[R-pkg-devel] ERROR from R CMD check that I have never seen before

On 25.05.2015 19:28, Richard M. Heiberger wrote:

I will send it.  what is the best way?  direct to you? posting it on my
website?

Website so others can look at it as well?

Best,
Uwe

On Mon, May 25, 2015 at 1:21 PM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> wrote:

On 25.05.2015 18:59, Richard M. Heiberger wrote:

I am still working on your suggestions.  While doing so I found a more
general concern.

I am now trapped in incompatible circular dependencies.  I don't know
how to resolve them.

The immediate specific is that ggplot2::layer and latticeExtra::layer
are incompatible.

Due to these dependencies I don't think I have control over which one
has precedence.

You have: import selectively from these packages using importFrom()
directives rather than simple import(). So you only import the layer
version
you actually need in your package (if any).
Try to get rid of Depends and solve all dependenciy issues via imports,
i.e.
NAMESPACE directives, where possible.

I depend on lattice and latticeExtra and gridExtra.
I import Hmisc and Rcmdr

Hmisc Depends:  lattice and ggplot2
Imports: latticeExtra,  gridExtra

gridExtra suggests ggplot2 and lattice

Rcmdr imports abind,
      suggests e1071, Hmisc

The message I am seeing with HH (which I cannot interpret by myself)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
    there is no package called 'abind'
seems to be a consequence of importing Rcmdr.
Since I do have this package the message is confusing at best.  Can
you rephrase the message?

Perhaps a bug in another package? ANyway, can you give us the HH version
that triggers these problems?

Perhaps by listing which specific line in which file is triggering it.

I also sometime get a similar complaint about e1071 which I don't use
at all but is suggested by Rcmdr.

If a function in e1071 that needs it is called from a function in your
package, you may need to suggest it as well.

I also get a complaint about TeachingDemos, which I have but don't use
in HH.  I haven't spotted
where that dependency is coming from.  However I see that
TeachingDemos suggests both lattice and ggplot2.

Don't know, again, I'd need the full package in order to say more.

Best,
Uwe

Rich

On Mon, May 25, 2015 at 3:44 AM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> wrote:

Two ideas:

1. Solve the first error at first:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck =
vI[[j]]) :
    there is no package called 'abind'
Error: package or namespace load failed for 'HH'
Execution halted

Looks like you forgot to declare abind as an Imports in your
DESCRIPTION
file?


2. If you still get the other problems, please make a version of your
package available so that someone else can check and debug this.

Best,
Uwe Ligges





On 25.05.2015 05:01, Richard M. Heiberger wrote:

The problem is still there.  I am working on both Windows and
Macintosh.

The packages I have check clean using R-3.1.2 on Windows.
They "INSTALL --build" and "build" using 3.3.0-devl on Windows and
3.2.0
on Mac,

I downloaded R-devel for Windows this afternoon and updated to
Rtools33.
I have attached two R CMD check log files with this combination
* using R Under development (unstable) (2015-05-22 r68399)
* using platform: i386-w64-mingw32 (32-bit)


The 3.1-15 is the version currently on CRAN.
It complains it can't find Hmisc.  Hmisc is installed.
The built package inside the Rcheck directory loads.
Package check results on CRAN don't show this warning.


The 3.1-17 is the version I am working on.
It complains it can't find abind.  abind is installed.
It gives 6 versions of this message.
Error in validObject(.Object) :
     invalid class "ObjectsWithPackage" object: superclass
"atomicVector"
not defined in the environment of the object's class
I don't understand what is triggering them.
The built package inside the Rcheck directory loads.

On Sat, May 23, 2015 at 9:02 AM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> wrote:

Can you try a more recent version of R-devel with all relevant
packages
you
depend on re-installed?

Looks like either a bug in that months old version of R-devel or an
inconsistancy of installed packages and the version of the methods
package
or so.

Best,
Uwe Ligges




On 23.05.2015 05:29, Richard M. Heiberger wrote:

followup.

I backed up to R-3.1.2 and fixed the problems it found.
Then I tried again with R-3.2.0 and I am still getting these
messages

Error in validObject(.Object) :
      invalid class "ObjectsWithPackage" object: superclass
"atomicVector"
not defined in the environment of the object's class
Calls: <Anonymous> ... metaNameUndo -> new -> initialize ->
initialize
-> validObject
Execution halted

On Fri, May 22, 2015 at 8:08 PM, Richard M. Heiberger
<rmh at temple.edu>
wrote:

I am updating the HH package and have series of messages that I
don't
recognize.

bash-3.2$ R CMD check HH2
* using log directory
'/Users/rmh/WindowsC/HOME/rmh/HH-R.package/HH2.Rcheck'
* using R Under development (unstable) (2015-02-12 r67812)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: ASCII
* checking for file 'HH2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HH' version '3.1-17'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
      .DS_Store
      inst/.DS_Store
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'HH' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated
dependencies
...
OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated
dependencies
... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Error in validObject(.Object) :
      invalid class "ObjectsWithPackage" object: superclass
"atomicVector"
not defined in the environment of the object's class
Execution halted

I have two questions about it.
1. What is it checking?  There are no words in the message that
indicate which of my
functions is being looked at.

I am getting 6 of these.  They are all identically worded.
sometimes
they are
NOTE ERROR WARNING

Thanks
Rich

2. How can I run R CMD check, or its components, in a way that will
stop
and
let me investigate from the point?  I am looking for the equivalent
of
the R option
option(error=recover)