DESeq2 installation error
1
0
Entering edit mode
2.5 years ago
Forough ▴ 10

Hello, I am trying to install DESeq2 package but repeatedly I face different errors. In my last try I entered bellow command:

BiocManager::install("DESeq2")

it was the output:

ERROR: configuration failed for package ‘openssl’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/openssl’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/httr’
ERROR: dependency ‘httr’ is not available for package ‘KEGGREST’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/KEGGREST’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/AnnotationDbi’
ERROR: dependencies ‘AnnotationDbi’, ‘httr’ are not available for package ‘annotate’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/annotate’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/genefilter’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/genetics/R/x86_64-pc-linux-gnu-library/4.2/DESeq2’

The downloaded source packages are in
‘/tmp/RtmpPetVxO/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
MASS, spatial, 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 ‘KEGGREST’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘AnnotationDbi’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘annotate’ had non-zero exit status
6: In install.packages(...) :
installation of package ‘genefilter’ had non-zero exit status
7: In install.packages(...) :
installation of package ‘geneplotter’ had non-zero exit status
8: In install.packages(...) :
installation of package ‘DESeq2’ had non-zero exit status

I would be appreciated if you help me?

DESeq2 RNA-Seq ubuntu • 2.0k views
ADD COMMENT
0
Entering edit mode

Installation paths not writeable..

start Rstudio with a sudo rstudio

That way you will get the right to write the packages

ADD REPLY
3
Entering edit mode
2.5 years ago

You might need to install the OpenSSL library.

sudo apt-get update
sudo apt-get install libssl-dev

Or the equivalent command on your flavor of linux.

ADD COMMENT
1
Entering edit mode

Thank you very much. your guidance worked and I installed DESeq2 successfully.

ADD REPLY

Login before adding your answer.

Traffic: 2038 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6