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mskilab-org / JaBbA

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
MIT License
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Sequenza has been removed from CRAN #91

Closed p-smirnov closed 11 months ago

p-smirnov commented 1 year ago

Describe the bug It seems like Sequenza has been removed from CRAN earlier this year, and its a dependency of this package. Therefore, normal package installation fails.

To Reproduce Try to install the package in a new environment without any dependencies available.

Suggestions to resolve: Either change to depend on the bitbucket hosted version of Sequenza, provide instructions on how to install from CRAN archive (or work around the dependency).

tpersse commented 1 year ago

Our group had similar issues. Resolved by doing the following in R, after changing R version to 4.0.2 (more recent versions might work, but this one was mentioned in a yaml file in the repository):

install.packages("BiocManager") install.packages('testthat') BiocManager::install(c("copynumber", "iotools", "squash", "seqminer")) # dependencies for sequenza

install.packages("~/sequenza_3.0.0.tar.gz", repos = NULL, type="source")

We had to install an archived version of sequenza from this link

Additionally, we ended up having to install DelayedArray and VariantAnnotation packages through BiocManager, then installing 'mskilab-org/gTrack' and 'mskilab-org/gGnome' before installing JaBbA. Hope this can help.