Question

Cannot install DESeq2

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mhz • 0

@mhz-7526

Last seen 5.8 years ago

United States

Hi, I have a problem with installing DESeq2. The R version is 3.2.3. I got errors as below.

Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/home/mhz/R/x8664-pc-linux-gnu-library/3.2/XML’ ERROR: dependency ‘XML’ is not available for package ‘annotate’ * removing ‘/home/mhz/R/x8664-pc-linux-gnu-library/3.2/annotate’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/home/mhz/R/x8664-pc-linux-gnu-library/3.2/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’ * removing ‘/home/mhz/R/x8664-pc-linux-gnu-library/3.2/geneplotter’ ERROR: dependencies ‘RcppArmadillo’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’ * removing ‘/home/mhz/R/x86_64-pc-linux-gnu-library/3.2/DESeq2’

The downloaded source packages are in ‘/tmp/RtmpGFjut1/downloaded_packages’ Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'rpart', 'survival' Update all/some/none? [a/s/n]: n 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 ‘annotate’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘genefilter’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘geneplotter’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DESeq2’ had non-zero exit status

I actually also tried to install DESeq2 under a R version 3.5.0, using the code on Bioconductor DESeq2 page. However, I got the same errors. When I tried to install DESeq2 on a laptop with R version 3.3.3, it worked. I am very confused. Could anyone advise?

Thanks a lot!!

deseq2 • 2.7k views

ADD COMMENT • link updated 5.8 years ago by Mike Smith ★ 6.6k • written 5.8 years ago by mhz • 0

score 1 · Answer 1 · 2019-02-05

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Mike Smith ★ 6.6k

@mike-smith

Last seen 10 hours ago

EMBL Heidelberg

You need to install the xml2 system library. If you're running Ubuntu you can do this by entering the following in a command line terminal:

sudo apt-get install libxml2-dev

and for Redhat / CentOS it's something like:

sudo yum install libxml2-devel.

Since this is a system library it will affect both R-3.2.3 and R-3.5.0. I'd recommend using the most up-to-date version of R you can, otherwise you'll also be using a very out dated version of DESeq2 since Bioconductor releases are tied to specific versions of R.

ADD COMMENT • link 5.8 years ago Mike Smith ★ 6.6k

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Thank you so much! The XML was fixed. However, I still got an error said 'RcppArmadillo' is not available.

    Warning: replacing previous import by ‘RSQLite::Id’ when loading ‘AnnotationDbi’
* DONE (geneplotter)
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’

I tried to install it but could not. I searched and used install.packages. Do I need to install in another way?

Thanks again!

ADD REPLY • link 5.8 years ago mhz • 0

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You'll need to show us the output from install.packages('RcppArmadillo'), otherwise it's impossible to diagnose what has failed.

ADD REPLY • link 5.8 years ago Mike Smith ★ 6.6k

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Thanks for responding again!

The output is:

    > install.packages("RcppArmadillo")
Installing package into ‘/home/mhz/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning message:
package ‘RcppArmadillo’ is not available (for R version 3.2.3)

I found the RcppArmadillo requires R 3.3.0 and above. I will try to upgrade and see if it works.

Thanks again!

ADD REPLY • link 5.8 years ago mhz • 0