Question: DEXSeq Installation Error
0
gravatar for deepak18
12 months ago by
deepak1810
deepak1810 wrote:

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.

ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 12 months ago by deepak1810

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.

ADD REPLYlink written 12 months ago by WouterDeCoster44k

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
`
ADD REPLYlink modified 12 months ago • written 12 months ago by deepak1810

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.

ADD REPLYlink modified 12 months ago • written 12 months ago by ATpoint40k
1
gravatar for WouterDeCoster
12 months ago by
Belgium
WouterDeCoster44k wrote:

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

ADD COMMENTlink written 12 months ago by WouterDeCoster44k

Yes installing libssl-dev worked. Thanks.

ADD REPLYlink written 12 months ago by deepak1810
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