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koustav-pal / HiCBricks

HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.
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Vignette examples cannot be followed #13

Closed mdozmorov closed 4 years ago

mdozmorov commented 4 years ago

Hi,

I installed HiCBricks as BiocManager::install("HiCBricks", version = "3.9") (also, tried the latest version from GitHub). Then, I tried following the vignette. The first command:

Bintable_path <- system.file(file.path("extdata",
"Bintable_100kb.bins"), package = "HiCBricks")

gives empty Bintable_path. 

> Bintable_path
[1] ""

OK, one can download the file manually from GitHub Bintable_100kb.bins.

The second command also fails:

> HiCBricks::Create_many_Bricks(BinTable = Bintable_path, 
...                    bin_delim=" ", output_directory = out_dir, 
...                    file_prefix = "HiCBricks_vignette_test", remove_existing=TRUE, 
...                    experiment_name = "HiCBricks vignette test", resolution = 100000)
Error: 'Create_many_Bricks' is not an exported object from 'namespace:HiCBricks'

What may be wrong?

koustav-pal commented 4 years ago

Hey @mdozmorov,

Sorry to hear that you are having so much trouble. I think the problem is that you are using the HiCBricks package from Bioconductor release 3.9 with the vignette from release 3.10. Can you please try out these commands?

First, make sure that you are using R 3.6.0. Next, run

BiocManager::install("HiCBricks", version = "3.10")

This should fail because you are still using many dependencies from the previous release. To fix this, run BiocManager::install(version="3.10") to update all packages.

After this is complete, run BiocManager::install("HiCBricks", version = "3.10")

mdozmorov commented 4 years ago

Thanks, @koustav-pal, that was indeed the problem. Good the README was updated. Will continue playing with the package.