Dockerfile fails to build

[mjmansfi]

The current version of the Dockerfile fails to build (below).

I have written an alternative Dockerfile that goes through the process of installing the appropriate dependencies via apt, CRAN, and so on manually.

Note also that the dependencies libbz2-dev, liblzma-dev, and libfftw3-dev are currently missing from the instructions.

I have made these changes in the following branch and will submit a PR if desired:

https://github.com/oist/GenomicBreaks/tree/dockerfile_manual_install

> docker build  .

Sending build context to Docker daemon  10.65MB
Step 1/3 : FROM bioconductor/bioconductor_docker:RELEASE_3_13
RELEASE_3_13: Pulling from bioconductor/bioconductor_docker
35807b77a593: Pull complete 
765af7b305b2: Pull complete 
47299a17438e: Pull complete 
02782102bff3: Pull complete 
1cc728779689: Pull complete 
77e79bd7a547: Pull complete 
02dc39cd2d4e: Pull complete 
be310f0bcd62: Pull complete 
6e3f6a2d645d: Pull complete 
fb912e359468: Pull complete 
a49649d56f66: Pull complete 
d8ff0af25b9b: Pull complete 
9387799dfa7e: Pull complete 
65c9bbda106d: Pull complete 
23c068cb3e38: Pull complete 
Digest: sha256:f6b9fc2c7fa85cfaffeb36b64188d7986a807978285f55ad7ba317d7c02bdebb
Status: Downloaded newer image for bioconductor/bioconductor_docker:RELEASE_3_13
 ---> 39cb1274f9a5
Step 2/3 : LABEL authors="[email protected]"       description="GenomicBreaks package in the Bioconductor Docker image"
 ---> Running in 6e11e0ad03e2
Removing intermediate container 6e11e0ad03e2
 ---> 63a2dd4269c6
Step 3/3 : RUN R CMD INSTALL .
 ---> Running in 4c2f499f9289
Warning: invalid package ‘.’
Error: ERROR: no packages specified
The command '/bin/sh -c R CMD INSTALL .' returned a non-zero code: 1

[charles-plessy]

Hi Mike, sorry, the Dockerfile is completely bitrotten. I have been using Singularity exclusively for more than a year. I will either update it for the next Bioconductor release or just delete it.