLY • link updated 2.5 years ago by shepherl 4.1k • written 2.5 years ago by fabianalanadearaujo • 0

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Bioconductor does not support the Apple M1 (a.k.a. arm64) architecture in native mode yet. Some information on this similar post: problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0 This is also indicated on the release announcement https://bioconductor.org/news/bioc_3_15_release/ .

ADD REPLY • link 2.5 years ago shepherl 4.1k

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You could try saying yes to install from source but no guarantees

ADD REPLY • link 2.5 years ago shepherl 4.1k

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You didn't answer "yes" to the "Do you want to attempt to install..." -- instead, the response given is "library(EBImage)" -- please look closely and try again.

ADD REPLY • link 2.5 years ago Vincent J. Carey, Jr. 6.7k