[R-pkg-devel] Strange error from CRAN on package submission
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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Function editGrob not found unless grid is in Depends
Dear all,
I have recently been trying to write a plotting function where a external PNG
file is drawn onto a ggmap object.
I managed to achieve this by using ggmap::inset , inputting as a grob the
result of applying grid::rasterGrob to the image rotated with
magick::image_rotate .
I therefore added ggmap, ggplot2, grid and magick to Imports in DESCRIPTION,
and added the corresponding imports in NAMESPACE
However, when running R CMD check, I got an error saying 'could not find
function editGrob', when running the example code for the mentioned plotting
function.
I confirmed the error also happens if I install and load the package in a fresh
R session.
If I then load explicitly grid through library(grid), the error disappears.
I tried to add explicitly importFrom("grid", editGrob) to NAMESPACE, but that
made no difference.
I have only been able to solve the problem by adding "grid" to Depends in
DESCRIPTION instead of Imports.
The code for the problematic plotting function can be found at
https://github.com/Rafael-Ayala/openSkies/blob/main/R/openSkies_plottingFunctions.R
(lines 61 to 91)
I would greatly appreciate if anybody could clarify why "grid" needs to be
added to Depends in this case, and why not even adding NAMESPACE
importFrom("grid", editGrob) fixes the problem if "grid" is left in Imports!
Thanks a lot in advance
Best wishes,
Rafa
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Re: [R-pkg-devel] Strange error from CRAN on package submission
You have to suggest flexmix. Best, Uwe Ligges On 11.11.2020 14:44, 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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
Hi Uwe, Thanks for the suggestion. I thought of that idea last night, and tried it with the latest submission of version 0.11.4 of Mercator. That version is still in the submission queue waiting for manual inspection, but it gave the same error message. (See https://win-builder.r-project.org/incoming_pretest/Mercator_0.11.4_2020_014655/Debian/00check.log) I think I may try to "Import" or "Depend" on flexmix to force it to be available. Is there some reason why my program should even need to know that flexmix is suggested several layers down the dependency hierarchy? For building and installing the package (or running R CMD check ---as-cran), I tried on my machine when flexmix is not even installed, and got no errors or warnings. There is clearly something I don't understand about namespaces, and I'd like to learn it to avoid this kind of situation in the future. Best, Kevin On 11/11/2020 11:14 AM, Uwe Ligges wrote: You have to suggest flexmix. Best, Uwe Ligges On 11.11.2020 14:44, 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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
Next guess is that you need more, because you may have an object that needs the flexmix, so likely something S4 related? I can take a closer look. Best, Uwe Ligges On 11.11.2020 17:30, 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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
HI Uwe,
That might be the key observation. The change to Mercator in this
package was to add a "show" method to an S4 class. In its NAMESPACE, the
flexmix package also exports a "show" method.
Both "flexmix" and "Mercator" have an
import("methods")
directive in their NAMESPACE files, which is where the base method for
"show" comes from. Also, if you just type show at the command prompt to
see the definition, you get the parenthetical note that
"(This generic function excludes non-simple inheritance' see ?setIs.)"
I don't completely understand what this parenthetical remark means, but
I have a suspicion that it is highly relevant to my problem.
If I run
library("Mercator")
showMethods("show")
on a system where flexmix is installed, then the "show" method for
flexmix (and related objects) is listed, because the flexmix NAMESPACE
has been attached. If I run the same code on an R system where flexmix
is not installed, then, of course, neither the NAMESPACE nor the method
is available.
I suspect (but am by no means certain) that the combination of that
parenthetical remark above and the existence of the "show" method in the
suggested package is why I am getting errors on some systems.
But I don't really understand why. My package doesn't need the flexmix
version of show. And (as Uwe said in an earlier comment), I thought that
"Suggests" isn't supposed to be inherited. I don't want the flexmix
NAMESPACE attached, since nothing in my package nor in the packages I
directly want (Thresher by "Depends" and then moVMF by "Imports")
actually requires it.
Why does the flexmix NAMESPACE get attached if some other package down
the line merely suggests it? Is that supposed to happen? To me, it feels
like a bug in the sense that it surprises the user (i.e., the package
developer). And I guess is potentially a bug for the ultimate user of
the package, since it adds a NAMESPACE that was not specifically
requested by the top level package being loaded.
In any event, what's the best advice now on how to proceed?
Thanks again,
Kevin
On 11/11/2020 11:34 AM, Uwe Ligges wrote:
Next guess is that you need more, because you may have an object that
needs the flexmix, so likely something S4 related? I can take a closer
look.
Best,
Uwe Ligges
On 11.11.2020 17:30, 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 ''
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
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Re: [R-pkg-devel] Strange error from CRAN on package submission
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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
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 '' 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Strange error from CRAN on package submission
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 '' 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'
Re: [R-pkg-devel] Strange error from CRAN on package submission
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 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 '' 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 install
