[R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On Sun, Feb 25, 2018 at 1:41 AM, Duncan Murdoch
On 24/02/2018 7:26 PM, Marius Hofert wrote:
On Sun, Feb 25, 2018 at 1:09 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
On 25 February 2018 at 00:45, Marius Hofert wrote:
| A package 'foo' uses a package 'bar' (in Imports). 'bar' has been
| archived and the maintainer of 'foo' was asked to fix the dependency
| on 'bar' according to WRE 1.1.3.1.
|
| Working with 'bar::' everywhere (and requireNamespace("bar", quietly =
| TRUE)), as well as moving 'bar' from Imports to Suggests seems to work
| but is not accepted on submission. Removing 'bar' also from Suggests
| leads to
|
| '::' or ':::' import not declared from: ?bar?
| 'loadNamespace' or 'requireNamespace' call not declared from: ?bar?
|
| Does this mean it is not possible to use 'bar' anymore in 'foo'?

Your title says "conditionally".

Does your code actually behave conditionally, ie does foo check if bar is
available, and only use its code if it is?
Hi Dirk,

nice to hear from you and thanks for helping!

Yes, 'foo' essentially has one main function with an argument 'method
= c("b", "ba", "bar")'. If the user chooses to call the function with
method = "bar", then it is checked whether "bar" is installed (as
described in WRE) and an error is thrown if not.
Don't throw an error, work around it.
Hi,

the 'workaround' is the error: to tell the user not to use it (but one
of the other available methods).

To be more precise: 'bar' is the package 'loon' for dynamic graphics
(and 'foo' is 'zenplots'). If that's not installed, the user can
choose to work with the other (non-dynamic) graphics packages. If a
user actively chooses to do the plotting with loon but doesn't have
loon installed, the error is a logical consequence.
If you have no alternative code,
then don't test the "bar" code unless "bar" is installed.
The main plotting function in zenplots uses:

    if(pkg == "loon" && !requireNamespace("loon", quietly = TRUE))
        stop("Package 'loon' is not available.")

... and if it's installed, it will call various further functions from
loon (now all used via "loon::..."). There are no tests or examples
that fail, everything works -- it's just that the use of "::"
generates the warning I mentioned which is (most likely) unacceptable
for upload to CRAN.
The basic idea is that your package should pass tests without errors
even if "bar" is not available.
It does -- except for the 'warning':

'::' or ':::' import not declared from: ?bar?
'loadNamespace' or 'requireNamespace' call not declared from: ?bar?
I think Dirk is wrong saying that "bar" has to be available; CRAN isn't
going to go looking for it.  But they do want your package to pass all
tests even if none of the Suggests packages is available.
'loon' is not in Suggests. It originally was in 'Imports', then I put
But you still have
Suggests: loon,
Please fix and resubmit.

... so it shouldn't appear in 'Suggests' either (I guess). That's why
I also removed it from Suggests, but then (because of the above
warning), I can't submit either.

Not sure how to solve this (... and thought that others might have a
similar problem with archived packages -- thus this post).

Cheers,
Marius
Duncan Murdoch

One additional difficulty may be that even for Suggests, it still has to be
accessible "somewhere" .
The full story is this: 'bar' has been archived because 'problems were
not corrected despite reminders'. 'bar' is mainly developed on github
and is probably easy to fix, but I also couldn't reach the maintainer
and I thought it's better to 'decrease' the dependency on 'bar' as
much as possible. 'bar' is actually quite intrusive to install/use
(requires R to be configured with tcltk). However, 'bar' provides some
nice features which the other methods ("b", "ba") don't have -- would
be a pity to completely remove 'bar' from 'foo'.

So 'bar' is on github (and thus could be installed from there + 'foo'
could make use of 'bar' conditionally... just don't know how to submit
'foo' to CRAN because of the warning)

Cheers,
M

And "archived" is not.  You could just move bar
onto a drat repo you set yp -- we have done the same for data packages and
have a R Journal paper describing it:

    https://journal.r-project.org/archive/2017/RJ-2017-026/index.html

Hth, Dirk

--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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R-package-devel at r-project.org mailing list
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On Sun, Feb 25, 2018 at 1:41 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
On 24/02/2018 7:26 PM, Marius Hofert wrote:
On Sun, Feb 25, 2018 at 1:09 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
On 25 February 2018 at 00:45, Marius Hofert wrote:
| A package 'foo' uses a package 'bar' (in Imports). 'bar' has been
| archived and the maintainer of 'foo' was asked to fix the dependency
| on 'bar' according to WRE 1.1.3.1.
|
| Working with 'bar::' everywhere (and requireNamespace("bar", quietly =
| TRUE)), as well as moving 'bar' from Imports to Suggests seems to work
| but is not accepted on submission. Removing 'bar' also from Suggests
| leads to
|
| '::' or ':::' import not declared from: ?bar?
| 'loadNamespace' or 'requireNamespace' call not declared from: ?bar?
|
| Does this mean it is not possible to use 'bar' anymore in 'foo'?

Your title says "conditionally".

Does your code actually behave conditionally, ie does foo check if bar is
available, and only use its code if it is?
Hi Dirk,

nice to hear from you and thanks for helping!

Yes, 'foo' essentially has one main function with an argument 'method
= c("b", "ba", "bar")'. If the user chooses to call the function with
method = "bar", then it is checked whether "bar" is installed (as
described in WRE) and an error is thrown if not.
Don't throw an error, work around it.
Hi,

the 'workaround' is the error: to tell the user not to use it (but one
of the other available methods).

To be more precise: 'bar' is the package 'loon' for dynamic graphics
(and 'foo' is 'zenplots'). If that's not installed, the user can
choose to work with the other (non-dynamic) graphics packages. If a
user actively chooses to do the plotting with loon but doesn't have
loon installed, the error is a logical consequence.

If you have no alternative code,
then don't test the "bar" code unless "bar" is installed.
The main plotting function in zenplots uses:

     if(pkg == "loon" && !requireNamespace("loon", quietly = TRUE))
         stop("Package 'loon' is not available.")

... and if it's installed, it will call various further functions from
loon (now all used via "loon::..."). There are no tests or examples
that fail, everything works -- it's just that the use of "::"
generates the warning I mentioned which is (most likely) unacceptable
for upload to CRAN.

The basic idea is that your package should pass tests without errors
even if "bar" is not available.
It does -- except for the 'warning':

'::' or ':::' import not declared from: ?bar?
'loadNamespace' or 'requireNamespace' call not declared from: ?bar?
That's because 'bar' is not in Suggests.

I think Dirk is wrong saying that "bar" has to be available; CRAN isn't
going to go looking for it.  But they do want your package to pass all
tests even if none of the Suggests packages is available.
'loon' is not in Suggests. It originally was in 'Imports', then I put
it to 'Suggests', but when I submitted, Uwe wrote:

But you still have
Suggests: loon,
Please fix and resubmit >
... so it shouldn't appear in 'Suggests' either (I guess). That's why
I also removed it from Suggests, but then (because of the above
warning), I can't submit either.
I suspect you didn't run an --as-cran check with no 'loon' available, 
and if you had, you would have received warnings or errors.

If you did run that check and it didn't give warnings or errors, then 
things have changed; sorry for misleading you.

Duncan Murdoch
Not sure how to solve this (... and thought that others might have a
similar problem with archived packages -- thus this post).

Cheers,
Marius

Duncan Murdoch

One additional difficulty may be that even for Suggests, it still has to be
accessible "somewhere" .
The full story is this: 'bar' has been archived because 'problems were
not corrected despite reminders'. 'bar' is mainly developed on github
and is probably easy to fix, but I also couldn't reach the maintainer
and I thought it's better to 'decrease' the dependency on 'bar' as
much as possible. 'bar' is actually quite intrusive to install/use
(requires R to be configured with tcltk). However, 'bar' provides some
nice features which the other methods ("b", "ba") don't have -- would
be a pity to completely remove 'bar' from 'foo'.

So 'bar' is on github (and thus could be installed from there + 'foo'
could make use of 'bar' conditionally... just don't know how to submit
'foo' to CRAN because of the warning)

Cheers,
M

And "archived" is not.  You could just move bar
onto a drat repo you set yp -- we have done the same for data packages and
have a R Journal paper describing it:

     https://journal.r-project.org/archive/2017/RJ-2017-026/index.html

Hth, Dirk

--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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