can't install cummeRbund
Hello!
I try to install cummerbund. Ubuntu 18.04, R 3.6.3, Bioconductor version 3.10 (BiocManager 1.30.10) using this page https://www.bioconductor.org/packages/3.10/bioc/html/cummeRbund.html for help. But it has errors:
ERROR: configuration failed for package ‘XML’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/XML’
ERROR: dependency ‘XML’ is not available for package ‘biomaRt’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/biomaRt’
ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/GenomicFeatures’
ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/BSgenome’
ERROR: dependencies ‘rtracklayer’, ‘BSgenome’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/VariantAnnotation’
ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘ensembldb’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/ensembldb’
ERROR: dependencies ‘Hmisc’, ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/cummeRbund’
The downloaded source packages are in
‘/tmp/RtmpWkh5H9/downloaded_packages’
What i do wrong and what should i do to install it? thank you for your help.
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ERROR: configuration failed for package ‘XML’Seems that this package couldn't be installed. Try to install it and to pay attention to the error log. You will probably be missing some ubuntu libraries. When you detect the missing library, then google the name and see how to install it (almost sure you can do it with
apt get install)Thanks, i installed xml. Now trying install cummerbund i see that: ERROR: dependency ‘foreign’ is not available for package ‘Hmisc’ * removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/Hmisc’ ERROR: dependency ‘Hmisc’ is not available for package ‘biovizBase’ * removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/biovizBase’ ERROR: dependency ‘biovizBase’ is not available for package ‘Gviz’ * removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/Gviz’ ERROR: dependency ‘Gviz’ is not available for package ‘cummeRbund’ * removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/3.6/cummeRbund’
I understand that it asks to install foreign, but package ‘foreign’ is not available (for R version 3.6.3 RC)
i tried to update r like here https://unix.stackexchange.com/questions/538915/installing-updating-r-3-6-on-ubuntu-18-04
sudo apt update sudo apt-get install r-base-dev but still R --version R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Then i type apt-cache policy r-base and see
r-base: Installed: r-base: Installed: 4.0.3-1.1804.0 Candidate: 4.0.3-1.1804.0
but -- version still 3.6.3
See this post. Then you can try to reinstall the problematic packages.