Forking and adapting an R package

Duncan Murdoch <murdoch.duncan at gmail.com> hat am 12. Juli 2016 um 19:38
geschrieben:

On 12/07/2016 7:28 AM, timo at timogrossenbacher.ch wrote:

Hello.

I'm trying to adapt the package ?hexbin? to suit my needs. This is the first
time I do this. I've read a bit through Hadley's ?R packages?, but now I'm
pretty lost (from a workflow point of view). I am using RStudio and Hadley's
devtools.

So I forked the repo I want to adapt: https://github.com/grssnbchr/hexbin
and
cloned it using RStudio (I created a new project). What I basically want to
do
is adapt the package slightly and use the adapted source on my use case (an
Rmd
file in another location) - ideally, I would call the respective function
(hexbin::grid.hexagons) in the Rmd and the source code of ?hexbin? would be
called and debugged (just for understanding what the package ?hexbin?
actually
does in that case, I do not have to build it yet, or even publish it). What
is
the workflow for this?

This is more of an R-devel question, so I've posted my followup there 
(as well as a private copy to you).

The fact that you've forked the package shouldn't matter. You are 
working in RStudio, so the way to work with a package is:

1. Open the project consisting of your local package.
2. In the Build pane, click on "Build and Reload".

What "Build and reload" does is to install the package from the source 
in the project, then restart R and load the installed package.

Test your code in this new R session. If you're working on a vignette, 
you can open the vignette, and execute the code chunks one by one.

If they all succeed in that context, they still might not when you run 
checks: it *won't* have your package loaded when it compiles a 
vignette. You need to put an explicit

library(hexbin)

in one of the code chunks.

Duncan Murdoch

Also, I tried running devtools::check() and it already fails there:
R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"

Platform: x86_64-pc-linux-gnu (64-bit)

devtools::check()

Updating hexbin documentation
Loading hexbin
Creating a generic function for ?plot? from package ?graphics? in package
?hexbin?
Creating a generic function for ?summary? from package ?base? in package
?hexbin?
Setting env vars
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
CFLAGS : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building hexbin
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
--quiet
CMD build '/home/tgrossen/R/hexbin' --no-resave-data --no-manual

* checking for file ?/home/tgrossen/R/hexbin/DESCRIPTION? ... OK
* preparing ?hexbin?:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR

Error: processing vignette 'hexagon_binning.Rnw' failed with diagnostics:
chunk 1 (label = comphexsq)
Error in eval(expr, envir, enclos) : could not find function ?hexbin?
Execution halted
Error: Command failed (1)

As you can see, I am very much lost. I googled for "adapt R package and
debug"
and so forth but couldn't find any tutorial or anything.

Thanks,

Timo

Duncan Murdoch <murdoch.duncan at gmail.com> hat am 12. Juli 2016 um 19:38
geschrieben:

On 12/07/2016 7:28 AM, timo at timogrossenbacher.ch wrote:

Hello.

I'm trying to adapt the package ?hexbin? to suit my needs. This is the

first

time I do this. I've read a bit through Hadley's ?R packages?, but now

I'm

pretty lost (from a workflow point of view). I am using RStudio and

Hadley's

devtools.

So I forked the repo I want to adapt:

https://github.com/grssnbchr/hexbin

and
cloned it using RStudio (I created a new project). What I basically

want to

do
is adapt the package slightly and use the adapted source on my use

case (an

Rmd
file in another location) - ideally, I would call the respective

function

(hexbin::grid.hexagons) in the Rmd and the source code of ?hexbin?

would be

called and debugged (just for understanding what the package ?hexbin?
actually
does in that case, I do not have to build it yet, or even publish it).

What

is
the workflow for this?

This is more of an R-devel question, so I've posted my followup there
(as well as a private copy to you).

Okay, I'm now subscribed to this list, too.

The fact that you've forked the package shouldn't matter. You are
working in RStudio, so the way to work with a package is:

1. Open the project consisting of your local package.
2. In the Build pane, click on "Build and Reload".

This works. devtools::build() though throws the same error with the
vignette as
with devtools::check(). See below.

What "Build and reload" does is to install the package from the source
in the project, then restart R and load the installed package.

Test your code in this new R session. If you're working on a vignette,
you can open the vignette, and execute the code chunks one by one.

Ok. But how do I debug the source code of that package? I.e. I want to
call a
function from that package from another, external script (that is not part
of
that project), and then jump into the function execution and debug it.
Because when it's built it's no longer "plain source code", or am I
completely
wrong with this? Or/and do I have to make the  external script part of the
hexbin project?

If they all succeed in that context, they still might not when you run
checks: it *won't* have your package loaded when it compiles a
vignette. You need to put an explicit

library(hexbin)

This is actually done in the chunk that fails (it fails on the last line
here).

library("grid")
library("hexbin")
x <- rnorm(1000)
y <- rnorm(1000)
##-- Hexagon Bins: --
hbin <- hexbin(x,y, xbins = 25)

in one of the code chunks.

Duncan Murdoch

Also, I tried running devtools::check() and it already fails there:
R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"

Platform: x86_64-pc-linux-gnu (64-bit)

devtools::check()

Updating hexbin documentation
Loading hexbin
Creating a generic function for ?plot? from package ?graphics? in

package

?hexbin?
Creating a generic function for ?summary? from package ?base? in

package

?hexbin?
Setting env vars

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

CFLAGS : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building hexbin

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
--quiet
CMD build '/home/tgrossen/R/hexbin' --no-resave-data --no-manual

* checking for file ?/home/tgrossen/R/hexbin/DESCRIPTION? ... OK
* preparing ?hexbin?:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR

Error: processing vignette 'hexagon_binning.Rnw' failed with

diagnostics:

chunk 1 (label = comphexsq)
Error in eval(expr, envir, enclos) : could not find function ?hexbin?
Execution halted
Error: Command failed (1)

As you can see, I am very much lost. I googled for "adapt R package and
debug"
and so forth but couldn't find any tutorial or anything.

Thanks,

Timo