On 30/04/19 11:08 AM, Bert Gunter wrote:> Offlist, as this might be complete baloney.Thanks Bert. I am CC-ing this reply to the r-help list since your suggestion is *NOT* complete baloney at all!> What dependencies does your package have? -- is it possible that some of > these dependent packages have made changes or added features that have > ggplot2 etc. dependencies that cause these issues?<SNIP> The package has no dependencies as such, but "Imports" a number of packages. I tried loading these, one by one, and when I did library(brms) I got the message that was triggered by loading my package. So that is the source of the problem. If it is indeed a problem. The question remains: is this message something that I (or the maintainer of brms) should be worried about? cheers, Rolf> On Mon, Apr 29, 2019 at 3:55 PM Rolf Turner <r.turner at auckland.ac.nz > <mailto:r.turner at auckland.ac.nz>> wrote: > > > I just installed the latest version of R on my laptop (running Ubuntu > 18.04; used "sudo apt-get install r-base".) > > Now when I load a package that I have written I get a message on screen: > > > Registered S3 methods overwritten by 'ggplot2': > >? ?method? ? ? ? ?from > >? ?[.quosures? ? ?rlang > >? ?c.quosures? ? ?rlang > >? ?print.quosures rlang > > Registered S3 method overwritten by 'dplyr': > >? ?method? ? ? ? ? ? ? ?from > >? ?as.data.frame.tbl_df tibble > > Registered S3 method overwritten by 'xts': > >? ?method? ? ?from > >? ?as.zoo.xts zoo > > What is the import of this (mysterious and cryptic) pronouncement?? I > don't understand it at all.? My package makes no use of ggplot2, dplyr > or xts. > > Should I be worried?? Are there adjustments that I should make to my > package (e.g. to NAMESPACE)? > > Thanks for any tips. > > cheers, > > Rolf Turner > > -- > Honorary Research Fellow > Department of Statistics > University of Auckland > Phone: +64-9-373-7599 ext. 88276 > > ______________________________________________ > R-help at r-project.org <mailto:R-help at r-project.org> mailing list -- > To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
Hi Guys, I suspect that this entry from news() for 3.6.0 is relevant: "When loading namespaces, S3 method registrations which overwrite previous registrations are now noted by default (using packageStartupMessage())." Always a good idea to read the NEWS file with a x.y point release. Peter usually includes it in his release announcement e-mail: https://stat.ethz.ch/pipermail/r-help/2019-April/462510.html Regards, Marc Schwartz> On Apr 29, 2019, at 7:32 PM, Rolf Turner <r.turner at auckland.ac.nz> wrote: > > > On 30/04/19 11:08 AM, Bert Gunter wrote: > >> Offlist, as this might be complete baloney. > > Thanks Bert. > > I am CC-ing this reply to the r-help list since your suggestion is *NOT* complete baloney at all! > >> What dependencies does your package have? -- is it possible that some of these dependent packages have made changes or added features that have ggplot2 etc. dependencies that cause these issues? > > <SNIP> > > The package has no dependencies as such, but "Imports" a number of packages. I tried loading these, one by one, and when I did > > library(brms) > > I got the message that was triggered by loading my package. So that is the source of the problem. If it is indeed a problem. > > The question remains: is this message something that I (or the maintainer of brms) should be worried about? > > cheers, > > Rolf > >> On Mon, Apr 29, 2019 at 3:55 PM Rolf Turner <r.turner at auckland.ac.nz <mailto:r.turner at auckland.ac.nz>> wrote: >> I just installed the latest version of R on my laptop (running Ubuntu >> 18.04; used "sudo apt-get install r-base".) >> Now when I load a package that I have written I get a message on screen: >> > Registered S3 methods overwritten by 'ggplot2': >> > method from >> > [.quosures rlang >> > c.quosures rlang >> > print.quosures rlang >> > Registered S3 method overwritten by 'dplyr': >> > method from >> > as.data.frame.tbl_df tibble >> > Registered S3 method overwritten by 'xts': >> > method from >> > as.zoo.xts zoo >> What is the import of this (mysterious and cryptic) pronouncement? I >> don't understand it at all. My package makes no use of ggplot2, dplyr >> or xts. >> Should I be worried? Are there adjustments that I should make to my >> package (e.g. to NAMESPACE)? >> Thanks for any tips. >> cheers, >> Rolf Turner >> -- Honorary Research Fellow >> Department of Statistics >> University of Auckland >> Phone: +64-9-373-7599 ext. 88276
Since you now have this indirect dependency, you should make sure you have updated this gaggle of packages. I have found that the dependencies do not necessarily update when I update the package that relies on them. It can take a few passes of reading error/warming messages to get them all updated. I suspect you have old versions of packages that now delegate certain functions to lower-level packages, and these errors should go away when you have them all current. On April 29, 2019 4:32:05 PM PDT, Rolf Turner <r.turner at auckland.ac.nz> wrote:> >On 30/04/19 11:08 AM, Bert Gunter wrote: > >> Offlist, as this might be complete baloney. > >Thanks Bert. > >I am CC-ing this reply to the r-help list since your suggestion is >*NOT* >complete baloney at all! > >> What dependencies does your package have? -- is it possible that some >of >> these dependent packages have made changes or added features that >have >> ggplot2 etc. dependencies that cause these issues? > ><SNIP> > >The package has no dependencies as such, but "Imports" a number of >packages. I tried loading these, one by one, and when I did > >library(brms) > >I got the message that was triggered by loading my package. So that is > >the source of the problem. If it is indeed a problem. > >The question remains: is this message something that I (or the >maintainer of brms) should be worried about? > >cheers, > >Rolf > >> On Mon, Apr 29, 2019 at 3:55 PM Rolf Turner <r.turner at auckland.ac.nz >> <mailto:r.turner at auckland.ac.nz>> wrote: >> >> >> I just installed the latest version of R on my laptop (running >Ubuntu >> 18.04; used "sudo apt-get install r-base".) >> >> Now when I load a package that I have written I get a message on >screen: >> >> > Registered S3 methods overwritten by 'ggplot2': >> >? ?method? ? ? ? ?from >> >? ?[.quosures? ? ?rlang >> >? ?c.quosures? ? ?rlang >> >? ?print.quosures rlang >> > Registered S3 method overwritten by 'dplyr': >> >? ?method? ? ? ? ? ? ? ?from >> >? ?as.data.frame.tbl_df tibble >> > Registered S3 method overwritten by 'xts': >> >? ?method? ? ?from >> >? ?as.zoo.xts zoo >> >> What is the import of this (mysterious and cryptic) >pronouncement?? I >> don't understand it at all.? My package makes no use of ggplot2, >dplyr >> or xts. >> >> Should I be worried?? Are there adjustments that I should make to >my >> package (e.g. to NAMESPACE)? >> >> Thanks for any tips. >> >> cheers, >> >> Rolf Turner >> >> -- >> Honorary Research Fellow >> Department of Statistics >> University of Auckland >> Phone: +64-9-373-7599 ext. 88276 >> >> ______________________________________________ >> R-help at r-project.org <mailto:R-help at r-project.org> mailing list >-- >> To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible >code. >>-- Sent from my phone. Please excuse my brevity.
On 30/04/19 12:19 PM, Jeff Newmiller wrote:> Since you now have this indirect dependency, you should make sure you > have updated this gaggle of packages. I have found that the > dependencies do not necessarily update when I update the package that > relies on them. It can take a few passes of reading error/warming > messages to get them all updated. I suspect you have old versions of > packages that now delegate certain functions to lower-level packages, > and these errors should go away when you have them all current.Nope. Doesn't work. I reinstalled brms and the messages still appeared when I loaded brms. cheers, Rolf -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
On 30/04/19 12:01 PM, Marc Schwartz wrote:> Hi Guys, > > I suspect that this entry from news() for 3.6.0 is relevant: > > "When loading namespaces, S3 method registrations which overwrite > previous registrations are now noted by default (using > packageStartupMessage())." > > > Always a good idea to read the NEWS file with a x.y point release. > Peter usually includes it in his release announcement e-mail: > > https://stat.ethz.ch/pipermail/r-help/2019-April/462510.htmlOK. This seems to be the issue. Basically I guess I could just ignore the messages --- but I'd really rather not see them. The news() says they are printed by "default". How can I move away from the default? I presume that I need to invoke the suppressPackageStartupMessages() function, but it is not at all clear to me just how I should do this. Perhaps I should put a call to this function in a *.R file (e.g. "First.R") in my R directory. I've experimented with various ideas; none so far have worked. The function suppressPackageStartupMessages() takes an argument "expr". It is not clear what "expr" should be in this context. Perhaps I am barking up the wrong tree. Any advice? cheers, Rolf -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276