server module missing biocLite

mdozmorov / genome_runner

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server module missing biocLite #101

Closed mdozmorov closed 8 years ago

mdozmorov commented 9 years ago

When starting the server, got

python -m grsnp.server -r /home/mdozmorov/Documents/ -g hg19 -d /home/mdozmorov/db_5.00_07-22-2015/ use 'source("http://bioconductor.org/biocLite.R")' to update 'BiocInstaller' after 'utils' package is attached Error: could not find function "biocLite"

mdozmorov commented 8 years ago

Cured by installing Bioconductor. Add to the installation file: 1) Start R. May use sudo, to install packages system-wide 2) source("http://bioconductor.org/biocLite.R") 3) biocLite() - this will install everything needed. Takes time.

mdozmorov commented 8 years ago

The issue caused by the machine-specific .Rprofile. Declaring loading biocLite solves the issue