[R-pkg-devel] Strange error from CRAN on package submission

Kevin R. Coombes kev|n@r@coombe@ @end|ng |rom gm@||@com
Thu Nov 12 17:39:09 CET 2020


Hi Martin,

I think you may be right that it is something odd about the 
configuration on the test machine, since I haven't been able to 
reproduce it anywhere else. But Duncan did say he could reproduce it in 
R-devel but not R-4.0.3, so there's that.

The error message is buried deep in this thread, but it was:

Check: whether package can be installed.
Result: WARN
     Found the following significant  warnings:
     Warning: namespace ‘flexmix’ is  not available and has been replaced

Check: data for non-ASCII characters
Result: WARN
     Warning: namespace 'flexmix'  is not available and has been replaced
     by .GlobalEnv when processing  object '<unknown>'

Best,
   Kevin

On 11/12/2020 10:13 AM, Martin Morgan wrote:
> This seems more like a problem with the CRAN test machine, with the movMF package installed with flexmix available but loaded with flexmix not available, maybe interacting with a caching mechanism used by the methods package to avoid re-computing methods tables? Otherwise how would movMF ever know to create the flexmix class / method?
>
> It seems like this could cause problems for the user if they installed movMV with flexmix available, but removed flexmix. This seems like a subtler variation of 'I installed package A but then removed dependency B and now A doesn't work', which could be a bug in R's remove.packages() but....
>
> I tried to emulate the scenario of installing movMF and then removing flexmix in an interactive session, and then looking for the warning reported below. I was not successful, but the build report with the error is no longer available so I don't know what I'm looking for...
>
> Martin Morgan
>
> On 11/11/20, 4:44 PM, "R-package-devel on behalf of Duncan Murdoch" <r-package-devel-bounces using r-project.org on behalf of murdoch.duncan using gmail.com> 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 web
>      >>>> site.
>      >>>>
>      >>>> 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 existing
>      >>>>> version 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 to
>      >>>>>> my package was to add a "show" method to one of the S4 classes, which
>      >>>>>> was requested by a reviewer of the paper we submitted. The
>      >>>>>> inability to
>      >>>>>> get this updated package into CRAN  is the only thing holding up the
>      >>>>>> revision (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.html
>      >>>>>>
>      >>>>>> I get warnings from the two fedora machine instances (clang and gcc).
>      >>>>>> They both report
>      >>>>>>
>      >>>>>>> Check: whether package can be installed.
>      >>>>>>> Result: WARN
>      >>>>>>>         Found the following significant  warnings:
>      >>>>>>>         Warning: namespace ‘flexmix’ is  not available and has been
>      >>>>>>> replaced
>      >>>>>>     >
>      >>>>>>     > Check: data for non-ASCII characters
>      >>>>>>> Result: WARN
>      >>>>>>>          Warning: namespace 'flexmix'  is not available and has been
>      >>>>>>> replaced
>      >>>>>>>          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 or
>      >>>>>> warnings even if flexmix is not available (which I believe to be the
>      >>>>>> correct behavior). On R-Forge, both the Windows and LINUX versions
>      >>>>>> build
>      >>>>>> and install with no errors or warnings. On R-Hub, tested on multiple
>      >>>>>> LINUX 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: flexmix
>      >>>>>> into the DESCRIPTION file for Mercator, but this didn't help fix the
>      >>>>>> problem 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 using r-project.org mailing list
>      >>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>      >>>>>>
>      >>>>>
>      >>>>
>      >>>
>      >>
>      >
>
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