R devel - Jul 2009 - strange bug? with R CMD check

Hello,

I am trying to get a package to pass R CMD check on an iMac running  
Mac OS X.  When the package is named safeBinaryRegression I get the  
following warning from R CMD check:

* checking whether the name space can be loaded with stated  
dependencies ... WARNING
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   function 'make_lp' not provided by package 'lpSolveAPI'
Calls: loadNamespace -> library.dynam -> dyn.load
Execution halted

A namespace must be able to be loaded with just the base namespace  
loaded:
otherwise if the namespace gets loaded by a saved object, the session  
will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.


Here is the contents of the DESCRIPTION:

Package: safeBinaryRegression
Version: 0.1-2
Date: 2009-07-01
Title: Safe Binary Regression
Author: Kjell Konis <kjell.konis at epfl.ch>
Maintainer: Kjell Konis <kjell.konis at epfl.ch>
Depends: R (>= 2.9.1), lpSolveAPI (>= 5.5.0.14)
LinkingTo: lpSolveAPI
Description: Overloads the stats::glm function so that a test for the  
existence of
   the maximum likelihood estimate is computed as part of the fitting  
procedure for
   binary regression models.
License: GPL-2


Here is the contents of the NAMESPACE:

export(glm)
useDynLib(safeBinaryRegression, linprog, reducedLP)


The strange thing is that if I change the length of the package name  
(for example safeBinaryRegression to safeBinaryRegress) the warning  
goes away and R CMD check completes successfully.  Also, regardless of  
the package name, the package installs and runs as expected.  I'm at a  
loss trying to figure out what's going on.

To reproduce:

(1) check out the sbr package (which passes R CMD check)

   svn checkout svn://svn.r-forge.r-project.org/svnroot/sbr/pkg  
safeBinaryRegression

(2) replace sbr with safeBinaryRegression in DESCRIPTION and NAMESPACE

(3) run R CMD check


Session Info:

 > sessionInfo()
R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1

locale:
fr_CH.UTF-8/en_US.UTF-8/C/C/fr_CH.UTF-8/fr_CH.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Thanks,
Kjell

Yes, I managed to work around the problem. You can still reproduce the  
strange behavior with revision 5 of the package though.

svn checkout svn://svn.r-forge.r-project.org/svnroot/sbr/pkg at 5  
safeBinaryRegression

Kjell


On 22 juil. 09, at 07:31, Paul Johnson wrote:
> I am guessing you solved this, because I just downloaded your svn
> files and there's no more "sbr" and the check passes on my
system.
>
> Right?
>
> pj
>
> On Tue, Jul 21, 2009 at 8:32 AM, Kjell Konis<kjell.konis at epfl.ch>
> wrote:
>> Hello,
>>
>> I am trying to get a package to pass R CMD check on an iMac running  
>> Mac OS
>> X.  When the package is named safeBinaryRegression I get the  
>> following
>> warning from R CMD check:
>>
>> * checking whether the name space can be loaded with stated  
>> dependencies ...
>> WARNING
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  function 'make_lp' not provided by package
'lpSolveAPI'
>> Calls: loadNamespace -> library.dynam -> dyn.load
>> Execution halted
>>
>> A namespace must be able to be loaded with just the base namespace  
>> loaded:
>> otherwise if the namespace gets loaded by a saved object, the  
>> session will
>> be unable to start.
>>
>> Probably some imports need to be declared in the NAMESPACE file.
>>
>>
>> Here is the contents of the DESCRIPTION:
>>
>> Package: safeBinaryRegression
>> Version: 0.1-2
>> Date: 2009-07-01
>> Title: Safe Binary Regression
>> Author: Kjell Konis <kjell.konis at epfl.ch>
>> Maintainer: Kjell Konis <kjell.konis at epfl.ch>
>> Depends: R (>= 2.9.1), lpSolveAPI (>= 5.5.0.14)
>> LinkingTo: lpSolveAPI
>> Description: Overloads the stats::glm function so that a test for the
>> existence of
>>  the maximum likelihood estimate is computed as part of the fitting
>> procedure for
>>  binary regression models.
>> License: GPL-2
>>
>>
>> Here is the contents of the NAMESPACE:
>>
>> export(glm)
>> useDynLib(safeBinaryRegression, linprog, reducedLP)
>>
>>
>> The strange thing is that if I change the length of the package  
>> name (for
>> example safeBinaryRegression to safeBinaryRegress) the warning goes  
>> away and
>> R CMD check completes successfully.  Also, regardless of the  
>> package name,
>> the package installs and runs as expected.  I'm at a loss trying to
>> figure
>> out what's going on.
>>
>> To reproduce:
>>
>> (1) check out the sbr package (which passes R CMD check)
>>
>>  svn checkout svn://svn.r-forge.r-project.org/svnroot/sbr/pkg
>> safeBinaryRegression
>>
>> (2) replace sbr with safeBinaryRegression in DESCRIPTION and  
>> NAMESPACE
>>
>> (3) run R CMD check
>>
>>
>> Session Info:
>>
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> fr_CH.UTF-8/en_US.UTF-8/C/C/fr_CH.UTF-8/fr_CH.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> Thanks,
>> Kjell
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
>
> -- 
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas