Re: Please review a number of R libraries

[Thomas Klausner <thomasklausner%users.sourceforge.net@localhost>]

On Tue, Jan 01, 2013 at 03:02:59AM +0200, Mike M. Volokhov wrote:
> >> R-BiocGenerics     Generic functions for Bioconductor
> >> R-Rgraphviz        Plotting capabilities for R graph objects
> > 
> > configure: Using default directory /usr/local, consider specifiying 
> > --with-graphviz
> > configure: error: /usr/local/bin/dot not found.  Check Graphviz 
> > installation.
> > 
> > Probably needs to be given the path to graphviz.
> 
> This requires to pass --configure-args='--with-graphviz=${PREFIX}' to
> R_PKG_INSTALL_ARGS of math/R/Makefile.extension, which currently is
> impossible. IMHO it should be enough to use += variable assignment
> modifier, or add support of CONFIGURE_ARGS:
> http://mail-index.netbsd.org/tech-pkg/2013/01/01/msg010554.html
> 
> This is a misc package, so please skip it for a while.

I see you've committed this change now, and R-graphviz compiles fine for me.

> >> R-VGAM             Vector Generalized Linear and Additive Models
> > 
> > => Bootstrap dependency digest>=20010302: found digest-20111104
> > => Fetching VGAM_0.8-7.tar.gz
> > => Total size: 2004921 bytes
> > ftp: Error retrieving file `404 Not Found'
> > fetch: Unable to fetch expected file VGAM_0.8-7.tar.gz
> 
> Updated to 0.9.0.

Works now.

> >> R-biganalytics     Library of utilities for big.matrix objects of package 
> >> bigmemory
> >> R-bigmemory        Manage massive matrices with shared memory and 
> >> memory-mapped files
> >> R-bigtabulate      R table, tapply, and split-like functionality for 
> >> (big.)matrix objects
> >> R-bnlearn  Bayesian network structure learning, parameter learning and 
> >> inference
> > 
> > => Fetching bnlearn_3.1.tar.gz
> > => Total size: 1014087 bytes
> > ftp: Error retrieving file `404 Not Found'
> > fetch: Unable to fetch expected file bnlearn_3.1.tar.gz
> 
> Updated to 3.2.

Same here.

> >> R-doParallel       Foreach parallel adaptor for the parallel package
> >> R-entropy  Entropy and Mutual Information Estimation
> >> R-foreach  Foreach looping construct for R
> >> R-gmp              Multiple Precision Arithmetic for R
> >> R-graph            R package to handle graph data structures
> >> R-gsl              R wrapper for the Gnu Scientific Library
> >> R-iterators        Iterator construct for R
> >> R-mclust   Model-based clustering and normal mixture modeling
> > 
> > WARNING: [license.mk] Every package should define a LICENSE.
> > => Fetching mclust_3.4.8.tar.gz
> > => Total size: 226824 bytes
> > ftp: Error retrieving file `404 Not Found'
> > fetch: Unable to fetch expected file mclust_3.4.8.tar.gz
> 
> Updated to 4.0.

Same here.

> The most common reason for breakage is outdated packages: as soon as
> a new version released the old tarball is moved to archive -
> http://cran.r-project.org/src/contrib/Archive/.
> 
> I wrote separate letter to tech-pkg@ on this issue:
> http://mail-index.netbsd.org/tech-pkg/2013/01/01/msg010556.html

While everyone was preparing a hangover, you were writing emails? :)

Looks good to me.

I browsed the files and found a few minor issues:

general: Please move LICENSE below COMMENT, that's where it usually is.

R-Rgraphviz: instead of
--with-graphviz=${PREFIX}
it is better to use:
--with-graphviz=${BUILDLINK_PREFIX.graphviz}

R-doParallel/bl3.mk (and others): When API and ABI depends are the
same, you can remove the ABI line.

Don't forget to update the paths pointing to wip to point somewhere
else when importing (Makefile, buildlink3.mk).

Other than that, please go ahead and import them to pkgsrc!

Thanks,
 Thomas

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