Re: [Bioc-devel] Package checks with WARNING
On 12/10/2022 13:42, Lapuente Santana, Oscar wrote: Hi Hervé, Thanks for your suggestion. The package rstatix which I used and it's set as an import, calls the coin package but this one is defined as a suggests in the description file of rstatix package (https://github.com/kassambara/rstatix/blob/master/DESCRIPTION). In particular, I am calling two two functions from this package: rstatix::wilcox_test and rstatix::wilcox_effsize. The later uses several functions from the coin package and one is called the same way which is coin::wilcox_test and then the warning arises. Given this situation, I would feel more comfortable importing the full coin package. What are your thoughts? I see. But still, you're only supposed to import what your code uses _directly_. In this case your code doesn't make any call to coin or doesn't use any symbol defined in coin. The code in rstatix does, but not your code. One concern is that you want to make sure that coin is installed on the user machine, so it needs to be listed as a dependency. One way to achieve this is to move coin to Depends, and to not import anything from it. I just tried this but R CMD check now produces: * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘coin’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. IMO this is actually a legitimate use of Depends, so I'd say it's ok. At least now you get a NOTE instead of a WARNING ;-) A more hacky solution is to keep coin in Imports and to import an arbitrary symbol from it. Could be anything, except 'wilcox_test' of course, to avoid the clash with importFrom(rstatix,wilcox_test). That should produce a clean R CMD check. Hope this helps, H. Cheers, Óscar On 12/10/2022, 20:07, "Hervé Pagès" wrote: Hi Óscar, On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote: > Dear Bioconductor developers/maintainers, > > My package ‘easier’ checks with WARNING in both the current 3.15 release and the devel version. > I am just checking in to see if that’s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency) Sure but you can get rid of it by importing only what you need from the coin package. Right now you import the full coin namespace, by having import(coin) in your NAMESPACE file, and that introduces a clash with importFrom(rstatix,wilcox_test) that you also have in there. I'm actually not sure what you need coin for (I was not able to find a place in your code where you make any use of it). So maybe you could just drop that dependency entirely? Best, H. > > Thanks in advance, > Cheers, Óscar > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=05%7C01%7C%7Cb6a12862a3d34c6fc57608daac7c93b1%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C0%7C638011948302682925%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=zX2HiEuNhlfF8IQ1N61wbAyt1Sd2k4hiVISTMJXA3qk%3Dreserved=0 -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package checks with WARNING
Hi Hervé, Thanks for your suggestion. The package rstatix which I used and it's set as an import, calls the coin package but this one is defined as a suggests in the description file of rstatix package (https://github.com/kassambara/rstatix/blob/master/DESCRIPTION). In particular, I am calling two two functions from this package: rstatix::wilcox_test and rstatix::wilcox_effsize. The later uses several functions from the coin package and one is called the same way which is coin::wilcox_test and then the warning arises. Given this situation, I would feel more comfortable importing the full coin package. What are your thoughts? Cheers, Óscar On 12/10/2022, 20:07, "Hervé Pagès" wrote: Hi Óscar, On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote: > Dear Bioconductor developers/maintainers, > > My package ‘easier’ checks with WARNING in both the current 3.15 release and the devel version. > I am just checking in to see if that’s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency) Sure but you can get rid of it by importing only what you need from the coin package. Right now you import the full coin namespace, by having import(coin) in your NAMESPACE file, and that introduces a clash with importFrom(rstatix,wilcox_test) that you also have in there. I'm actually not sure what you need coin for (I was not able to find a place in your code where you make any use of it). So maybe you could just drop that dependency entirely? Best, H. > > Thanks in advance, > Cheers, Óscar > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=05%7C01%7C%7Cb6a12862a3d34c6fc57608daac7c93b1%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C0%7C638011948302682925%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=zX2HiEuNhlfF8IQ1N61wbAyt1Sd2k4hiVISTMJXA3qk%3Dreserved=0 -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package checks with WARNING
Hi Óscar, On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote: Dear Bioconductor developers/maintainers, My package ‘easier’ checks with WARNING in both the current 3.15 release and the devel version. I am just checking in to see if that’s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency) Sure but you can get rid of it by importing only what you need from the coin package. Right now you import the full coin namespace, by having import(coin) in your NAMESPACE file, and that introduces a clash with importFrom(rstatix,wilcox_test) that you also have in there. I'm actually not sure what you need coin for (I was not able to find a place in your code where you make any use of it). So maybe you could just drop that dependency entirely? Best, H. Thanks in advance, Cheers, Óscar [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package checks with WARNING
Ideally all warnings and notes would be addressed. However as long as the package currently is not in an ERROR or TIMEOUT state this is okay; especially if it comes from a dependency of a dependency. Please keep an eye on all warnings and make sure there is not anything new or anything that can (and then should) be addressed. 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 Lapuente Santana, Oscar via Bioc-devel Sent: Wednesday, October 12, 2022 4:09 AM To: Anestis Gkanogiannis via Bioc-devel Subject: [Bioc-devel] Package checks with WARNING Dear Bioconductor developers/maintainers, My package �easier� checks with WARNING in both the current 3.15 release and the devel version. I am just checking in to see if that�s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency) Thanks in advance, Cheers, �scar [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1z9TwmP02ciIng0M5eHpUlHpjIwpxLiKtANaU_PXH6E5yEYKl8mTjAmdFZsb8yVpehtNYriEa90us07yim1-sZSGuMaxIjBnzc5PChq-taUyUXLKwjYg_uci79RwiCL7joAT6KTKJ2om_bcyRbecLYBEWRbjNEz_MTzKLpnCZSxMv9QEfFK2hIK24NuQMsGhHyCM1jPwC8CcHqUun0eN2a6Gx2dJaCLB-S9kc6JM8U051Moc7UuJ1Yodn158OG4fhpK-N_cTEM9BL4329kzegrjsSKrrthEUtG2YR52O8SJldBORg48N_NGTkvdP_S9m-/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] Package checks with WARNING
Dear Bioconductor developers/maintainers, My package ‘easier’ checks with WARNING in both the current 3.15 release and the devel version. I am just checking in to see if that’s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency) Thanks in advance, Cheers, Óscar [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
