Re: [R-pkg-devel] What's recommended to do on "Suggests or Enhances not in mainstream repositories: ..."?

2016-05-22 Thread Balamuta, James Joseph
Greetings and Salutations Marius,

For implementation help with “Additional_repositories”, which lacks a bit of 
documentation, please see: 
http://thecoatlessprofessor.com/programming/r-data-packages-in-external-data-repositories-using-the-additional_repositories-field/

Under this approach, I am able use `imudata` package 
[https://github.com/smac-group/imudata] to build the vignettes within the 
`gmwm` package [https://github.com/smac-group/gmwm] with the suggests field 
filled in as: “Suggests: imudata”. Otherwise, CRAN would not accept the `gmwm` 
package as-is. 

(Regarding the package size claim, there really are not that many packages 
greater than 5 mb… For some figures on this, see: 
http://thecoatlessprofessor.com/programming/size-and-limitations-of-packages-on-cran/
 )

Sincerely,

JJB

On 5/21/16, 10:22 AM, "R-package-devel on behalf of Marius Hofert" 
 
wrote:

>Hi,
>
>I have (co-)developed two packages: 'qrmtools' and 'qrmdata'. The
>latter contains data sets and is currently only available on R-Forge
>(as it is larger than 5MB and thus not accepted for CRAN [although
>there are much larger packages, but that's a different story...]).
>'qrmtools' contains mainly tools that show what can be done with data
>such as the one contained in 'qrmdata' -- and thus has 'qrmdata' in
>Suggests. The check shows 'Suggests or Enhances not in mainstream
>repositories: qrmdata'; I also added 'Additional_repositories:
>http://r-forge.r-project.org/' to DESCRIPTION but of course
>winbuilder reports errors as it can't find 'qrmdata'.
>
>I'm wondering about what I am supposed to do: Remove everything about
>'qrmdata' from 'qrmtools'? Clearly, the easiest solution, but that's a
>bit dull as the 'qrmtools' can be nicely used to deal with the data
>from 'qrmdata'.
>
>How 'severe' is this issue for vignettes? I guess since they are
>checked as well, one would run into the same problem. But then a
>vignette even more so should show/replicate the functionality of a
>paper, say, and there one would definitely like to work with the
>data...
>
>The only partially related thread I found was
>https://stat.ethz.ch/pipermail/r-package-devel/2015q2/02.html
>
>In any case, I continue to pray to the R gods in the hope that the 5MB
>limit will change for data-related packages (which are updated very
>rarely) at some point in the future... Some 'adaptive limits' would be
>nice: The less often you submit, the larger the data package can be
>(for example), up to a certain larger limit more suitable for
>data-related packages.
>
>Any ideas on (all of) that?
>
>Cheers,
>Marius
>
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Re: [R-pkg-devel] CRAN note: src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS

2018-08-20 Thread Balamuta, James Joseph
In short, the default Makevars{.win} file should be updated with:

CXX_STD = CXX11
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

c.f. 
https://github.com/RcppCore/RcppArmadillo/blob/58b11c738d31b9e8d9fa6b39e2290b2ac08aefc4/inst/skeleton/Makevars#L11-L14

Sincerely,

JJB

On 8/20/18, 5:40 PM, "R-package-devel on behalf of Dirk Eddelbuettel" 
 wrote:


On 20 August 2018 at 22:14, Georgi Boshnakov wrote:
| Hi,
| 
| Recently the results page of my package on CRAN at
| https://cran.r-project.org/web/checks/check_results_sarima.html,
| started to show the NOTE below for some systems.
| I am using Rcpp/RcppArmadillo without any manual interventions on my 
side. 
| 
| Is it reasonable to expect that the NOTE will disappear if I rebuild the 
package with an up-to-date version of  Rcpp
| and maybe rerunning RcppAttributes().?

No you have to edit src/Makevars{,win} yourself.

| ==
| 
| Check: use of SHLIB_OPENMP_*FLAGS in Makefiles 
| Result: NOTE 
|  src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but 
not in PKG_LIBS
|  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in 
PKG_CFLAGS
|  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS 
but not in PKG_LIBS
|  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but 
not in PKG_CFLAGS

Basically just use SHLIB_OPENMP_CXXFLAGS in PKG_LIBS as well. As the
paragraph quoted below suggests.

Our initial example in RcppArmadillo was sloppy was mix *_CFLAGS and
*_CXXFLAGS use, and that is no longer liked at the CRAN side.

Dirk

| Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
| Extensions'. The macros for different languages may differ so the
| matching macro must be used in PKG_CXXFLAGS (etc) and match that used
| in PKG_LIBS (except for F77: see the manual).
| 
| 
| 
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-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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