Hi! Hope this finds you well! I was told to contact this mailing list about preparing/changing a package for Bioconductor submission. My question is: How should I store large dependency files - 6GB large (e.g. 1000 genomes reference LD data) - for the package on Bioconductor? My package wraps multiple methods of cell-typing GWAS summary statistics. The problem is that the methods wrapped by my package require dependency files for analyses to run, and those dependency files are very large. In my github package, I simply made a function that downloads and formats all of the data in the package's system path, in the data folder: paste0(system.file(package="GWASCellTyper"), "/data/") Link to the package in its current state: https://bitbucket.org/alexandru_ioan_voda/cell_typing_package/src/master/ With best wishes, Alexandru Ioan Voda
[Bioc-devel] Dependency files question
2 messages · Alexandru Voda, Shepherd, Lori
2 days later
We would probably recommended having an associated data package that utilizes ExperimentHub. Please see http://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html Please let me know if you have any follow up questions. Cheers Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Alexandru Voda <alexandru.voda at seh.ox.ac.uk>
Sent: Monday, March 2, 2020 6:51 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Dependency files question
Sent: Monday, March 2, 2020 6:51 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Dependency files question
Hi! Hope this finds you well! I was told to contact this mailing list about preparing/changing a package for Bioconductor submission. My question is: How should I store large dependency files - 6GB large (e.g. 1000 genomes reference LD data) - for the package on Bioconductor? My package wraps multiple methods of cell-typing GWAS summary statistics. The problem is that the methods wrapped by my package require dependency files for analyses to run, and those dependency files are very large. In my github package, I simply made a function that downloads and formats all of the data in the package's system path, in the data folder: paste0(system.file(package="GWASCellTyper"), "/data/") Link to the package in its current state: https://bitbucket.org/alexandru_ioan_voda/cell_typing_package/src/master/ With best wishes, Alexandru Ioan Voda [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.