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Is it fine to download all available packages for R?

Hello,

I am trying to download genefu package in R, and constantly got the error that certain dependencies are not available for biomaRt. I was therefore wondering if it is fine to download all available packages for R? If yes, is there a way to download all packages at once or do I have to mention each package one at a time?

TIA :)

r bio-conductor
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updated by lakhujanivijay lakhujanivijay • written by vinayjrao vinayjrao

I think this will take a loooong time and will use up a lot of your hard disk space. I would suggest to install the package you need only.

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written by dago dago

Thanks, but what do I do when it keeps saying that the dependencies are not available?

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written by vinayjrao vinayjrao

1 answer

You can do like this; example installing an arbitrary package called "foo" along with its dependencies:

install.packages("foo", dependencies=TRUE)
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written by lakhujanivijay lakhujanivijay

genefu is a bioconductor package, so I did the following -

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

The error I got was -

checking for xml2-config... no

Cannot find xml2-config

ERROR: configuration failed for package ‘XML’ * removing ‘/home/vinay/R/x86_64-pc-linux-gnu-library/3.4/XML’ * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked

checking for curl-config... no

Cannot find curl-config

ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/vinay/R/x86_64-pc-linux-gnu-library/3.4/RCurl’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’ *removing ‘/home/vinay/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’ ERROR: dependency ‘biomaRt’ is not available for package ‘genefu’ * removing ‘/home/vinay/R/x86_64-pc-linux-gnu-library/3.4/genefu’

The downloaded source packages are in ‘/tmp/RtmpLcsZFf/downloaded_packages’ installation path not writeable, unable to update packages: foreign, spatial Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RCurl’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘biomaRt’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘genefu’ had non-zero exit status

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written by vinayjrao vinayjrao

share session information by running:

> sessionInfo()
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written by lakhujanivijay lakhujanivijay

The problem is with xml2-config. Check this Also there are many dependencies. Do biocLite() and update, then try one more time.

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written by venu venu

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