Re: Please review a number of R libraries

["Mike M. Volokhov" <mike.volokhov%gmail.com@localhost>]

28 Dec 2012, 02:03, Thomas Klausner wrote:

> On Thu, Aug 30, 2012 at 10:11:37PM +0300, Mike M. Volokhov wrote:
>> Could anybody take a look to the following packages, please.
> 
> Sure. Sorry for the delay.

Hey, many thanks for doing this kind of dirty, but very important job!

>> 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.

>> 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.

>> 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.

>> 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.

> The others seem to be fine.
> Can you please fix the issues?

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

Thank you!

--
Mishka.



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