Help finding source of warnings

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Help finding source of warnings

Prof J C Nash (U30A)
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

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Re: Help finding source of warnings

Kurt Hornik-5
>>>>> 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

> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: Help finding source of warnings

Dirk Eddelbuettel
In reply to this post by Prof J C Nash (U30A)

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 | [hidden email]

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Re: Help finding source of warnings

Prof J C Nash (U30A)
In reply to this post by Kurt Hornik-5
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
>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel

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