R devel - Jan 2015 - Help finding source of warnings

I've been implementing a wrapper to the 2011 Fortran version of 
L-BFGS-B. In optim(), R uses a C translation of a Fortran version (the 
version number does not appear to be documented by the original 
authors). The authors of the original Fortran code have updated it and 
published the reasons in ACM TOMS due to inefficiencies and a bug.

In running the checks on the resulting package (which is on R-forge 
under the optimizer project), I'm getting a number of warning messages 
of the type

Warning in file.copy(file.path(.Library, pkg, "DESCRIPTION"), pd) :
   problem copying /usr/lib/R/library/mgcv/DESCRIPTION to 
/tmp/Rtmp0kkeHo/RLIBS_1214765d1c5f/mgcv/DESCRIPTION: No such file or 
directory

which reference DESCRIPTIONs for a number of packages other than the one 
being checked -- here mgcv -- and which are not referenced in my package 
as far as I can determine.

Possibly unrelated, when I run the code on a problem, it works for one 
run, then gives a NAMESPACE error and failure on the second try. Apart 
from this, checks and unit tests appear to work correctly.

Does anyone have pointers where I might find some ideas on the origin of 
the issue(s)? I suspect the warning messages are not particularly 
indicative of the source of the warnings, but that I have some subtle 
glitch in the setup and call to the Fortran.

I suspect this is not platform dependent, but I'm running Linux Mint 
17.1 (ubuntu derivative), and  R 3.1.2.

Cheers, JN

>>>>> Prof J C Nash (U30A) writes:
> I've been implementing a wrapper to the 2011 Fortran version of 
> L-BFGS-B. In optim(), R uses a C translation of a Fortran version (the 
> version number does not appear to be documented by the original 
> authors). The authors of the original Fortran code have updated it and 
> published the reasons in ACM TOMS due to inefficiencies and a bug.
> In running the checks on the resulting package (which is on R-forge 
> under the optimizer project), I'm getting a number of warning messages 
> of the type
> Warning in file.copy(file.path(.Library, pkg, "DESCRIPTION"), pd)
:
>    problem copying /usr/lib/R/library/mgcv/DESCRIPTION to 
> /tmp/Rtmp0kkeHo/RLIBS_1214765d1c5f/mgcv/DESCRIPTION: No such file or 
> directory
> which reference DESCRIPTIONs for a number of packages other than the one 
> being checked -- here mgcv -- and which are not referenced in my package 
> as far as I can determine.
> Possibly unrelated, when I run the code on a problem, it works for one 
> run, then gives a NAMESPACE error and failure on the second try. Apart 
> from this, checks and unit tests appear to work correctly.
> Does anyone have pointers where I might find some ideas on the origin of 
> the issue(s)? I suspect the warning messages are not particularly 
> indicative of the source of the warnings, but that I have some subtle 
> glitch in the setup and call to the Fortran.
> I suspect this is not platform dependent, but I'm running Linux Mint 
> 17.1 (ubuntu derivative), and  R 3.1.2.
John: maybe you did not install the recommended packages?
(On Debian, the corresponding package would be r-recommended.)

Best
-k
> Cheers, JN
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

On 18 January 2015 at 09:03, Prof J C Nash (U30A) wrote:
| I've been implementing a wrapper to the 2011 Fortran version of 
| L-BFGS-B. In optim(), R uses a C translation of a Fortran version (the 
| version number does not appear to be documented by the original 
| authors). The authors of the original Fortran code have updated it and 
| published the reasons in ACM TOMS due to inefficiencies and a bug.
| 
| In running the checks on the resulting package (which is on R-forge 
| under the optimizer project), I'm getting a number of warning messages 
| of the type

If you were so kind to share the __name of the subpackage__ you fail to test,
one could attempt to help you.
 
| Warning in file.copy(file.path(.Library, pkg, "DESCRIPTION"), pd) :
|    problem copying /usr/lib/R/library/mgcv/DESCRIPTION to 
| /tmp/Rtmp0kkeHo/RLIBS_1214765d1c5f/mgcv/DESCRIPTION: No such file or 
| directory
| 
| which reference DESCRIPTIONs for a number of packages other than the one 
| being checked -- here mgcv -- and which are not referenced in my package 
| as far as I can determine.

I've seen that when R tries to be too clever by half -- somehow .libPaths()
ends up being partial.  Following the high-level decision by Hornik, Leisch
and Eddelbuettel made circa 2003 in a pub in Vienna, the Debian packages use
three entries, and if you have recommended packages installed via apt, R may
now pretend they don't exist.  

I could work on an alternate setup via Github and Travis but as you managed
to make this non-reproducible I cannot actually try that ...

Dirk

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

Kurt pointed to the issue. Thanks. I did install r-recommended, but it 
seems something went wrong at some point. A reinstall got rid of the 
warnings.

Thanks to Dirk for his offer of help.

Now I'm still getting a namespace issue on the second run of an 
optimization problem. However, I think I need to do some more digging to 
narrow down where this issue is lurking. It may be some local matter, as 
with the r-recommended links failing.

Best, JN

On 15-01-18 09:27 AM, Kurt Hornik wrote:
>>>>>> Prof J C Nash (U30A) writes:
>
>> I've been implementing a wrapper to the 2011 Fortran version of
>> L-BFGS-B. In optim(), R uses a C translation of a Fortran version (the
>> version number does not appear to be documented by the original
>> authors). The authors of the original Fortran code have updated it and
>> published the reasons in ACM TOMS due to inefficiencies and a bug.
>
>> In running the checks on the resulting package (which is on R-forge
>> under the optimizer project), I'm getting a number of warning
messages
>> of the type
>
>> Warning in file.copy(file.path(.Library, pkg, "DESCRIPTION"),
pd) :
>>     problem copying /usr/lib/R/library/mgcv/DESCRIPTION to
>> /tmp/Rtmp0kkeHo/RLIBS_1214765d1c5f/mgcv/DESCRIPTION: No such file or
>> directory
>
>> which reference DESCRIPTIONs for a number of packages other than the
one
>> being checked -- here mgcv -- and which are not referenced in my
package
>> as far as I can determine.
>
>> Possibly unrelated, when I run the code on a problem, it works for one
>> run, then gives a NAMESPACE error and failure on the second try. Apart
>> from this, checks and unit tests appear to work correctly.
>
>> Does anyone have pointers where I might find some ideas on the origin
of
>> the issue(s)? I suspect the warning messages are not particularly
>> indicative of the source of the warnings, but that I have some subtle
>> glitch in the setup and call to the Fortran.
>
>> I suspect this is not platform dependent, but I'm running Linux
Mint
>> 17.1 (ubuntu derivative), and  R 3.1.2.
>
> John: maybe you did not install the recommended packages?
> (On Debian, the corresponding package would be r-recommended.)
>
> Best
> -k
>
>> Cheers, JN
>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel