Issues installing packages miniconda environment
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cpat • 0
@cpat-15192
Last seen 3.6 years ago

Hi,

I installed R and Rstudio in miniconda3 on Unbuntu 17.10. I have issues downloading packages (eg DESeq2) using Bioconductor/bioclite on both R and R studio.

Here is a piece of the ERROR:

 

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------------------------------------------------

ERROR: configuration failed for package ‘curl’

 

Of note, libcurl is already installed. I really don't know how to proceed!

Thanks a lot in advance!

Celine

bioclite deseq2 miniconda packages • 839 views
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@mikelove
Last seen 23 hours ago
United States

Sorry, can't help much here. Looks like you could ask the conda team about how to install the necessary libraries. BTW the libraries are not sufficient in some cases but you require the _dev or -devel version as well. See this frequently asked question in the DESeq2 vignette:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#i-have-trouble-installing-deseq2-on-ubuntulinux

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cpat • 0
@cpat-15192
Last seen 3.6 years ago

Thanks Michael :)

I've got the all the dev tools installed but doesn't help. Will check with the conda team!

Celine

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