Error installing AnnotationHub on Fedora
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Entering edit mode
barashe ▴ 10
@barashe-8770
Last seen 6.1 years ago
European Union

I attempted to install the AnnotationHub package for the coursera bioconductor course. I am using Fedora 21.

I did the following:

  • Made sure R is up to date (typed sudo yum install R).
  • Downloaded and installed an up-to-date version of RStudio.
  • Installed biocondoctor:
    • source("http://www.bioconductor.org/biocLite.R")
    • biocLite()
    • created a personal library since I didn't start RStudio as sudo.
    • biocLite("AnnotationHub") (personal library again, update all old packages).
When it finished, I got the following:

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘curl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘httr’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationHub’ had non-zero exit status

-----------------------------------------------------------------------------------------------------------------------------

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 21 (Twenty One)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.18.4

loaded via a namespace (and not attached):
[1] tools_3.2.1

-----------------------------------------------------------------------------------------------------------------------

Thanks!

Annotationhub curl httr fedora • 1.3k views
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3
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

You need curl and curl-devel. For Redhat I believe the correct incantation is

sudo yum install curl curl-devel
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0
Entering edit mode

Thanks, worked like a charm.

curl was already installed, but curl-devel wasn't.

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anastazie.d ▴ 20
@anastazied-10696
Last seen 4 months ago
Czechia

Or

sudo apt-get install libcurl4-openssl-dev

for Ubuntu

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