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rocker-org / rocker-versioned2

Run current & prior versions of R using docker. rocker/r-ver, rocker/rstudio, rocker/shiny, rocker/tidyverse, and so on.
https://rocker-project.org
GNU General Public License v2.0
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Issue installing alakazam #833

Closed ramirobarrantes closed 4 months ago

ramirobarrantes commented 4 months ago

Not sure if this is the best place to ask ,but I have a simple docker recipe that uses rocker rstudio:

FROM rocker/rstudio:4.4

RUN install2.r -e rmarkdown ggplot2 kableExtra dplyr readxl stringr reshape2 httr BiocManager parallel

RUN R -e 'BiocManager::install(ask = F)'
RUN R -e 'BiocManager::install(c("biomaRt","XVector","Biostrings","GenomicAlignments","DECIPHER",ask = F))'

RUN install2.r -e alakazam

But when I try to build it:

docker build -t moonshot . --no-cache It breaks in the last step, alakazam, it says:

ERROR: dependencies ‘Biostrings’, ‘GenomicAlignments’ are not available for package ‘alakazam’

Any suggestions?

eddelbuettel commented 4 months ago

That usually means that your attempted installation was unsuccessful so that loading of the (hence not installed) library fails. You will have to debug why it failed.

As an aside, rocker's r2u has these as binaries for Ubuntu and in a Docker container.

ramirobarrantes commented 4 months ago

Got it! As easy as not using the install2.r but rather good old fashioned install.packages()!!!

# Base R image
FROM rocker/rstudio:4.4

MAINTAINER Ramiro Barrantes <ramiro.barrantes@med.uvm.edu>

RUN install2.r -e rmarkdown ggplot2 kableExtra dplyr readxl stringr reshape2 httr BiocManager parallel

RUN R -e 'BiocManager::install(ask = F)'
RUN R -e 'BiocManager::install(c("biomaRt","XVector","Biostrings","GenomicAlignments","DECIPHER",ask = F))'

RUN R -e "install.packages('alakazam',dependencies=TRUE, repos='http://cran.rstudio.com/')"