Re: [Rd] problem with vignettes when S4 classes in packages overlap
On Tue, 18 Sep 2012, Paul Gilbert wrote:
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
Thanks for bringing this up. This is caused by maptools avoiding: Depends:
spatstat, which might create circularities. maptools and spatstat (which
defines the classes that maptools and trip augment by adding coercion to
and from their own or sp classes) mutually Suggest: each other. trip
Depends: spatstat, but out of the box has no NAMESPACE - I haven't
investigated whether adding one helps.
Adding maptools to trip::Depends removes the warnings; check passes as
before, so no side-effects I can see. The auto-generated NAMESPACE is
then:
# Default NAMESPACE created by R
# Remove the previous line if you edit this file
# Export all names
exportPattern(".")
# Import all packages listed as Imports or Depends
import(
methods,
sp,
spatstat,
maptools
)
Since trip was last updated in May 2011, it is missing both a NAMESPACE
file, and suggestion of the correct adehabitat?? package(s) - adehabitat
is deprecated. I don't think that this is an S4 problem, I think it is
about keeping packages in sync with the R engine, especially with regard
to NAMESPACE, etc., and with packages named in DESCRIPTION. This may carry
over to the main case here, but I haven't checked.
Roger
I am writing a vignette which loads RMySQL and RPostgreSQL. This produces the
warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “dbObjectId” in package ‘RPostgreSQL’ seems
equivalent to one from package ‘RMySQL’ and is not turning on duplicate class
definitions for this class
This can be reproduced by running
R CMD Sweave --pdf Atest.Stex
where the file Atest.Stex has the lines
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\begin{Scode}
library("RMySQL")
library("RPostgreSQL")
\end{Scode}
\end{document}
These warnings only happen in a vignette. They are not produced if the lines
are entered in an R session.
(Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on Ubuntu)
Paul
--
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Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: roger.biv...@nhh.no
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Re: [Rd] problem with vignettes when S4 classes in packages overlap
On 9/18/2012 5:53 PM, Duncan Murdoch wrote:
On 12-09-18 7:50 PM, Spencer Graves wrote:
On 9/18/2012 4:23 PM, Duncan Murdoch wrote:
On 12-09-18 5:40 PM, Paul Gilbert wrote:
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
I am writing a vignette which loads RMySQL and RPostgreSQL. This
produces the warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “dbObjectId” in package ‘RPostgreSQL’
seems
equivalent to one from package ‘RMySQL’ and is not turning on
duplicate
class definitions for this class
This can be reproduced by running
R CMD Sweave --pdf Atest.Stex
where the file Atest.Stex has the lines
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\begin{Scode}
library("RMySQL")
library("RPostgreSQL")
\end{Scode}
\end{document}
These warnings only happen in a vignette. They are not produced if the
lines are entered in an R session.
(Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on
Ubunt
You'll get the warning in a regular session if you set
options(warn=1). I think Sweave is probably doing this so that
warnings show up around the time of the chunk they correspond to. It
does it in the command line version, but not in the Sweave() function
(which would save them up to the end).
I don't know if the warning is something you should worry about or not.
On August 30, 2012, CRAN maintainers rejected the latest version
of "fda", and I understood them to say it was rejected because the
current CRAN policy did not accept packages reporting either "Notes" or
"Warnings". As part of my efforts to comply with this, I started the
thread on [Rd] subject: "if(--as-cran)?" I added a function "CRAN" to
"fda", and I thought someone had added a more general function to the
development version of R. Unfortunately, I can't find documentation of
that more general function now.
I don't remember for sure, but I don't think your warning or note was
the same as Paul's. Generally it's not a good idea to suppress
warnings. Someone should fix things so there's no warning. I don't
know if that should be RCore because the methods package is issuing a
bogus warning, or the maintainer of one of the database packages, or
Paul. (From his example, it doesn't look like it should be Paul,
unless docs somewhere say that RMySQL and RPostgreSQL can't be used
together.)
In general, as a package user, I don't want people to be able to
suppress checks on CRAN. I want things fixed.
So I am pretty sure there won't ever be a reliable "CRAN-detector" put
into R. It would devalue the brand.
Our primary use of the "CRAN" function is to reduce test time:
Some of our "\examples" ran over 10 seconds on CRAN, and the package was
rejected on that basis.
With now over 4,000 packages on CRAN, maintaining it is taxing
the commitments of our volunteer CRAN maintainers. I believe the world
would be better off if people like Brian Ripley, Kurt Hornik, and Uwe
Ligges could hire (more) competent systems administrators and buy (more)
hardware to manage the details, so Ripley, Hornik, Ligges and others
could spend more time developing new statistical algorithms and helping
others with their responses on this list.
Assuming money is part of the problem, Jim Ramsay suggested that
CRAN issue a pro forma invoice to CRAN package maintainers for, say, 100
Euros each. Maintainers would be asked to pay it if they have a grant
that would support that but would be invited to plead poverty if they
don't. This would be similar to the current page charges with some
journals, which are forgiven for authors who would have to pay out of
their own pockets. Ramsay said he would happily pay some reasonable
amount, but he needs an invoice.
The same goes for R-Forge: It's a great service to the R
Community -- benefiting the entirety of humanity through the improved
decisions that R facilitates. They, too, could offer a better service
if they had a larger budget, I think.
Best Wishes,
Spencer
Duncan Murdoch
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Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
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Re: [Rd] problem with vignettes when S4 classes in packages overlap
On 18 September 2012 at 16:50, Spencer Graves wrote: |On August 30, 2012, CRAN maintainers rejected the latest version | of "fda", and I understood them to say it was rejected because the | current CRAN policy did not accept packages reporting either "Notes" or | "Warnings". That is not what the "CRAN Repository Policy" document says: * Please ensure that R CMD check --as-cran has been run on the tarball to be uploaded before submission. This should be done with the current release of R or (preferably) R-devel or R-patched. As “Writing R Extensions” says Please ensure that you can run through the complete procedure with only warnings that you understand and have reasons not to eliminate. In principle, packages must pass R CMD check without warnings or significant notes to be admitted to the main CRAN package area. If there are warnings or notes you cannot eliminate (for example because you believe them to be spurious) send an explanatory note as part of your covering email. Notr the qualifier "significant" in front of notes, so it is not "all notes" as you imply. Now, if would of course help if CRAN could specify what "significant notes" were ... Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] problem with vignettes when S4 classes in packages overlap
On 12-09-18 7:50 PM, Spencer Graves wrote:
On 9/18/2012 4:23 PM, Duncan Murdoch wrote:
On 12-09-18 5:40 PM, Paul Gilbert wrote:
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
I am writing a vignette which loads RMySQL and RPostgreSQL. This
produces the warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “dbObjectId” in package ‘RPostgreSQL’
seems
equivalent to one from package ‘RMySQL’ and is not turning on duplicate
class definitions for this class
This can be reproduced by running
R CMD Sweave --pdf Atest.Stex
where the file Atest.Stex has the lines
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\begin{Scode}
library("RMySQL")
library("RPostgreSQL")
\end{Scode}
\end{document}
These warnings only happen in a vignette. They are not produced if the
lines are entered in an R session.
(Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on Ubunt
You'll get the warning in a regular session if you set
options(warn=1). I think Sweave is probably doing this so that
warnings show up around the time of the chunk they correspond to. It
does it in the command line version, but not in the Sweave() function
(which would save them up to the end).
I don't know if the warning is something you should worry about or not.
On August 30, 2012, CRAN maintainers rejected the latest version
of "fda", and I understood them to say it was rejected because the
current CRAN policy did not accept packages reporting either "Notes" or
"Warnings". As part of my efforts to comply with this, I started the
thread on [Rd] subject: "if(--as-cran)?" I added a function "CRAN" to
"fda", and I thought someone had added a more general function to the
development version of R. Unfortunately, I can't find documentation of
that more general function now.
I don't remember for sure, but I don't think your warning or note was
the same as Paul's. Generally it's not a good idea to suppress
warnings. Someone should fix things so there's no warning. I don't
know if that should be RCore because the methods package is issuing a
bogus warning, or the maintainer of one of the database packages, or
Paul. (From his example, it doesn't look like it should be Paul,
unless docs somewhere say that RMySQL and RPostgreSQL can't be used
together.)
In general, as a package user, I don't want people to be able to
suppress checks on CRAN. I want things fixed.
So I am pretty sure there won't ever be a reliable "CRAN-detector" put
into R. It would devalue the brand.
Duncan Murdoch
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Re: [Rd] problem with vignettes when S4 classes in packages overlap
On 12-09-18 07:23 PM, Duncan Murdoch wrote:
On 12-09-18 5:40 PM, Paul Gilbert wrote:
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
I am writing a vignette which loads RMySQL and RPostgreSQL. This
produces the warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “dbObjectId” in package ‘RPostgreSQL’ seems
equivalent to one from package ‘RMySQL’ and is not turning on duplicate
class definitions for this class
This can be reproduced by running
R CMD Sweave --pdf Atest.Stex
where the file Atest.Stex has the lines
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\begin{Scode}
library("RMySQL")
library("RPostgreSQL")
\end{Scode}
\end{document}
These warnings only happen in a vignette. They are not produced if the
lines are entered in an R session.
(Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on Ubunt
You'll get the warning in a regular session if you set options(warn=1).
I think Sweave is probably doing this so that warnings show up around
the time of the chunk they correspond to. It does it in the command
line version, but not in the Sweave() function (which would save them up
to the end).
I don't know if the warning is something you should worry about or not.
It doesn't interfere with producing the vignette, but for submitting to
CRAN it is better not to have warnings coming from my package, even
though they are caused by a problem with other packages. Now that I know
why it only happens in the vignette, I guess I can suppress it (but it
would be nice to see the other packages fixed).
Thanks,
Paul
Duncan Murdoch
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Re: [Rd] problem with vignettes when S4 classes in packages overlap
On 9/18/2012 4:23 PM, Duncan Murdoch wrote:
On 12-09-18 5:40 PM, Paul Gilbert wrote:
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
I am writing a vignette which loads RMySQL and RPostgreSQL. This
produces the warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “dbObjectId” in package ‘RPostgreSQL’
seems
equivalent to one from package ‘RMySQL’ and is not turning on duplicate
class definitions for this class
This can be reproduced by running
R CMD Sweave --pdf Atest.Stex
where the file Atest.Stex has the lines
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\begin{Scode}
library("RMySQL")
library("RPostgreSQL")
\end{Scode}
\end{document}
These warnings only happen in a vignette. They are not produced if the
lines are entered in an R session.
(Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on Ubunt
You'll get the warning in a regular session if you set
options(warn=1). I think Sweave is probably doing this so that
warnings show up around the time of the chunk they correspond to. It
does it in the command line version, but not in the Sweave() function
(which would save them up to the end).
I don't know if the warning is something you should worry about or not.
On August 30, 2012, CRAN maintainers rejected the latest version
of "fda", and I understood them to say it was rejected because the
current CRAN policy did not accept packages reporting either "Notes" or
"Warnings". As part of my efforts to comply with this, I started the
thread on [Rd] subject: "if(--as-cran)?" I added a function "CRAN" to
"fda", and I thought someone had added a more general function to the
development version of R. Unfortunately, I can't find documentation of
that more general function now.
Spencer
Duncan Murdoch
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Re: [Rd] problem with vignettes when S4 classes in packages overlap
On 12-09-18 5:40 PM, Paul Gilbert wrote:
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
I am writing a vignette which loads RMySQL and RPostgreSQL. This
produces the warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “dbObjectId” in package ‘RPostgreSQL’ seems
equivalent to one from package ‘RMySQL’ and is not turning on duplicate
class definitions for this class
This can be reproduced by running
R CMD Sweave --pdf Atest.Stex
where the file Atest.Stex has the lines
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\begin{Scode}
library("RMySQL")
library("RPostgreSQL")
\end{Scode}
\end{document}
These warnings only happen in a vignette. They are not produced if the
lines are entered in an R session.
(Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on Ubunt
You'll get the warning in a regular session if you set options(warn=1).
I think Sweave is probably doing this so that warnings show up around
the time of the chunk they correspond to. It does it in the command
line version, but not in the Sweave() function (which would save them up
to the end).
I don't know if the warning is something you should worry about or not.
Duncan Murdoch
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