Recommended R Version and chromVAR installation issues

[joreynajr]

Hi Sankaran Lab,

Is there an R version that you would recommend/is a dependency? I've been trying to install some of the dependencies but I'm running into problems mainly with chromVAR. I've been following instructions on Bioconductor to install chromVAR (https://bioconductor.org/packages/release/bioc/html/chromVAR.html) and it does say that R >=3.4 is ok but I'm wondering if it's better to use an R version closer to R 3.4.0? Currently I don't have the error warnings to share but I'm in the process of re-running the installation of chromVAR with R 3.5.1. I'll update soon with those error messages.

Thanks in advance,

Joaquin

[joreynajr]

I actually just got the error messages. I ran the following command:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chromVAR")

But after about 50 minutes I get the following error messages:

ERROR: dependency ‘httr’ is not available for package ‘KEGGREST’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/KEGGREST’
ERROR: dependencies ‘lifecycle’, ‘rlang’, ‘tibble’, ‘tidyselect’, ‘vctrs’, ‘pillar’ are not available for package ‘dplyr’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/dplyr’
ERROR: dependencies ‘digest’, ‘isoband’, ‘mgcv’, ‘rlang’, ‘scales’, ‘tibble’ are not available for package ‘ggplot2’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/ggplot2’
ERROR: dependency ‘BiocParallel’ is not available for package ‘Rsamtools’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/Rsamtools’
ERROR: dependencies ‘shiny’, ‘htmltools’ are not available for package ‘miniUI’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/miniUI’
ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/SummarizedExperiment’
ERROR: dependencies ‘SummarizedExperiment’, ‘Rsamtools’, ‘BiocParallel’ are not available for package ‘GenomicAlignments’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/GenomicAlignments’
ERROR: dependencies ‘hms’, ‘lifecycle’, ‘rlang’, ‘tibble’, ‘vroom’, ‘tzdb’ are not available for package ‘readr’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/readr’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/annotate’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘GO.db’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/GO.db’
ERROR: dependencies ‘dplyr’, ‘ellipsis’, ‘lifecycle’, ‘purrr’, ‘rlang’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘tidyr’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/tidyr’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/rtracklayer’
ERROR: dependencies ‘ggplot2’, ‘scales’, ‘httr’, ‘digest’, ‘htmltools’, ‘htmlwidgets’, ‘tidyr’, ‘dplyr’, ‘vctrs’, ‘tibble’, ‘rlang’, ‘crosstalk’, ‘purrr’, ‘promises’ are not available for package ‘plotly’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/plotly’
ERROR: dependencies ‘RSQLite’, ‘rtracklayer’, ‘GenomicAlignments’, ‘readr’, ‘reshape2’, ‘ggplot2’, ‘annotate’, ‘GO.db’, ‘KEGGREST’ are not available for package ‘CNEr’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/CNEr’
ERROR: dependencies ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘BSgenome’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/BSgenome’
ERROR: dependencies ‘BiocParallel’, ‘BSgenome’, ‘caTools’, ‘CNEr’, ‘RSQLite’, ‘rtracklayer’, ‘TFMPvalue’ are not available for package ‘TFBSTools’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/TFBSTools’
ERROR: dependencies ‘ggplot2’, ‘BiocParallel’, ‘TFBSTools’, ‘Rsamtools’, ‘plotly’, ‘shiny’, ‘miniUI’, ‘DT’, ‘SummarizedExperiment’, ‘BSgenome’, ‘RcppArmadillo’ are not available for package ‘chromVAR’
* removing ‘/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/mambaforge/envs/scavenge-3.5.0/lib/R/library/chromVAR’

The downloaded source packages are in
        ‘/mnt/beegfs/scratch/herman-login3/Rtmpj1HoHi/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
There were 50 or more warnings (use warnings() to see the first 50)```

[fl-yu]

Hi Joaquin! Thank you for your interest in our tool!

Sorry for the failed installation of chromVAR but I can not figure out the reason based on the error message, it may be worth contacting the authors of chromVAR package. I have successfully installed all the R packages in R versions both 3.6 and 4.0. Can you try with a clean conda environment for R and corresponding package installation?

[joreynajr]

Thanks for the reply and tool as well! When you use anaconda do you use R (https://anaconda.org/r/r) or r-base (https://anaconda.org/conda-forge/r-base)?

[joreynajr]

There's also a chromvar available through conda, do you use this one? I've been trying to install like this:

mamba install -c bioconda bioconductor-chromvar # using mamba instead of conda

but also from Bioconductor directly.

[fl-yu]

Either one could be good! After you installed R 3.6 or 4.0 in a clean conda env, you may proceed to install R packages using Bioconductor in R session

[joreynajr]

Sounds good, I'll give that a try!

[ldcato]

@joreynajr did you get to the bottom of this problem Joaquin? I've found in the past that installing chromVAR from the github page directly will allow me to install it on more recent versions of R (>4.0). The command looks something like this: devtools::install_github("GreenleafLab/chromVAR")