[Rd] Non-GPL packages for R
Dirk Eddelbuettel
edd at debian.org
Fri Sep 11 17:44:42 CEST 2009
On 11 September 2009 at 16:37, Peter Dalgaard wrote:
| who have responded on the list do not necessarily speak for CRAN. In the
| final analysis, the maintainers must decide what is maintainable.
Fully agreed. As 'maintainers' of cran2deb, Charles and I decided to 'shoot
first, ask questions later' as we clearly wanted to avoid creating any sort
of trouble for our generous CRAN hosts (currently just the Vienna master) are
effectively re-distributing our compilations (of its own content).
So we pro-actively chose to excludes some packages. To put some meat on this
particular bone, the current set packages blacklistes for 'nonfree-ness' is:
sqlite> select package, explanation from blacklist_packages where nonfree;
package explanation
-------------------- ----------------------------------------
mclust non-commercial license
mclust02 non-commercial license
ConvCalendar no modification or distribution rights
SDDA non-commercial CSIRO license
conf.design non-commercial license
isa2 non-commercial creative commons license
optmatch non-commercial license
rankreg non-commercial license
realized non-commercial license
rngwell19937 non-commercial license
tnet non-commercial creative commons license
spatialkernel contains non-commercial gpc code
Bhat non-commercial license
PTAk non-commercial license
PredictiveRegression non-commercial license
RLadyBug contains some code under non-commercial
mapproj non-commercial license
mathgraph non-commercial license
sqlite>
| (Even within the Free Software world there are current issues with,
| e.g., incompatibilities between GPL v.2 and v.3, and also with the
| Eclipse license. Don't get me started...)
Yes. There is a potential problem with gcc 4.4 compilation of GPL-2 code. If
that comes to a boil we all (as in: GPL 2 users) are in a spot of bother.
On 11 September 2009 at 07:48, Robert Gentleman wrote:
| It is also the case that things are not so simple, as dependencies
| can make a package unusable even if it is itself GPL-compatible. This
Yes, in the case of cran2deb / CRAN there are just three blacklists because
of dependencies on nonfree CRAN content, most often it is dependencies on
other stuff incl BioC which we do not include (for mostly technical /
historical reasons; contact Charles or me offline if you'd like to work on
changing this)
sqlite> select package,explanation from blacklist_packages where unsatisfied_dependency;
package explanation
-------------------- ----------------------------------------
ROracle requires Oracle to build and run
Rlsf requires LSF cluster/grid system librari
Rsge requires SGE cluster/grid system librari
CarbonEL requires OS X system
VhayuR requires Vhayu database system
gputools requires Nvidia CUDA compiler and GPU-en
klaR requires SVMlight which is non-free
wgaim requires asreml-R
svGUI requires Komodo from OpenKomodo.org whic
RScaLAPACK requires MPICH2 and Blacs and ScaLAPACK
caMassClass requires PROcess from BioConductor
Rcplex requires CPLEX libraries
ADaCGH BioC depends: tilingArray
DAAGbio BioC depends: limma
GFMaps BioC depends: affy
GOSim BioC depends: GO.db
Metabonomic BioC depends: PROcess
classGraph BioC depends: Rgraphviz
gcExplorer BioC depends: Rgraphviz
logilasso BioC depends: Rgraphviz
pcalg BioC depends: Rgraphviz
celsius BioC depends: BioBase
multtest BioC depends: BioBase
hopach BioC depends: BioBase
GExMap BioC depends: multtest,BioBase
LMGene BioC depends: multtest,BioBase
PCS BioC depends: multtest,BioBase
SubpathwayMiner BioC depends: KEGG.db
gene2pathway BioC depends: KEGG.db
PhViD BioC depends: LBE
SNPMaP BioC depends: affxparser
qdg BioC depends: pcalg,Rgraphviz
lsa Ohat depends: Rstem
mpm BioC depends: geneplotter
sisus BioC depends: annotate
metaMA BioC depends: limma
clustTool non-free depends: mclust02
clustvarsel non-free depends: mclust02
SpectralGEM non-free depends: optmatch
bayesCGH BioC depends: snapCGH
crosshybDetector missing depends: marray
FEST needs MERLIN <http://www.sph.umich.edu/c
aroma.affymetrix BioC depends: aroma.light
aroma.core BioC depends: aroma.light
aroma.apd BioC depends: aroma.light
sqlite>
| also makes the notion of some simple split into free and non-free (or
| what ever split you want) less trivial than is being suggested.
That sounds like the Ostrich defense :) Nobody claimed it was easy or
non-controversial, but it seems some of us feel that it should be discussed
as the status quo may be something we can improve upon.
E.g. I think that 'License: file LICENSE' is not good enough. Some sort of
marker at the DESCRIPTIOn level would help. How many levels we put into an
appropriate factor variable is open for discussion. But for argument's sake:
why don't we start with a binary toggle of whether or not one of the licenses
in http://www.r-project.org/Licenses/ aka share/licenses/ is met?
CRAN has been a huge success (and I am sure the success puts a strain on its
maintainers). Given that it has become the 800 pound gorilla, may not use
some of that weight to nudge folks to a set of common licenses?
Dirk
--
Three out of two people have difficulties with fractions.
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