Installing Ggbio

Question

[simonconti]

bioconductor used to install ggbio without issue. It seems as though since the installation of R 3.0.0 this no longer works. It gives the following error messages.

** preparing package for lazy loading
Error : package 'bitops' was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package 'Rsamtools'
* removing '..........x86_64-pc-linux-gnu-library/3.0/Rsamtools'
ERROR: dependency 'RSQLite' is not available for package 'AnnotationDbi'
* removing '...........x86_64-pc-linux-gnu-library/3.0/AnnotationDbi'
ERROR: dependency 'RCurl' is not available for package 'biomaRt'
* removing '...........x86_64-pc-linux-gnu-library/3.0/biomaRt'
ERROR: dependency 'munsell' is not available for package 'scales'
* removing '...........x86_64-pc-linux-gnu-library/3.0/scales'
ERROR: dependencies 'RCurl', 'Rsamtools' are not available for package 'rtracklayer'
* removing '............x86_64-pc-linux-gnu-library/3.0/rtracklayer'
ERROR: dependency 'scales' is not available for package 'ggplot2'
* removing '..............x86_64-pc-linux-gnu-library/3.0/ggplot2'
ERROR: dependencies 'AnnotationDbi', 'RSQLite', 'rtracklayer', 'biomaRt', 'RCurl' are not available for package 'GenomicFeatures'
* removing '............x86_64-pc-linux-gnu-library/3.0/GenomicFeatures'
ERROR: dependencies 'scales', 'Rsamtools', 'GenomicFeatures' are not available for package 'biovizBase'
* removing '..............x86_64-pc-linux-gnu-library/3.0/biovizBase'
ERROR: dependencies 'Rsamtools', 'AnnotationDbi', 'GenomicFeatures' are not available for package 'VariantAnnotation'
* removing '..............x86_64-pc-linux-gnu-library/3.0/VariantAnnotation'
ERROR: dependencies 'ggplot2', 'biovizBase', 'GenomicFeatures', 'Rsamtools', 'scales', 'VariantAnnotation', 'rtracklayer' are not available for package 'ggbio'
* removing '...............x86_64-pc-linux-gnu-library/3.0/ggbio'

The downloaded source packages are in
    '/tmp/RtmphFekSZ/downloaded_packages'
There were 14 warnings (use warnings() to see them)

Thanks!

Answer 1

[Sean Davis]

It looks like you have a mix of packages built for different R versions and have some packages that do not have their dependencies installed correctly. I have seen this when folks have tried to install a new version of R without reinstalling all packages or have been installing packages "by hand" rather than using biocLite(). I would encourage you to use biocLite() as suggested on the Bioconductor website. You may want to start over from scratch (remove your R packages and reinstall).

[Alastair Kerr]

I agree it looks like a package version problem. Before reinstalling however make sure to use the argument "checkbuild=T" when upgrading your packages.

Answer 2

[simonconti]

I have been using biocLite to install these packages. It is my university's public server actually...so every time I log in i'm starting from scratch and have to reinstall ggbio, BSgenome, methylkit...etc..

[Steve Lianoglou]

This should have been a comment to Sean Davis's answer, not your own answer. There seems to be a lot of things wrong with your install -- but you can see that it starts with the "bitops" package, as you are loading one that was built on a version of R that is lower than 3.0. Reinstall that package, load it, and see if it works .. .then continue from there.