Re: [Bioc-devel] How to deal with external software dependencies
Hi Ran, First of all, please note that direct calls to external commands via system() or system2() are not ideal so should only be used when there is no other alternative. For example, if a CRAN or Bioconductor package already provides the functionality that you are after, you should use that instead. Now if your package **absolutely** must rely on external software then you need to make sure that those requirements are listed in the SystemRequirements field of the DESCRIPTION file of the package. These requirements should be "reasonable" requirements, that is, trusted software only, open source, and relatively easy to install. Additionally we ask that the package contains an INSTALL file (in the top-level folder) that provides instructions for installing the external software on the 3 major OS that we support: Linux, Windows, and Mac. This will not only help your users get the external software on their machines, but it will also help us install it on the build machines if it's not already there. May I ask what those external tools are? Thanks, H. On Mon, Dec 19, 2022 at 3:13 PM RAN HU wrote: > Hi all, > > I am developing a new R package that relies on some external software. > There are some system calls written in the R function that requires the > path to those external software tools. > > I am not sure what is the best practice to using external software in R > Bioconductor packages. If the external software paths are required for the > functions to run successfully, will the package fail the BiocCheck? > > Any suggestions would be appreciated and thank you in advance for your > help!!! > > Best, > Ran > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] data extension preference
Personally: I think it depends on the use case and the type of data being provided as well as the size. Raw data is probably more adaptable for various usage even extending beyond expected use however it can be large; processed data can be saved compressed and greatly reduce package/data size. Again it will largely depend on what you are doing with the data provided. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Park, Adam Keebum Sent: Wednesday, December 21, 2022 11:42 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] data extension preference Dear whom it may concern, I want to check if reviewers have a preference in data formats for data included in a package. Is rda strongly recommended over csv? Sincerely, Adam. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1TPdwAVqVZuSe4StGWM5cZ069tkkEd2TzRyilsxSECEjqUKvno8Zdb1ADlxRO16lYeghEAcxQKUbYlHrN2KDXvokdAcDZyHHQnbzpmvtEdR5-LnOnPQTBydfgzsrqt_wvHLCCkfIR2dca1h0yDT6Tx8KsV-vXAoxjLyP0YTvVpcrOsqRabwJF7P7y5ntz29eeFVAqTNjXA6XilRqlKO8HMidxVRRAWSypOTO7X1oscKhmxUKWQgBLGrn9p8rF7XA9tjsaOAg5-1kEcC4Cbqu0T7qqPX0bGD1spEdDqAv2q2Vz-Cpwm-xniK7e7w7xeI5J/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Large vignettes
Dear community, I hope wonderful things happen to you in the new year. I guess this issue is well-known. BiocCheck works on a output of R CMD build, which means vignettes are rendered in html forms. Those sometimes include many images easily exceeding 5mb limit, failing the BiocCheck with a warning. Could anyone give advice for it? I don't consider using any sort of pre-computed images. Sincerely, Adam. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
