[Bioc-devel] Imports, depends and warnings
With the minimal working example, alone the importing of NMF raises the warning, so I guess this is due to that particular package. Should I contact the author of that in hope he adapts its NAMESPACE to have some nicer behavior? (or would be *just that* warning "fine" for the Bioc ecosystem?) Cheers, Federico
On 02.03.16 20:41, Morgan, Martin wrote:
I think the only unavoidable case is when the package you import 'does it wrong'. If that's not the case, then please provide an (easy-to-reproduce -- start with a simple package.skeleton() and add a couple of Imports: and import() statements, rather than providing your current package). Martin
________________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Federico Marini <marinif at uni-mainz.de> Sent: Wednesday, March 2, 2016 10:53 AM To: bioc-devel at r-project.org Subject: [Bioc-devel] Imports, depends and warnings Hi Bioconductors, I'm on a good way to finalize the pcaExplorer package I presented at the recent Bioc Developers Meeting. Trying to keep check and BiocCheck always in the background of my head, as well as trying to be a good 'package neighbour', I am dealing with the issue of some "Warning: replacing previous import by..." messages, when building/loading/checking. From my understanding, there might be some cases where this can not be fixed, probably because an imported package in turn imports itself another one entirely, making my own import redundant (e.g., ggplot2 for plotting and NMF for aheatmap give this part: Warnung: replacing previous import by ?ggplot2::unit? when loading ?NMF? Warnung: replacing previous import by ?ggplot2::arrow? when loading ?NMF? This happens even if I specifically just use importFrom in the NAMESPACE. I'm kind of puzzled on this, so I thought I'd better ask out for some expert advice on the ML. If required, I could put the package in a GitHub repository. Thank you in advance for any help you can provide! Federico -- Federico Marini, M.Sc. Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) Division Biostatistics and Bioinformatics University Medical Center of the Johannes Gutenberg University Mainz Postal address: 55101 Mainz Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz Phone: +49 (0) 6131 17-8108 Fax: +49 (0) 6131 17-2968 Web: www.imbei.uni-mainz.de E-Mail: marinif at uni-mainz.de _______________________________________________ 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.
Federico Marini, M.Sc. Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) Division Biostatistics and Bioinformatics University Medical Center of the Johannes Gutenberg University Mainz Postal address: 55101 Mainz Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz Phone: +49 (0) 6131 17-8108 Fax: +49 (0) 6131 17-2968 Web: www.imbei.uni-mainz.de E-Mail: marinif at uni-mainz.de