Dear Lori, Thanks for your quick reply!
Yes, I was referring to the snapshot date of the PhyloProfileData data package. I have updated the raw data on the hosted server. In the inst/scripts/ directory of the data package I have two files make-data.R and make-metadata.R, which generate the .RData files and the metadata.csv, respectively. I will try updating the data version in the metadata file and submit again. Currently, neither the devel nor the release version reflexes the changes. I understand the importance of consistency and reproducibility. However, this data package is used solely as a demo data for the Bioconductor PhyloProfile package. In order to fully demonstrate the feature of the current version of PhyloProfile, we need to update the data, even in the release version. Many thanks again for your support! Best, Vinh -------------------------------- Dr. Vinh Tran Applied Bioinformatics Group Inst. of Cell Biology and Neuroscience Goethe University Max-von-Laue Str. 13 D-60438 Frankfurt am Main Germany Biologicum, Room 3.209 Phone +49 (0)69/798-42118 > On 20. Jun 2025, at 14:08, Kern, Lori <lori.sheph...@roswellpark.org> wrote: > > So a few follow up questions and comments > > It seems like you a referencing an ExperimentHub data package with the > snapshot date; is that correct? > > And if so, you mentioned you updated the raw data; you have updated those > files on the hosted server? And did you request an update to the metadata in > the experiment hub database. The data files would need to be updated in > order to have the correct download and access. > > The update will only be available using Bioconductor devel 3.22; a snapshot > of 4-12-2025 is for release not devel so you would have to use devel in > order to see the change. It is possible to update release but it is not > recommended for consistency and to keep release as stable and reproducible > for users as possible. > > If you need further assistance with updating the experiment hub data; I > suggest reaching out to h...@bioconductor.org <mailto:h...@bioconductor.org> > > Cheers, > > > > 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 <bioc-devel-boun...@r-project.org > <mailto:bioc-devel-boun...@r-project.org>> on behalf of Vinh Tran > <t...@bio.uni-frankfurt.de <mailto:t...@bio.uni-frankfurt.de>> > Sent: Friday, June 20, 2025 7:54 AM > To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> > <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>> > Subject: [Bioc-devel] Help updating data in ExperimentHub > > Greetings, > > I would like to update the data in our PhyloProfileData package. I have > updated the raw data and also made changes to the make-data.R file which > generates the .RData files for the package. However, after the latest build, > the data remains unchanged, even after reinstalling R and all related > packages. I also noticed that the snapshot date is still set to 12 April > 2025, while the latest build was on 19 June 2025. > > Could anyone please help me figure out what might be missing? Many thanks in > advance! > > Best regards, > Vinh > >  > > -------------------------------- > Dr. Vinh Tran > > Applied Bioinformatics Group > Inst. of Cell Biology and Neuroscience > Goethe University > Max-von-Laue Str. 13 > D-60438 Frankfurt am Main > Germany > > Biologicum, Room 3.209 > Phone +49 (0)69/798-42118 > > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://secure-web.cisco.com/1etTV5ILfZjNJrSXx7fXpVxg8WYX3Xvp6TGMvaIZP6NCJGuJBzPTj3NggCepWiUBEYjNbO8jDwxpWL0zOqo9x6mUkmGb9tSkLNd44zduAiGSeuYItup1Rz_Ix0cL3yIlFRtnR9Da_6NzxNPF7MwpM_kG3t4kx8nW4j0jtZ9_pHbhv64pUXKNxuMz91zU04UUl455AvzlItPfzlRmZ5Ahg4ZlbptZrSwLHcf7xm0OyaPxcN4uiAQ9GSMVlzWZJLnrzYFw3sBZay1mvTqrK5mkQqCP7mlmZxNLdMffYpufCn7SO63Pz6S6DUwsDUNxVHY_2/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
