SomaticSignatures for Bioconductor 3.6 (R 3.4.3) depends on NMF, which is not available for R 3.4.3
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samuel.fux • 0
@samuelfux-15169
Last seen 6.1 years ago

Bioconductor 3.6 requires R 3.4.3

SomaticSignatures depends on NMF from CRAN

CRAN removed NMF from their repository, therefore it is not available for R 3.4.3, which makes it impossible to install SomaticSignatures for Bioconductor 3.6

> biocLite("SomaticSignatures")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘SomaticSignatures’
Warning: dependency ‘NMF’ is not available
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/SomaticSignatures_2.14.0.tar.gz'
Content type 'application/x-gzip' length 1938379 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

ERROR: dependency ‘NMF’ is not available for package ‘SomaticSignatures’
* removing ‘/cluster/apps/bioconductor/3.6/x86_64/lib64/R/library/SomaticSignatures’

The downloaded source packages are in
        ‘/tmp/RtmpzU4brW/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SomaticSignatures’ had non-zero exit status

 

> install.packages("NMF")

Warning message:

package ‘NMF’ is not available (for R version 3.4.3)

NMF somaticsignatures R 3.4.3 • 1.0k views
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Entering edit mode
shepherl 3.8k
@lshep
Last seen 14 hours ago
United States

It looks like NMF became available on CRAN today.  Please try again.  

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