[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 '<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]]

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]]

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 '<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]]

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]]

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]]

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]]

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 '<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]]

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]]

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]]

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]]

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]]

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 at r-project.org on behalf of murdoch.duncan at 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 at r-project.org mailing list
     >>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
     >>>>>>

     >>>>>

     >>>>

     >>>

     >>

     >

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 at r-project.org on behalf of murdoch.duncan at 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 at r-project.org mailing list
     >>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
     >>>>>>

     >>>>>

     >>>>

     >>>

     >>

     >