I use the following:
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Bioconductor 3.8, BiocManager 1.30.4
I have tried to install scater in a multiple of different ways now, and I always end up with a variant of the following warning message:
Installing package(s) 'scater' The downloaded source packages are in '/tmp/RtmpE6nZpa/downloaded_packages' There were 13 warnings (use warnings() to see them) >> warnings() Warning messages: 12: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package 'scater' had non-zero exit status
I have tried to install through https and http,and got either the warning message from above or a problem with connecting to the SSL (when using https, sorry I forgot to save that error message).
I also tried to install it as recommended from your website: https://www.bioconductor.org/install/#install-bioconductor-packages but recieved the same warnings.
>> BiocManager::install()The downloaded source packages are in '/tmp/RtmpE6nZpa/downloaded_packages' Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'edgeR' had non-zero exit status >> install.packages("edgeR") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) Warning message: package 'edgeR' is not available (for R version 3.5.1) >> BiocManager::install(c("scater")) Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing package(s) 'scater' The downloaded source packages are in '/tmp/RtmpE6nZpa/downloaded_packages' There were 13 warnings (use warnings() to see them)
And finally, i checked if scater existed at all, and found the following:
>>BiocManager::available()  "SCAT"  "scatr"  "scatterD3"  "scatterpie"  "scatterplot3d"
What is this supposed to mean? Have scater changed name, or is it not available any more?