hg38 not exported object from namespace:GenomicDistributionsData

[kloot]

Happens consistently with all tutorial and test files.
Distribution plot files are created but have no content
Example here for tutorial1

The seems to be my final issue ... (hopefully) ... many thanks for taking a look!

Target to produce: /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_chromosome_distribution.pdf

Rscript /home/APPS/pepatac_tutorial//tools/pepatac/tools/PEPATAC.R anno -p chromosome -i /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak -f /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed -g hg38 -o /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_chromosome_distribution.pdf (1161033)

ERROR: Error: 'chromSizes_hg38' is not an exported object from 'namespace:GenomicDistributionsData'
Unable to produce chromosome distribution plot!

Command completed. Elapsed time: 0:00:10. Running peak memory: 3.51GB.
PID: 1161033; Command: Rscript; Return code: 0; Memory used: 0.412GB

Peak chromosome distribution QC_hg38/tutorial1_peak_chromosome_distribution.pdf Peak chromosome distribution QC_hg38/tutorial1_peak_chromosome_distribution.png PEPATAC OBJ
Target to produce: /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_TSS_distribution.pdf

Rscript /home/APPS/pepatac_tutorial//tools/pepatac/tools/PEPATAC.R anno -p tss -i /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak -f /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed -g hg38 -o /home/APPS/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_TSS_distribution.pdf (1161140)

calcFeatureDistRefTSS(): Error: 'TSS_hg38' is not an exported object from 'namespace:GenomicDistributionsData'

Unable to produce tss distribution plot!






[PEPATAC_log.md.txt](https://github.com/databio/pepatac/files/9836867/PEPATAC_log.md.txt)

[jpsmith5]

Hi @kloot, this has been an issue with GenomicDistributionsData before, and there are likely a few possible causes and solutions.

1. Ensure GenomicDistributions and GenomicDistributionsData are the most current packages (e.g. GenomicDistributionsData_1.2.0 & GenomicDistributions_1.4.6).
   Both can now be installed directly from BiocManager

BiocManager::install('GenomicDistributions')
BiocManager::install('GenomicDistributionsData')

Depending on your version of R, you may also need to install GenomicDistributions directly from the tarball:
e.g.

wget http://www.bioconductor.org/packages/release/bioc/src/contrib/GenomicDistributions_1.4.6.tar.gz
Rscript -e 'install.packages("GenomicDistributions_1.4.6.tar.gz")'

Additionally, ExperimentHub has updated over time, and the previous cache location can change and lead to issues here. See https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html#default-caching-location-update

Finally, if installing older versions, as discussed over in databio/GenomicDistributions#111 (comment),
it is not uncommon for a timeout to occur in the direct install process for the Data package. It is not always obvious that there was a timeout in the install process and you can still then perform the library("GenomicDistributionsData") call in R.

To help with the timeout process, you can grab the Data package separately first, then install using this local copy.

wget http://big.databio.org/GenomicDistributionsData/GenomicDistributionsData_0.0.2.tar.gz
Rscript -e 'install.packages("GenomicDistributionsData_0.0.2.tar.gz", type="source", repos=NULL)'

[alkrup]

Piggybacking off this related issue, I'm finding I am unable to download any of the resources from big.databio.org (tutorial fastqs nor the GenomicDistributionsData_....tar.gz noted above). The HTTP request gets sent but times out while awaiting response with a 504 gateway timeout error. Are there alternative ways to access these datasets?