[R-pkg-devel] Calls not declared

I am developing my first package and found these errors when checking it.

Any help?


* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
   ?qgraph? ?semPlot? ?sna? ?xlsx?

On 11/03/2019 9:53 a.m., Elias Carvalho wrote:

I am developing my first package and found these errors when checking

it.

Any help?


* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
   ?qgraph? ?semPlot? ?sna? ?xlsx?

Without seeing your package I might be wrong, but I believe this says 
that you have something like

library(qgraph)

somewhere in your R code, without listing

Depends: qgraph

in your DESCRIPTION file.

HOWEVER, fixing this warning will lead to a different one, because 
that's not the recommended way to do things now.  There are two 
possibilities:

1.  Your package is useless without the dependency.

In this case, you should put

Imports:  qgraph, ...

in the DESCRIPTION file (where ... lists the other packages with the 
same status), and list the functions in those packages in your
NAMESPACE 
file, using

importFrom(qgraph, ...)

etc.  (If you use Roxygen, you use comments in the source to get it to 
put this into your NAMESPACE file.)

2.  Your package works without the dependency, but you may want to
issue 
errors or warnings if it is missing.

Then you should put

Suggests:  qgraph, ...

in the DESCRIPTION file, and to use a function from it, use something
like

if (requireNamespace("qgraph")) {
  qgraph::foo(...)
} else
  warning("qgraph is not available.")

Duncan Murdoch

I did not see any mention of the distinction between Depends and Imports in the DESCRIPTION file... which is always a risk when duplicating existing documentation in an email. Imports is preferred because the user does not have to put definitions only needed inside your package into their public search path (easier to make under-the-hood changes to the package implementation), but Depends is better when they cannot make use of your package without those definitions (e.g. you return a ggplot object from one of your functions).

So do keep reading the documentation... email is just a kickstart.

On March 11, 2019 8:19:33 AM PDT, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

On 11/03/2019 9:53 a.m., Elias Carvalho wrote:

I am developing my first package and found these errors when checking

it.

Any help?


* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
    ?qgraph? ?semPlot? ?sna? ?xlsx?

Without seeing your package I might be wrong, but I believe this says
that you have something like

library(qgraph)

somewhere in your R code, without listing

Depends: qgraph

in your DESCRIPTION file.

HOWEVER, fixing this warning will lead to a different one, because
that's not the recommended way to do things now.  There are two
possibilities:

1.  Your package is useless without the dependency.

In this case, you should put

Imports:  qgraph, ...

in the DESCRIPTION file (where ... lists the other packages with the
same status), and list the functions in those packages in your
NAMESPACE
file, using

importFrom(qgraph, ...)

etc.  (If you use Roxygen, you use comments in the source to get it to
put this into your NAMESPACE file.)

2.  Your package works without the dependency, but you may want to
issue
errors or warnings if it is missing.

Then you should put

Suggests:  qgraph, ...

in the DESCRIPTION file, and to use a function from it, use something
like

if (requireNamespace("qgraph")) {
   qgraph::foo(...)
} else
   warning("qgraph is not available.")

Duncan Murdoch

On 11/03/2019 11:32 a.m., Jeff Newmiller wrote:

I did not see any mention of the distinction between Depends and

Imports in the DESCRIPTION file... which is always a risk when
duplicating existing documentation in an email. Imports is preferred
because the user does not have to put definitions only needed inside
your package into their public search path (easier to make
under-the-hood changes to the package implementation), but Depends is
better when they cannot make use of your package without those
definitions (e.g. you return a ggplot object from one of your
functions).

You don't need Depends to be able to handle ggplot2 objects. You'll get

the methods when the package is loaded, so they'll print fine without 
having ggplot2 on the search list.

There are very few cases nowadays where it makes sense to use Depends.

Duncan Murdoch

So do keep reading the documentation... email is just a kickstart.

On March 11, 2019 8:19:33 AM PDT, Duncan Murdoch

<murdoch.duncan at gmail.com> wrote:

On 11/03/2019 9:53 a.m., Elias Carvalho wrote:

I am developing my first package and found these errors when

checking

it.

Any help?


* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
    ?qgraph? ?semPlot? ?sna? ?xlsx?

Without seeing your package I might be wrong, but I believe this

says

that you have something like

library(qgraph)

somewhere in your R code, without listing

Depends: qgraph

in your DESCRIPTION file.

HOWEVER, fixing this warning will lead to a different one, because
that's not the recommended way to do things now.  There are two
possibilities:

1.  Your package is useless without the dependency.

In this case, you should put

Imports:  qgraph, ...

in the DESCRIPTION file (where ... lists the other packages with the
same status), and list the functions in those packages in your
NAMESPACE
file, using

importFrom(qgraph, ...)

etc.  (If you use Roxygen, you use comments in the source to get it

to

put this into your NAMESPACE file.)

2.  Your package works without the dependency, but you may want to
issue
errors or warnings if it is missing.

Then you should put

Suggests:  qgraph, ...

in the DESCRIPTION file, and to use a function from it, use

something

like

if (requireNamespace("qgraph")) {
   qgraph::foo(...)
} else
   warning("qgraph is not available.")

Duncan Murdoch

Ah, so as long as you don't need to call a normal function to make use of the returned object you don't need Depends. But in this example, the user would then need to call library(ggplot2) in order to, say, change an axis title.

A bit more subtle than I thought.

On March 11, 2019 10:07:12 AM PDT, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

On 11/03/2019 11:32 a.m., Jeff Newmiller wrote:

I did not see any mention of the distinction between Depends and

Imports in the DESCRIPTION file... which is always a risk when
duplicating existing documentation in an email. Imports is preferred
because the user does not have to put definitions only needed inside
your package into their public search path (easier to make
under-the-hood changes to the package implementation), but Depends is
better when they cannot make use of your package without those
definitions (e.g. you return a ggplot object from one of your
functions).

You don't need Depends to be able to handle ggplot2 objects. You'll get

the methods when the package is loaded, so they'll print fine without
having ggplot2 on the search list.

There are very few cases nowadays where it makes sense to use Depends.

Duncan Murdoch

So do keep reading the documentation... email is just a kickstart.

On March 11, 2019 8:19:33 AM PDT, Duncan Murdoch

<murdoch.duncan at gmail.com> wrote:

On 11/03/2019 9:53 a.m., Elias Carvalho wrote:

I am developing my first package and found these errors when

checking

it.

Any help?


* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
     ?qgraph? ?semPlot? ?sna? ?xlsx?

Without seeing your package I might be wrong, but I believe this

says

that you have something like

library(qgraph)

somewhere in your R code, without listing

Depends: qgraph

in your DESCRIPTION file.

HOWEVER, fixing this warning will lead to a different one, because
that's not the recommended way to do things now.  There are two
possibilities:

1.  Your package is useless without the dependency.

In this case, you should put

Imports:  qgraph, ...

in the DESCRIPTION file (where ... lists the other packages with the
same status), and list the functions in those packages in your
NAMESPACE
file, using

importFrom(qgraph, ...)

etc.  (If you use Roxygen, you use comments in the source to get it

to

put this into your NAMESPACE file.)

2.  Your package works without the dependency, but you may want to
issue
errors or warnings if it is missing.

Then you should put

Suggests:  qgraph, ...

in the DESCRIPTION file, and to use a function from it, use

something

like

if (requireNamespace("qgraph")) {
    qgraph::foo(...)
} else
    warning("qgraph is not available.")

Duncan Murdoch

On 11/03/2019 2:12 p.m., Jeff Newmiller wrote:

Ah, so as long as you don't need to call a normal function to make use

of the returned object you don't need Depends. But in this example, the
user would then need to call library(ggplot2) in order to, say, change an
axis title.

I think the current philosophy is that if a user wants to be able to use
ggplot2 functions, the user should ask for them, they shouldn't be
automagically added to the search list.  If a user wants to change the
axis title and doesn't want to have ggplot2 on their search list, that
is definitely possible:

ggplot2::qplot(1:10, 1:10) + ggplot2::xlab("new x label")

Duncan Murdoch

A bit more subtle than I thought.

On March 11, 2019 10:07:12 AM PDT, Duncan Murdoch <

murdoch.duncan at gmail.com> wrote:

On 11/03/2019 11:32 a.m., Jeff Newmiller wrote:

I did not see any mention of the distinction between Depends and

Imports in the DESCRIPTION file... which is always a risk when
duplicating existing documentation in an email. Imports is preferred
because the user does not have to put definitions only needed inside
your package into their public search path (easier to make
under-the-hood changes to the package implementation), but Depends is
better when they cannot make use of your package without those
definitions (e.g. you return a ggplot object from one of your
functions).

You don't need Depends to be able to handle ggplot2 objects. You'll get

the methods when the package is loaded, so they'll print fine without
having ggplot2 on the search list.

There are very few cases nowadays where it makes sense to use Depends.

Duncan Murdoch

So do keep reading the documentation... email is just a kickstart.

On March 11, 2019 8:19:33 AM PDT, Duncan Murdoch

<murdoch.duncan at gmail.com> wrote:

On 11/03/2019 9:53 a.m., Elias Carvalho wrote:

I am developing my first package and found these errors when

checking

it.

Any help?


* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
     ?qgraph? ?semPlot? ?sna? ?xlsx?

Without seeing your package I might be wrong, but I believe this

says

that you have something like

library(qgraph)

somewhere in your R code, without listing

Depends: qgraph

in your DESCRIPTION file.

HOWEVER, fixing this warning will lead to a different one, because
that's not the recommended way to do things now.  There are two
possibilities:

1.  Your package is useless without the dependency.

In this case, you should put

Imports:  qgraph, ...

in the DESCRIPTION file (where ... lists the other packages with the
same status), and list the functions in those packages in your
NAMESPACE
file, using

importFrom(qgraph, ...)

etc.  (If you use Roxygen, you use comments in the source to get it

to

put this into your NAMESPACE file.)

2.  Your package works without the dependency, but you may want to
issue
errors or warnings if it is missing.

Then you should put

Suggests:  qgraph, ...

in the DESCRIPTION file, and to use a function from it, use

something

like

if (requireNamespace("qgraph")) {
    qgraph::foo(...)
} else
    warning("qgraph is not available.")

Duncan Murdoch