Issues installing packages miniconda environment
2
0
Entering edit mode
cpat • 0
@cpat-15192
Last seen 6.7 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 • 2.1k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 day 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

ADD COMMENT
0
Entering edit mode
cpat • 0
@cpat-15192
Last seen 6.7 years ago

Thanks Michael :)

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

Celine

ADD COMMENT

Login before adding your answer.

Traffic: 780 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6