krunal.24.6 ▴ 10

@krunal246-23330

Last seen 3.7 years ago

 

Hi, I am trying to install DESeq/ DESeq2 but keep getting error for RCurl, i tried to resoled with multiple solutions available over repositories but failed, please help me to understand and resolve the issue. (I am using Ubuntu 18.04). Issue is After running the command -> "BiocManager::install("DESeq")" i received the below output:

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'DESeq'
also installing the dependencies ‘RCurl’, ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.1.tar.gz'
Content type 'application/x-gzip' length 699474 bytes (683 KB)
==================================================
downloaded 683 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz'
Content type 'application/x-gzip' length 1873132 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz'
Content type 'application/x-gzip' length 1421076 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz'
Content type 'application/x-gzip' length 1431450 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq_1.38.0.tar.gz'
Content type 'application/x-gzip' length 1692154 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/krunal/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘annotate’
* removing ‘/home/krunal/R/x86_64-pc-linux-gnu-library/3.6/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/krunal/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/krunal/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’
* removing ‘/home/krunal/R/x86_64-pc-linux-gnu-library/3.6/DESeq’

The downloaded source packages are in
    ‘/tmp/RtmpfOWb9z/downloaded_packages’
Installation path not writeable, unable to update packages: boot, foreign,
  nlme, survival
Warning messages:
1: In install.packages(...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘DESeq’ had non-zero exit status

Please help me to understand and resolve the issue with R.

Regards Krunal Pawar

Mike Smith ★ 6.2k

@mike-smith

Last seen 10 hours ago

EMBL Heidelberg

You need Curl installed on your system. Try running this in a command line terminal:

sudo apt-get install -y libcurl4-openssl-dev

Then give the package installation another try.

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