Hi Duncan,Thanks for the help. For now (since I want my package to get into CRAN so I can resubmit my paper), I'll add the "Import" clause, and write myself a note to try removing it later.
Best, Kevin On 11/11/2020 4:44 PM, Duncan Murdoch wrote:
Here's what I think is happening.In the movMF:::.onLoad function there's a test whether flexmix is installed. If found, then it is loaded and some methods are set. (I'm not sure what caused flexmix to be installed: I didn't intentionally install it, but it ended up in there when I installed enough stuff to check Mercator.)In the R-devel --as-cran checks, some checks are run with only strong dependencies of your package visible. Somehow I think that .onLoad function sees flexmix and loads it, but then some other part of the check can't see it.A workaround is to add flexmix to your Imports clause. This is a strong enough dependency to make it visible, and the error goes away.HOWEVER, to me this is pretty clearly an R-devel bug: you have no control over methods set by packages that you don't even use, so you shouldn't have to change your dependency lists if one of them sets a method that you're using.Duncan Murdoch On 11/11/2020 3:31 p.m., Kevin R. Coombes wrote:Oh, I forgot to mention explicitly that checking (with --as-cran) on the development version of R on Windows also produces no errors or warnings. On 11/11/2020 1:39 PM, Kevin R. Coombes wrote:Hi Duncan, I just sent a longer version of this message, but it looks to me like the underlying issue is the fact that flexmix and Mercator both define and export "show" methods for their S4 classes. What confuses me is why the NAMESPACE of a package that is merely Suggest'ed by something several layers down the hierarchy should get attached and cause an issue like this one. (The attached NAMESPACE happens in current versions of R.) Thanks, Kevin On 11/11/2020 1:07 PM, Duncan Murdoch wrote:Okay, I've tried testing on my Mac with R 4.0.3 and R-devel for the new one, 4.0.3 for the CRAN version. I'm not seeing any check error with the CRAN version. I get an error trying to check 0.11.4 from R-forge because I don't have flexmix installed. If I take flexmix out of the Suggests list, it checks with no error on 4.0.3, but I get the error you saw on R-devel when checked with --as-cran. I tried debugging this, and narrowed it down a bit. It happens when your package is installed, in particular in the do_install_source() function in src/library/tools/R/install.R. But that function runs a new R instance, and I didn't get to debugging that. I'll try again later today if nobody else figures it out. Duncan Murdoch On 11/11/2020 12:03 p.m., Kevin R. Coombes wrote:Hi Duncan,Oops; I didn't realize I had forgotten to push updates to the OOMPA website. The code for Mercator is contained as part of the Thresher project in the subversion repository on R-Forge. (https://r-forge.r-project.org/projects/thresher/) It's under pkg/Mercator below that URL Thanks, Kevin On 11/11/2020 11:30 AM, Duncan Murdoch wrote:Uwe suggested you suggest flexmix, but I see below you already tried that. I'd like to take a look, but I can't find your package. The existingversion on CRAN gives the URL as http://oompa.r-forge.r-project.org/,but I can't see it mentioned there. Duncan Murdoch On 11/11/2020 8:44 a.m., Kevin R. Coombes wrote:Hi, I am trying to figure out how to fix warnings from two of the CRAN machines on the submission of an update to a package. The only change tomy package was to add a "show" method to one of the S4 classes, whichwas requested by a reviewer of the paper we submitted. The inability toget this updated package into CRAN is the only thing holding up therevision (and probable acceptance) of the manuscript. The same "warnings"s were found in the previous version. The package is called Mercator, and the CRAN check results from the last version are here: https://cran.r-project.org/web/checks/check_results_Mercator.htmlI get warnings from the two fedora machine instances (clang and gcc).They both reportCheck: whether package can be installed. Result: WARN Found the following significant warnings:Warning: namespace ‘flexmix’ is not available and has beenreplaced> > Check: data for non-ASCII charactersResult: WARNWarning: namespace 'flexmix' is not available and has beenreplaced by .GlobalEnv when processing object '<unknown>'The relationships in the DESCRIPTION files are: 1. Mercator depends on Thresher 2. Thresher imports moVMF 3. moMVF suggests flexmix On my Windows machine, the package builds and installs with no errors orwarnings even if flexmix is not available (which I believe to be thecorrect behavior). On R-Forge, both the Windows and LINUX versions buildand install with no errors or warnings. On R-Hub, tested on multipleLINUX versions, the package builds and installs with no errors or warnings. And flexmix is still clearly available from CRAN: https://cran.r-project.org/web/packages/flexmix/index.html In the latest attempt to get things to work, I added Suggests: flexmixinto the DESCRIPTION file for Mercator, but this didn't help fix theproblem on CRAN. Is there anything I can do to fix this problem (other than moan here on this list and hope that CRAN can just install flexmix on those machines)? Thanks in advance for your help, Kevin [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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