ERROR configuration failed for package RCurl during installation of DESeq
1
1
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krunal.24.6 ▴ 10
@krunal246-23330
Last seen 17 months 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

ERROR: configuration failed for package ‘RCurl’ DESeq • 363 views
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Mike Smith ★ 5.1k
@mike-smith
Last seen 11 hours ago
EMBL Heidelberg / de.NBI

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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@Mike Thanks i already tried this but getting error :

... Reading package lists... Done Building dependency tree
Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:

The following packages have unmet dependencies: libcurl4-openssl-dev : Depends: libcurl4 (= 7.58.0-2ubuntu3.8) but it is not going to be installed E: Unable to correct problems, you have held broken packages.

...

Thanks

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Entering edit mode

Sounds like you need to find out why the package manager won't install libcurl4 for you. There are many possible reasons for that, and I'm not sure I can really off useful suggestions remotely.

I would approach this by using Synaptic Package Manager to take a look at what is conflicting with that package and try to resolve the conflict. There are some tips in https://help.ubuntu.com/community/SynapticHowto#Troubleshooting and take it slowly as it's easy to create an even worse mess by randomly removing things.

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