Error installing Deseq2
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Gime ▴ 10
@293af73d
Last seen 17 days ago
United States

I'm trying to install Deseq2 in my Linux computer. I have Ubuntu 20.04. But I got the following warning messages:

> warnings()
Warning messages:
1: In install.packages(...) :
  installation of package ‘curl’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘RCurl’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘openssl’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
10: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
11: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
12: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

Then, I installed libxml2-dev (sudo apt install libxml2-dev) and libcurl4-openssl-dev (sudo apt install libcurl4-openssl-dev) as suggested here: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#i-have-trouble-installing-deseq2-on-ubuntulinux.

But I still get 6 warning messages when I try to install Deseq2 again:

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 ‘annotate’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

Can someone help me find a solution to these remaining warning messages? Thank you for your help!!

DESeq2 R • 155 views
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ATpoint ▴ 640
@atpoint-13662
Last seen 40 minutes ago
Germany

Go through the error logs and find the first error, this is where you have to start debugging, this here is just the consequences of the initial error.

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Yes, this is the right approach.

Also if you google "openssl ubuntu" you will find others have posted code to help you here.

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Thank you for the advice

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