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DEXSeq Installation Error

I am trying to install DEXSeq on R version 3.6.1 but I am getting the following error:

ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’.

* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’
ERROR: dependencies ‘DESeq2’, ‘biomaRt’, ‘geneplotter’, ‘genefilter’ are not available for package ‘DEXSeq’
* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/DEXSeq’

The downloaded source packages are in
    ‘/tmp/RtmpJ2hksP/downloaded_packages’

Installation path not writeable, unable to update packages: boot, cluster,
  foreign, KernSmooth, MASS, Matrix, nlme, rpart, survival

Warning messages:
1: In install.packages(...) :
  installation of package ‘XML’ had non-zero exit status

2: In install.packages(...) :
  installation of package ‘openssl’ had non-zero exit status

3: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status

4: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status

5: In install.packages(...) :
  installation of package ‘biomaRt’ had non-zero exit status

6: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status

7: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status

8: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

9: In install.packages(...) :
  installation of package ‘DEXSeq’ had non-zero exit status

Will I have to install these dependencies one by one? If not then what can be done? Thanks in advance.

dexseq rna-seq alternative splicing
• 3,315 views • link
updated by Biostar Biostar • written by deepak18 • deepak18

It's just the xml package that can't find a dependency. You'll have to install something outside of R, but the exact name depends on your operating system.

Alternatively, use conda.

• 0 views • link
written by WouterDeCoster WouterDeCoster

What do I have to install outside of R? My OS is Ubuntu 19.04. After installing Anaconda2 I got this:

`------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl@1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/openssl’

ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/httr’

ERROR: dependency ‘httr’ is not available for package ‘biomaRt’
* removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/biomaRt’

The downloaded source packages are in
    ‘/tmp/Rtmp7ZgPvc/downloaded_packages’

Installation path not writeable, unable to update packages: boot, cluster,
  foreign, KernSmooth, MASS, Matrix, nlme, rpart, survival

Warning messages:
1: In install.packages(...) :
  installation of package ‘openssl’ had non-zero exit status

2: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status

3: In install.packages(...) :
  installation of package ‘biomaRt’ had non-zero exit status
`
• 0 views • link
written by deepak18 • deepak18

Can you please format your post with the code option 10101? It is visually not appealing. I already did that for the toplevel question. Also, use Add Reply or add that info to the question. The answer field is intended for answers only to keep everything organized.

• 0 views • link
written by ATpoint ATpoint

1 answer

In the current error message (please read it carefully) the cause of the problem comes from the openssl package:

Configuration failed because openssl was not found. Try installing: deb: libssl-dev (Debian, Ubuntu, etc)

You need libssl-dev, because you are on Ubuntu. You can install it with sudo apt install libssl-dev

• 0 views • link
written by WouterDeCoster WouterDeCoster

Yes installing libssl-dev worked. Thanks.

• 0 views • link
written by deepak18 • deepak18

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