R devel - Apr 2013 - Rebuild package on R 3.0.0 without source code?

R-developers,
I have a binary R package built using R 2.14.1 that I would like to run on R
3.0.0. Unfortunately, the original source code is unavailable, so I cannot
rebuild the package as R 3.0.0 requires.

Is there a straight forward way of converting the package (.rdb, .rdx and .rds
files) in the binary package from a 2.14.1 version to a 3.0.0 version without
the source code (perhaps uncompressing/recompressing somehow)?

Naturally, since the R code is visible, I know I can output all of the parsed
objects in the package to a text file to make a skeleton package that can then
be built/installed. Something like this:

       objs <- ls(envir=loadNamespace("binaryPkg"), all.names=TRUE)
       dump(objs, file="code.R",
envir=loadNamespace("binaryPkg"))

However, I'd still lose all the man pages, and since I get a couple of
"deparse may be incomplete" warnings, I worry that this may be
introducing additional bugs.
 
Is there a magic solution here, or is this a fool's errand?

Thanks, Robert

Robert McGehee, CFA
Geode Capital Management, LLC
One Post Office Square, 28th Floor | Boston, MA | 02109
Direct: (617)392-8396

On Apr 18, 2013, at 10:07 AM, "McGehee, Robert" <Robert.McGehee at
geodecapital.com> wrote:
> R-developers,
> I have a binary R package built using R 2.14.1 that I would like to run on
R 3.0.0. Unfortunately, the original source code is unavailable, so I cannot
rebuild the package as R 3.0.0 requires.
> 
> Is there a straight forward way of converting the package (.rdb, .rdx and
.rds files) in the binary package from a 2.14.1 version to a 3.0.0 version
without the source code (perhaps uncompressing/recompressing somehow)?
> 
> Naturally, since the R code is visible, I know I can output all of the
parsed objects in the package to a text file to make a skeleton package that can
then be built/installed. Something like this:
> 
>       objs <- ls(envir=loadNamespace("binaryPkg"),
all.names=TRUE)
>       dump(objs, file="code.R",
envir=loadNamespace("binaryPkg"))
> 
> However, I'd still lose all the man pages, and since I get a couple of
"deparse may be incomplete" warnings, I worry that this may be
introducing additional bugs.
> 
> Is there a magic solution here, or is this a fool's errand?
> 
> Thanks, Robert
Robert,

Which package? You might find some older version of the package source code
here:

  http://cran.us.r-project.org/src/contrib/Archive/

or have you already looked there?

Regards,

Marc Schwartz

On 18/04/2013 11:07 AM, McGehee, Robert wrote:
> R-developers,
> I have a binary R package built using R 2.14.1 that I would like to run on
R 3.0.0. Unfortunately, the original source code is unavailable, so I cannot
rebuild the package as R 3.0.0 requires.
>
> Is there a straight forward way of converting the package (.rdb, .rdx and
.rds files) in the binary package from a 2.14.1 version to a 3.0.0 version
without the source code (perhaps uncompressing/recompressing somehow)?
>
> Naturally, since the R code is visible, I know I can output all of the
parsed objects in the package to a text file to make a skeleton package that can
then be built/installed. Something like this:
>
>         objs <- ls(envir=loadNamespace("binaryPkg"),
all.names=TRUE)
>         dump(objs, file="code.R",
envir=loadNamespace("binaryPkg"))
>
> However, I'd still lose all the man pages, and since I get a couple of
"deparse may be incomplete" warnings, I worry that this may be
introducing additional bugs.
>   
> Is there a magic solution here, or is this a fool's errand?
I'd guess there's no magic solution.  Deparsing is not perfect, so just 
about any automatic solution may introduce additional bugs.

Use it as a lesson:  you shouldn't use closed-source software.

BTW, you're probably aware of this, but others might not be:  if this 
was a CRAN package, it quite likely does have the source for the old 
version still available.  Take a look around the "Archive" link on the
contributed packages page.  CRAN is very reluctant to delete sources 
once it has made them public. So it's quite safe to install binaries 
from CRAN, just not necessarily from other sources.

Duncan Murdoch

On 18/04/2013 16:07, McGehee, Robert wrote:
> R-developers,
> I have a binary R package built using R 2.14.1 that I would like to run on
R 3.0.0. Unfortunately, the original source code is unavailable, so I cannot
rebuild the package as R 3.0.0 requires.
>
> Is there a straight forward way of converting the package (.rdb, .rdx and
.rds files) in the binary package from a 2.14.1 version to a 3.0.0 version
without the source code (perhaps uncompressing/recompressing somehow)?
>
> Naturally, since the R code is visible, I know I can output all of the
parsed objects in the package to a text file to make a skeleton package that can
then be built/installed. Something like this:
>
>         objs <- ls(envir=loadNamespace("binaryPkg"),
all.names=TRUE)
>         dump(objs, file="code.R",
envir=loadNamespace("binaryPkg"))
>
> However, I'd still lose all the man pages, and since I get a couple of
"deparse may be incomplete" warnings, I worry that this may be
introducing additional bugs.
>
> Is there a magic solution here, or is this a fool's errand?
No magic solution, and the following may not work, but it might.

Make a simple package with the correct DESCRIPTION file.  Install that 
somewhere new.  Then use the installed DESCRIPTION file and 
Meta/package.rds to replace the versions you got from 2.14.1.


It is possible to extract the man pages: the key step is 
tools:::fetchRdDB.  On my system

names(tools:::fetchRdDB('/Users/ripley/R/R-devel/library/MASS/help/MASS'))
tools:::fetchRdDB('/Users/ripley/R/R-devel/library/MASS/help/MASS',
'rlm')

work: the layout of the pages is a little odd.


>
> Thanks, Robert
>
> Robert McGehee, CFA
> Geode Capital Management, LLC
> One Post Office Square, 28th Floor | Boston, MA | 02109
> Direct: (617)392-8396
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595