ExomeDepth installation error

Question

[Medha]

Hi all, I am trying to install ExomeDepth, my R version is 4.1.3. While using install.packages("ExomeDepth") I am facing error :

ERROR: dependencies ‘Biostrings’, ‘IRanges’, ‘Rsamtools’,‘GenomicRanges’, ‘GenomicAlignments’ are not available for package ‘ExomeDepth’

• removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-298031e1-1448-435c-a00f-5da4c903f9f6/ExomeDepth’ Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-298031e1-1448-435c-a00f-5da4c903f9f6’ (as ‘lib’ is unspecified)

  Warning: dependencies ‘Biostrings’, ‘IRanges’, ‘Rsamtools’, ‘GenomicRanges’, ‘GenomicAlignments’ are not available trying URL 'https://cloud.r-project.org/src/contrib/ExomeDepth_1.1.16.tar.gz' Content type 'application/x-gzip' length 1974890 bytes (1.9 MB)

I also tried devtools::install_github("vplagnol/ExomeDepth") which is giving same error. After this I also tried running library("ExomeDepth") as the first step provided in vignette but it shows: Error in library(ExomeDepth) : there is no package called ‘ExomeDepth’ That shows it wasnt installed successfully indeed.

I checked the version requirements too, using

                          Package        Version      Priority     Depends       
ExomeDepth "ExomeDepth"   "1.1.16"       NA        "R (>= 3.4.0)" 
ExomeDepth "ExomeDepth"    "1.1.16"      NA        "R (>= 3.4.0)"
                          Imports       
ExomeDepth  "Biostrings, IRanges, Rsamtools, GenomicRanges (>=1.23.0),\naod, VGAM (>= 0.8.4), methods, GenomicAlignments, dplyr,\nmagrittr" 
ExomeDepth "Biostrings, IRanges, Rsamtools, GenomicRanges (>= 1.23.0),\naod, VGAM (>= 0.8.4), methods, GenomicAlignments, dplyr,\nmagrittr"
                         LinkingTo Suggests Enhances License License_is_FOSS....

Now I do not understand what should be done to add these dependencies and successfully install the package. Can someone help me on this?

Answer 1

[jared.andrews07]

install.packages("BiocManager")
BiocManager::install(c("Biostrings", "IRanges", "Rsamtools", "GenomicRanges", "GenomicAlignments"))

Your install.packages("ExomeDepth") should then have what it needs to install. Note that you'll still need the system to have samtools installed for Rsamtools to function properly.

[Medha]

Hi jared.andrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rsamtools we need to install samtools is what you have suggested, so can I just simply do that as in this post: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04 But the problem is I am using cloud workspace on databricks, how will this change?

[jared.andrews07]

No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.

[Medha]

Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam files for exomedepth to run successfully (not caring for precision/accuracy)? or can we input 1 bam file?

[jared.andrews07]

Again, no idea, I haven't used this tool. You will at minimum need a reference to compare your single bam file to, so I expect you'd need at least two samples (a reference and a test). I'd read the vignette closely and just give it a shot.