Install package phyloseq
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Entering edit mode
layeb • 0
@layeb-15273
Last seen 4.4 years ago

Hi,

When trying to install phyloseq from :

source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")

I have got the following error :

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.4; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
> biocLite("phyloseq")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘phyloseq’
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/macosx/el-capitan/contrib/3.4:
  impossible d'ouvrir l'URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/annotation/bin/macosx/el-capitan/contrib/3.4:
  impossible d'ouvrir l'URL 'https://bioconductor.org/packages/3.4/data/annotation/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/macosx/el-capitan/contrib/3.4:
  impossible d'ouvrir l'URL 'https://bioconductor.org/packages/3.4/data/experiment/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/macosx/el-capitan/contrib/3.4:
  impossible d'ouvrir l'URL 'https://bioconductor.org/packages/3.4/extra/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
installing the source package ‘phyloseq’

essai de l'URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/phyloseq_1.19.1.tar.gz'
Content type 'application/x-gzip' length 3291400 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Error : Functions found when exporting methods from the namespace ‘S4Vectors’ which are not S4 generic: ‘sd’, ‘t’, ‘var’
ERROR: lazy loading failed for package ‘phyloseq’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/phyloseq’

The downloaded source packages are in
    ‘/private/var/folders/fs/vn6w_t8j1nj46ptf0k2gs2cw0000gn/T/Rtmp2BuXQ1/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘phyloseq’ had non-zero exit status
>

Could you help me with this ?

Many thanks in advance!

 

Leïla

installation phyloseq • 896 views
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0
Entering edit mode
@martin-morgan-1513
Last seen 1 day ago
United States

This error

** preparing package for lazy loading
Error : Functions found when exporting methods from the namespace ‘S4Vectors’ which are not S4 generic: ‘sd’, ‘t’, ‘var’

suggests that you have an installation that mixes Bioonductor versions. Try running

BiocInstaller::biocValid()

to confirm that your packages are all installed from the same version.

 

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