BiocManager non-zero exit status error

General
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1

Hello everyone, I am trying to install a dependency of the package GenomicRanges.
Unfortunately I get this non-zero exit status, due to a path not writable. Did anyone get the same issue?

BiocManager::install("GenomicRanges")
Bioconductor version 3.8 (BiocManager 1.30.10), R 3.5.2 (2018-12-20)
Installing package(s) 'GenomicRanges'
also installing the dependencies ‘RCurl’, ‘GenomeInfoDb’

  • installing source package ‘RCurl’ ...
    ** package ‘RCurl’ successfully unpacked and MD5 sums checked
    checking for curl-config... no
    Cannot find curl-config
    ERROR: configuration failed for package ‘RCurl’
  • removing ‘/home/usr/R/x86_64-pc-linux-gnu-library/3.5/RCurl’
    ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
  • removing ‘/home/usr/R/x86_64-pc-linux-gnu-library/3.5/GenomeInfoDb’
    ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
  • removing ‘/home/usr/R/x86_64-pc-linux-gnu-library/3.5/GenomicRanges’

The downloaded source packages are in
‘/tmp/RtmplstXY9/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet,
rpart, spatial, survival
Warning messages:
1: In install.packages(...) :
installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘GenomicRanges’ had non-zero exit status

2

You can try separately installing RCurl beforehand with install.packages("RCurl").

3

This suggests you are missing a system dependency (libcurl), on what Linux distribution are you?

1 Like
4

Thank you very much for your answers.
I am working on Ubuntu 20.04.1 LTS.

I have tried to install RCurl, as AlexisW suggested.
But I got another error message. I don't understand it, would anyone know what the source of the problem?

  • 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/usr/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
    Warning in install.packages :
    installation of package ‘RCurl’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpA0wgBE/downloaded_packages’

5

As I said, you are missing a system dependency. Try installing it by running this command on a terminal (not in R).

sudo apt install libcurl4-openssl-dev
1 Like
6

It did work! It took some dependencies to install and load before being able to load GenomicRanges, but here it is.

Thanks a lot andresrcs!

7

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