DEXSeq Installation Error

Question

[deepak18]

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.

[WouterDeCoster]

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.

[deepak18]

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
`

[ATpoint]

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.

Answer 1

[WouterDeCoster]

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

[deepak18]

Yes installing libssl-dev worked. Thanks.