Re: [R-pkg-devel] Rcpp.package.skeleton -- Rcmd check --as-cran Windows

[Peter Clifford [peter.cliff...@stats.ox.ac.uk]]

It's Rcpp 0.12.12 and R 3.4.1.   If nobody can reproduce this with Windows
7 (?), I'll assume it's something odd with my system.

Thanks

On Mon, Aug 28, 2017 at 7:48 PM, Uwe Ligges  wrote:

>
>
> On 28.08.2017 18:10, Peter Clifford [peter.cliff...@stats.ox.ac.uk]
> wrote:
>
>> On Mon, Aug 28, 2017 at 4:53 PM, Dirk Eddelbuettel 
>> wrote:
>>
>>
>>> On 28 August 2017 at 10:21, Peter Clifford [
>>> peter.cliff...@stats.ox.ac.uk]
>>> wrote:
>>> | R version 3.4.0 and 3.4.1 with Rcpp 0.12.12 Windows 7.
>>>
>>> Potentially wrong list here as it is an Rcpp question...
>>>
>>> | Trying to fix persistent "Found no calls to: 'R_registerRoutines',
>>> | 'R_useDynamicSymbols'" problem, when running Rcmd check --as-cran.
>>> |
>>> | Eventually gave up with my own package and tried the simplest possible
>>> case
>>> | using Rcpp.package.skeleton("test") with defaults, i.e. the hello_world
>>> | example.
>>> | That works fine with Rcmd build test and Rcmd check test_1.0.tar.gz,
>>> but
>>> if
>>> | I try Rcmd check --as-cran test_1.0.tar.gz I get the NOTE:
>>> |
>>> | File 'test/libs/x64/test.dll':
>>> |   Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
>>> |
>>> | It is good practice to register native routines and to disable symbol
>>> | search.
>>> |
>>> | I don't whether there really is a registration problem and if there is,
>>> how
>>> | to fix it.
>>> |
>>> | I'd be grateful for suggestions. Thanks.
>>>
>>> I cannot reproduce this.  Full log below -- new package, and running
>>> compileAttributes() creates the registration as it should.
>>>
>>> (For all the R Core members in the audience: We still need pre-build /
>>> post-build hooks like cleanup to have R CMD foo do more things. Happy to
>>> work
>>> on that if somewhat can work with me to shepherd this in ...)
>>>
>>> Dirk
>>>
>>>
>>> edd@bud:/tmp$ r -e 'Rcpp::Rcpp.package.skeleton("barePackage")'
>>> Creating directories ...
>>> Creating DESCRIPTION ...
>>> Creating NAMESPACE ...
>>> Creating Read-and-delete-me ...
>>> Saving functions and data ...
>>> Making help files ...
>>> Done.
>>> Further steps are described in './barePackage/Read-and-delete-me'.
>>>
>>> Adding Rcpp settings
>>>   >> added Imports: Rcpp
>>>   >> added LinkingTo: Rcpp
>>>   >> added useDynLib directive to NAMESPACE
>>>   >> added importFrom(Rcpp, evalCpp) directive to NAMESPACE
>>>   >> added example src file using Rcpp attributes
>>>   >> added Rd file for rcpp_hello_world
>>>   >> compiled Rcpp attributes
>>> edd@bud:/tmp$
>>> edd@bud:/tmp$ build.r barePackagePlus/# simple littler wrapper
>>> * checking for file ‘barePackagePlus/DESCRIPTION’ ... OK
>>> * preparing ‘barePackagePlus’:
>>> * checking DESCRIPTION meta-information ... OK
>>> * cleaning src
>>> * installing the package to process help pages
>>> * saving partial Rd database
>>> * cleaning src
>>> * checking for LF line-endings in source and make files
>>> * checking for empty or unneeded directories
>>> * building ‘barePackagePlus_1.0.tar.gz’
>>>
>>> edd@bud:/tmp$
>>> edd@bud:/tmp$ RD CMD check --as-cran barePackage_1.0.tar.gz
>>> * using log directory ‘/tmp/barePackage.Rcheck’
>>> * using R Under development (unstable) (2017-08-24 r73125)
>>> * using platform: x86_64-pc-linux-gnu (64-bit)
>>> * using session charset: UTF-8
>>> * using option ‘--as-cran’
>>> * checking for file ‘barePackage/DESCRIPTION’ ... OK
>>> * checking extension type ... Package
>>> * this is package ‘barePackage’ version ‘1.0’
>>> * checking CRAN incoming feasibility ... NOTE
>>> Maintainer: ‘Your Name ’
>>>
>>> New submission
>>> * 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 ... OK
>>> * checking for portable file names ... OK
>>> * checking for sufficient/correct file permissions ... OK
>>> * checking whether package ‘barePackage’ 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 loading without being on the library search path ... OK
>>> * checking use of S3 registration ... OK
>>> * checking 

Re: [R-pkg-devel] Rcpp.package.skeleton -- Rcmd check --as-cran Windows

[Uwe Ligges]

On 28.08.2017 18:10, Peter Clifford [peter.cliff...@stats.ox.ac.uk]  wrote:

On Mon, Aug 28, 2017 at 4:53 PM, Dirk Eddelbuettel  wrote:



On 28 August 2017 at 10:21, Peter Clifford [peter.cliff...@stats.ox.ac.uk]
wrote:
| R version 3.4.0 and 3.4.1 with Rcpp 0.12.12 Windows 7.

Potentially wrong list here as it is an Rcpp question...

| Trying to fix persistent "Found no calls to: 'R_registerRoutines',
| 'R_useDynamicSymbols'" problem, when running Rcmd check --as-cran.
|
| Eventually gave up with my own package and tried the simplest possible
case
| using Rcpp.package.skeleton("test") with defaults, i.e. the hello_world
| example.
| That works fine with Rcmd build test and Rcmd check test_1.0.tar.gz, but
if
| I try Rcmd check --as-cran test_1.0.tar.gz I get the NOTE:
|
| File 'test/libs/x64/test.dll':
|   Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
|
| It is good practice to register native routines and to disable symbol
| search.
|
| I don't whether there really is a registration problem and if there is,
how
| to fix it.
|
| I'd be grateful for suggestions. Thanks.

I cannot reproduce this.  Full log below -- new package, and running
compileAttributes() creates the registration as it should.

(For all the R Core members in the audience: We still need pre-build /
post-build hooks like cleanup to have R CMD foo do more things. Happy to
work
on that if somewhat can work with me to shepherd this in ...)

Dirk


edd@bud:/tmp$ r -e 'Rcpp::Rcpp.package.skeleton("barePackage")'
Creating directories ...
Creating DESCRIPTION ...
Creating NAMESPACE ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './barePackage/Read-and-delete-me'.

Adding Rcpp settings
  >> added Imports: Rcpp
  >> added LinkingTo: Rcpp
  >> added useDynLib directive to NAMESPACE
  >> added importFrom(Rcpp, evalCpp) directive to NAMESPACE
  >> added example src file using Rcpp attributes
  >> added Rd file for rcpp_hello_world
  >> compiled Rcpp attributes
edd@bud:/tmp$
edd@bud:/tmp$ build.r barePackagePlus/# simple littler wrapper
* checking for file ‘barePackagePlus/DESCRIPTION’ ... OK
* preparing ‘barePackagePlus’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘barePackagePlus_1.0.tar.gz’

edd@bud:/tmp$
edd@bud:/tmp$ RD CMD check --as-cran barePackage_1.0.tar.gz
* using log directory ‘/tmp/barePackage.Rcheck’
* using R Under development (unstable) (2017-08-24 r73125)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘barePackage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barePackage’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Your Name ’

New submission
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘barePackage’ 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... OK
* 

Re: [R-pkg-devel] Rcpp.package.skeleton -- Rcmd check --as-cran Windows

[Peter Clifford [peter.cliff...@stats.ox.ac.uk]]

On Mon, Aug 28, 2017 at 4:53 PM, Dirk Eddelbuettel  wrote:

>
> On 28 August 2017 at 10:21, Peter Clifford [peter.cliff...@stats.ox.ac.uk]
> wrote:
> | R version 3.4.0 and 3.4.1 with Rcpp 0.12.12 Windows 7.
>
> Potentially wrong list here as it is an Rcpp question...
>
> | Trying to fix persistent "Found no calls to: 'R_registerRoutines',
> | 'R_useDynamicSymbols'" problem, when running Rcmd check --as-cran.
> |
> | Eventually gave up with my own package and tried the simplest possible
> case
> | using Rcpp.package.skeleton("test") with defaults, i.e. the hello_world
> | example.
> | That works fine with Rcmd build test and Rcmd check test_1.0.tar.gz, but
> if
> | I try Rcmd check --as-cran test_1.0.tar.gz I get the NOTE:
> |
> | File 'test/libs/x64/test.dll':
> |   Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
> |
> | It is good practice to register native routines and to disable symbol
> | search.
> |
> | I don't whether there really is a registration problem and if there is,
> how
> | to fix it.
> |
> | I'd be grateful for suggestions. Thanks.
>
> I cannot reproduce this.  Full log below -- new package, and running
> compileAttributes() creates the registration as it should.
>
> (For all the R Core members in the audience: We still need pre-build /
> post-build hooks like cleanup to have R CMD foo do more things. Happy to
> work
> on that if somewhat can work with me to shepherd this in ...)
>
> Dirk
>
>
> edd@bud:/tmp$ r -e 'Rcpp::Rcpp.package.skeleton("barePackage")'
> Creating directories ...
> Creating DESCRIPTION ...
> Creating NAMESPACE ...
> Creating Read-and-delete-me ...
> Saving functions and data ...
> Making help files ...
> Done.
> Further steps are described in './barePackage/Read-and-delete-me'.
>
> Adding Rcpp settings
>  >> added Imports: Rcpp
>  >> added LinkingTo: Rcpp
>  >> added useDynLib directive to NAMESPACE
>  >> added importFrom(Rcpp, evalCpp) directive to NAMESPACE
>  >> added example src file using Rcpp attributes
>  >> added Rd file for rcpp_hello_world
>  >> compiled Rcpp attributes
> edd@bud:/tmp$
> edd@bud:/tmp$ build.r barePackagePlus/# simple littler wrapper
> * checking for file ‘barePackagePlus/DESCRIPTION’ ... OK
> * preparing ‘barePackagePlus’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to process help pages
> * saving partial Rd database
> * cleaning src
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building ‘barePackagePlus_1.0.tar.gz’
>
> edd@bud:/tmp$
> edd@bud:/tmp$ RD CMD check --as-cran barePackage_1.0.tar.gz
> * using log directory ‘/tmp/barePackage.Rcheck’
> * using R Under development (unstable) (2017-08-24 r73125)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * using option ‘--as-cran’
> * checking for file ‘barePackage/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘barePackage’ version ‘1.0’
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ‘Your Name ’
>
> New submission
> * 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 ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘barePackage’ 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 loading without being on the library search path ... OK
> * checking use of S3 registration ... OK
> * checking dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... OK
> * checking Rd metadata ... OK
> * checking Rd line widths ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated 

Re: [R-pkg-devel] Rcpp.package.skeleton -- Rcmd check --as-cran Windows

[Dirk Eddelbuettel]

On 28 August 2017 at 10:21, Peter Clifford [peter.cliff...@stats.ox.ac.uk]  
wrote:
| R version 3.4.0 and 3.4.1 with Rcpp 0.12.12 Windows 7.

Potentially wrong list here as it is an Rcpp question...
 
| Trying to fix persistent "Found no calls to: 'R_registerRoutines',
| 'R_useDynamicSymbols'" problem, when running Rcmd check --as-cran.
| 
| Eventually gave up with my own package and tried the simplest possible case
| using Rcpp.package.skeleton("test") with defaults, i.e. the hello_world
| example.
| That works fine with Rcmd build test and Rcmd check test_1.0.tar.gz, but if
| I try Rcmd check --as-cran test_1.0.tar.gz I get the NOTE:
| 
| File 'test/libs/x64/test.dll':
|   Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
| 
| It is good practice to register native routines and to disable symbol
| search.
| 
| I don't whether there really is a registration problem and if there is, how
| to fix it.
| 
| I'd be grateful for suggestions. Thanks.

I cannot reproduce this.  Full log below -- new package, and running
compileAttributes() creates the registration as it should.

(For all the R Core members in the audience: We still need pre-build /
post-build hooks like cleanup to have R CMD foo do more things. Happy to work
on that if somewhat can work with me to shepherd this in ...)

Dirk


edd@bud:/tmp$ r -e 'Rcpp::Rcpp.package.skeleton("barePackage")'
Creating directories ...
Creating DESCRIPTION ...
Creating NAMESPACE ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './barePackage/Read-and-delete-me'.

Adding Rcpp settings
 >> added Imports: Rcpp
 >> added LinkingTo: Rcpp
 >> added useDynLib directive to NAMESPACE
 >> added importFrom(Rcpp, evalCpp) directive to NAMESPACE
 >> added example src file using Rcpp attributes
 >> added Rd file for rcpp_hello_world
 >> compiled Rcpp attributes 
edd@bud:/tmp$ 
edd@bud:/tmp$ build.r barePackagePlus/# simple littler wrapper
* checking for file ‘barePackagePlus/DESCRIPTION’ ... OK
* preparing ‘barePackagePlus’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘barePackagePlus_1.0.tar.gz’

edd@bud:/tmp$ 
edd@bud:/tmp$ RD CMD check --as-cran barePackage_1.0.tar.gz 
* using log directory ‘/tmp/barePackage.Rcheck’
* using R Under development (unstable) (2017-08-24 r73125)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘barePackage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barePackage’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Your Name ’

New submission
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘barePackage’ 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/tmp/barePackage.Rcheck/00check.log’
for details.


edd@bud:/tmp$ 




-- 

[R-pkg-devel] Rcpp.package.skeleton -- Rcmd check --as-cran Windows

[Peter Clifford [peter.cliff...@stats.ox.ac.uk]]

R version 3.4.0 and 3.4.1 with Rcpp 0.12.12 Windows 7.

Trying to fix persistent "Found no calls to: 'R_registerRoutines',
'R_useDynamicSymbols'" problem, when running Rcmd check --as-cran.

Eventually gave up with my own package and tried the simplest possible case
using Rcpp.package.skeleton("test") with defaults, i.e. the hello_world
example.
That works fine with Rcmd build test and Rcmd check test_1.0.tar.gz, but if
I try Rcmd check --as-cran test_1.0.tar.gz I get the NOTE:

File 'test/libs/x64/test.dll':
  Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

I don't whether there really is a registration problem and if there is, how
to fix it.

I'd be grateful for suggestions. Thanks.

[[alternative HTML version deleted]]

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