Hello,
It would appear as though liftr is having difficulty with previous versions of Bioconductor and Bioconductor packages. Running the following .Rmd:
`
title: "Untitled"
output: html_document
liftr:
maintainer: "Maintainer Name"
email: "[email protected]"
from: "bioconductor/release_core2:R3.4.0_Bioc3.5"
pandoc: false
texlive: false
bioc:
- topGO/2.28.0
`
results in the following once the initial installation of bioconductor/release_core2:R3.4.0_Bioc3.5 completes:
Step 5/7 : RUN Rscript -e "source('http://bioconductor.org/biocLite.R');biocLite(c('topGO/2.28.0'))"
---> Running in 043d8fee39fe
�[91mBioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
�[0m�[91mA newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
�[0m�[91mBioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
�[0m�[91mA newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
�[0m�[91mtrying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/BiocInstaller_1.26.1.tar.gz'
�[0m�[91mContent type 'application/x-gzip'�[0m�[91m length 18347 bytes (17 KB)
�[0m�[91m================�[0m�[91m====�[0m�[91m===============�[0m�[91m===�[0m�[91m============
downloaded 17 KB
�[0m�[91mBioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
�[0m�[91mA newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
�[0m�[91m* installing source package ‘BiocInstaller’ ...
�[0m�[91m** R
�[0m�[91m** inst
�[0m�[91m** preparing package for lazy loading
�[0m�[91m** help
�[0m�[91m*** installing help indices
�[0m�[91m** building package indices
�[0m�[91m** testing if installed package can be loaded
�[0mBioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
�[91m* DONE (BiocInstaller)
�[0m�[91m
The downloaded source packages are in
‘/tmp/RtmpDHoPBn/downloaded_packages’
�[0m�[91mBioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
�[0m�[91mA newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
�[0m�[91m'BiocInstaller' updated to version 1.26.1
�[0m�[91mBioC_mirror: https://bioconductor.org
�[0m�[91mUsing Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
�[0m�[91mInstalling github package(s) ‘topGO/2.28.0’
�[0m�[91mDownloading GitHub repo topGO/2.28.0@master
from URL https://api.github.com/repos/topGO/2.28.0/zipball/master
�[0m�[91mInstallation failed: Not Found (404)
[0m�[91mOld packages: 'AnnotationDbi', 'AnnotationHub', 'backports', 'BH', 'Biobase',
'BiocGenerics', 'BiocParallel', 'BiocStyle', 'biomaRt', 'Biostrings',
'bookdown', 'BSgenome', 'checkmate', 'curl', 'data.table', 'DBI',
'DelayedArray', 'ensembldb', 'evaluate', 'foreign', 'Formula',
'GenomeInfoDb', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges',
'gridExtra', 'GSEABase', 'htmlwidgets', 'httr', 'IRanges', 'jsonlite',
'lambda.r', 'lazyeval', 'Matrix', 'mgcv', 'openssl', 'OrganismDbi', 'R6',
'Rcpp', 'RSQLite', 'rtracklayer', 'S4Vectors', 'scales', 'ShortRead',
'stringi', 'SummarizedExperiment', 'tibble', 'VariantAnnotation', 'XML'
�[0m ---> e64f91a7d127
Removing intermediate container 043d8fee39fe
Step 6/7 : RUN mkdir /liftrroot/
---> Running in 9c95cb7d4eca
---> 1dcb9ac6c7b3
Removing intermediate container 9c95cb7d4eca
Step 7/7 : WORKDIR /liftrroot/
---> f22056789c44
Removing intermediate container 7028e5fd2dc5
Successfully built f22056789c44
Successfully tagged test:latest
$container_name
[1] "liftr_container_a71c6c41_81a1_47eb_a525_1aedad258a80"
$image_name
[1] "test"
$docker_build_cmd
[1] "docker build --no-cache=true --rm=true -t="test" /Users/jasonserviss/Desktop/test"
$docker_run_cmd
[1] "docker run --rm --name "liftr_container_a71c6c41_81a1_47eb_a525_1aedad258a80" -u id -u $USER -v "/Users/jasonserviss/Desktop/test:/liftrroot/" test Rscript -e "library('knitr');library('rmarkdown');library('shiny');setwd('/liftrroot/');render(input = 'test.Rmd')""Loading required package: methods
|.................................................................| 100%
label: unnamed-chunk-1
processing file: test.Rmd
Quitting from lines 15-16 (test.Rmd)
Error in library(topGO) : there is no package called 'topGO'
Calls: render ... withCallingHandlers -> withVisible -> eval -> eval -> library
Execution halted
The topGO version corresponds with the Bioconductor image version (can be seen here: https://bioconductor.org/packages/3.5/bioc/html/topGO.html) although it would appear that liftr is looking for the package version in an invalid place (i.e. https://api.github.com/repos/topGO/2.28.0/zipball/master).
I had originally thought that this is due to the relatively recent Bioconductor switch to Github (from SVN) and noticed that the earliest version of topGO on GitHub is 3.0... although both https://api.github.com/repos/topGO/3.0/zipball/master and https://api.github.com/repos/topGO/release-3.0/zipball/master are also invalid urls which probably indicates that liftr would fail with that version as well.
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