numerous updates

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@231 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

diff --git a/PackagesWithIssues.txt b/PackagesWithIssues.txt
index 6dae78589f8b185b0098e0e8cadf51c2650dc9f8..8602a1f73ea0e5ab9d99a56550ffe0cedea9bfb1 100644 (file)
--- a/PackagesWithIssues.txt
+++ b/PackagesWithIssues.txt
@@ -5,28 +5,36 @@ Package               Needs                   License         Other
 
 RESOLVED
 ---------------------------------------------------------------------------------
-matlab                                 Rice U -- added                                 
+matlab                                 Rice U          added                                   
 rwt            matlab
 arrayImpute    matlab
-rtiff                                  tiff + gpl -- added
+rtiff                                  tiff + gpl      added
 sendplot       rtiff                   
-BARD                                   AGPL -- added
-DierckxSpline                                          new version built
-FAiR                                   AGPL -- added
-StatFingerprints                                       now builds
-WriteXLS                                               (lots of) sysreq ignore added
+BARD                                   AGPL            added
+DierckxSpline                                          new version builds
+FAiR                                   AGPL            added
+StatFingerprints tcltk2                                        now builds
+WriteXLS                                               (many) sysreq ignore added
 mlbench                                        added
 adabag         mlbench                                 
 ipred          mlbench                                 
+gwidgetsWWW    Rpad, rebuilt
+rgrs           xclip                   added alias_run,sysreq
+scagnostics                            scagnostics license -- added
+seewave                flac                                    added alias_run,sysreq                  
+snpXpert       tcltk2                                  now builds 
+tlnise                                 tlnise license added
+toosm          tlnise                                  now builds                                      
+SuppDists                                              build bombs, DESCRIPTION needs space, patch added
+qAnalyst       SuppDists
+survcomp       SuppDists
 
 OPEN ISSUES
 ---------------------------------------------------------------------------------
 ADaCGH         tilingArray (BioC)
 BayesTree                                              C++ patch ?
 DAAGbio                limma (BioC ?)
-multtest       BioBase (BioC ?)
-GExMap         multtest (BioC)
-LMGene         multtest (BioC)
+metaMA         limma (BioC ?)
 GFMaps         affy (BioC)
 GOSim          GO.db (BioC)
 Geneland       mapproj
@@ -34,26 +42,68 @@ HAPim                                                       odd build failure
 MatchIt                                                        need small patch
 Metabonomic    PROcess (BioC ?)
 PhViD          LBE ????
-RJaCGH                                                 contains zli, may need patch
+RJaCGH                                                 contains zlib, may need patch
 RLadyBug                                               needs small patch
 Rsymphony                                              build bombs, patch ?, Debian build
 SNPMaP         affxparser, SNPMaP.cdm (BioC)                                           
 SubpathwayMiner KEGG.db (BioC)
-SuppDists                                              build bombs, unclear why
+gene2pathway    KEGG.db (BioC)
 TSpaid                                                 build bombs, wild linking ?
 alphahull      removed ?
-                                                                                               
+ash                                    statlib ?
+bayesCGH       snapCGH (BioC ?)
+classGraoh     Rgraphviz (BioC ?)                      
+gcExplorer     Rgraphviz (BioC ?)                                                                                      
+logilasso      Rgraphviz (BioC ?)
+pcalg          Rgraphviz (BioC ?)
+qdg            pcalg -> Rgraphviz 
+celsius                BioBase (BioC ?)
+multtest       BioBase (BioC ?)
+hopach         BioBase (BioC ?)
+multtest       BioBase (BioC ?)
+GExMap         multtest (BioC)
+LMGene         multtest (BioC)
+crosshybDetector marray (disappread ?)
+dlmap          empty DESCRIPTION ?
+fPortfolio     RSymphony (which will be in Debian)
+lsa            Rstem ?
+mpm            geneplotter (BioC ?)
+mvgraph                statDA ?
+rSymPy                                                 small patch
+race                                                   remove debian/ from source tarball ?                            
+sabreR                                                 contains binary, lintian override ?
+seqinr                                                 contains zlib 
+sgeostat       license ? package gone ?
+sisus          annotate, Biobase (BioC ?)
+svSocket                                               small patch re tcl path
+
 REJECTED
 ---------------------------------------------------------------------------------------------
 gpclib                                 non-commercial
 AIGIS          gpclib                  non-commercial
+RSurvey                gpclib                  non-commercial
+aspace         gpclib
+tossm          gpclib
+spatstat       gpclib
 DSpat          spatstat -> gpclib      non-commercial
 SGCS           spatstat -> gpclib
-RSurvey                gpclib                  non-commercial
+arrayMissPattern spatstat -> gpclib
+ecespa         spatstat -> gpclib
+spatclus       spatstat -> gpclib
 CoCo                                   not-for-profit
+gmvalid                CoCo                    not-for-profit                  
 ConCalendar                            non-commercial
+mclust                                 non-free
 EMCC           mclust
 StatDA         mclust
+chemometrics   mclust
+clValid                mclust
+latentnetHRT   mclust
+sdcMicro       mclust
+vabayelMix     mclust
+mclust02                               non-free
+clustTool      mclust02
+clustvarsel    mclust02
 mapproj                                        non-commercial
 Geneland       mapproj                 non-commercial                  
 PTAk                                   non-commercial
@@ -61,6 +111,12 @@ SDDA                                        non-commercial  CSIRO license
 optmatch                               non-commercial
 SpectralGEM    optmatch                non-commercial                  
 realized                               non-commercial
+asypow                                 acm non-commercial
+caMassClass                            non-commercial
+mapproj                                        non-commercial
+rankreg                                        non-profit
+rngwell19937                           non-commercial
+spatialkernel                          gpc library in non-commercial
 
 CANNOT BUILD
 ----------------------------------------------------------------------------------------------
@@ -71,13 +127,12 @@ Rcplex                                                     CPLEX library
 Rlsf                                                   LSF required
 Rsge                                                   SGE required
 VhayuR                                                 Vhauy required
-
+gputools                                               nvcc (>= 2.1)                                           
+klar                                                   svmlight (non-commercial)
+rgrs                                                   xclip
+rimage                                                 C++ needs g++ 4.* update
+svGUI                                                  komodo
+wgaim                                                  asreml-r
+xgobi                                                  Xgobi
 
 TODO:
-,arrayMissPattern,ash,aspace,asypow,bayesCGH,caMassClass,celsius,
-chemometrics,clValid,classGraph,clustTool,clustvarsel,crosshybDetector,dlmap,ecesp
-a,fPortfolio,gWidgetsWWW,gcExplorer,gene2pathway,gmvalid,gpclib,gputools,hopach,
-ipred,klaR,latentnetHRT,logilasso,lsa,mapproj,mclust,mclust02,metaMA,mpm,multtest,mvgraph,
-pcalg,qAnalyst,qdg,rSymPy,race,rankreg,rgrs,rimage,rngwell19937,sabreR,scagnostics,
-sdcMicro,seewave,seqinr,sgeostat,sisus,snpXpert,spatclus,spatialkernel,spatstat
-survcomp,svGUI,svSocket,tlnise,tossm,tsModel,vabayelMix,wgaim,xgobi