Question: Cannot install DESeq2
0
gravatar for mhz
10 weeks ago by
mhz0
United States
mhz0 wrote:

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 • 124 views
ADD COMMENTlink modified 10 weeks ago by Mike Smith3.3k • written 10 weeks ago by mhz0
Answer: Cannot install DESeq2
1
gravatar for Mike Smith
10 weeks ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k wrote:

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 COMMENTlink written 10 weeks ago by Mike Smith3.3k

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 REPLYlink written 10 weeks ago by mhz0

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

ADD REPLYlink written 10 weeks ago by Mike Smith3.3k

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 REPLYlink written 10 weeks ago by mhz0
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