start allowing for local user cache configuration

[cran2deb.git] / PackagesWithIssues.txt

diff --git a/PackagesWithIssues.txt b/PackagesWithIssues.txt
index f589bf0fe9f7159332845118614cd9876b78f624..6bfd60dd121b8059af289b6b5ad837836820c4a2 100644 (file)
--- a/PackagesWithIssues.txt
+++ b/PackagesWithIssues.txt
@@ -25,34 +25,38 @@ seewave             flac                                    added alias_run,sysreq
 snpXpert       tcltk2                                  now builds 
 tlnise                                 tlnise license added
 tsModel                tlnise                                  now builds                                      
-SuppDists                                              build bombs, DESCRIPTION needs space, patch added
 qAnalyst       SuppDists
 survcomp       SuppDists
 BayesTree                                              added one-line C++ patch 
 HAPim                                                  added one-char DESCRIPTION patch
 MatchIt                                                        added one-line patch
+race                                                   remove debian/ from source tarball -- fixed in cran2deb 
+RJaCGH                                                 contains zlib, added patch to remove it
+seqinr                                                 contains zlib, added patch to remove it
+rSymPy                                                 small patch for python path
+svSocket                                               small patch re tcl path
+rgrs                                                   xclip sysreq/force added
+RLadyBug                                               added patch, now works
+dlmap                                                  now works
+TSpadi                                                 now works
+ash                                    statlib ?
+alphahull                                              now works
+sgeostat                                               now works
 
-OPEN ISSUES
+BLACKLISTED 
 ---------------------------------------------------------------------------------
 ADaCGH         tilingArray (BioC)
 DAAGbio                limma (BioC ?)
 metaMA         limma (BioC ?)
 GFMaps         affy (BioC)
 GOSim          GO.db (BioC)
-Geneland       mapproj
 Metabonomic    PROcess (BioC ?)
-PhViD          LBE ????
-RLadyBug                                               added small patch, still fails ??
-RJaCGH                                                 contains zlib, may need patch
-Rsymphony                                              build bombs, patch ?, Debian build
+PhViD          LBE (BioC)
 SNPMaP         affxparser, SNPMaP.cdm (BioC)                                           
 SubpathwayMiner KEGG.db (BioC)
 gene2pathway    KEGG.db (BioC)
-TSpaid                                                 build bombs, wild linking ?
-alphahull      removed ?
-ash                                    statlib ?
 bayesCGH       snapCGH (BioC ?)
-classGraoh     Rgraphviz (BioC ?)                      
+classGraph     Rgraphviz (BioC ?)                      
 gcExplorer     Rgraphviz (BioC ?)                                                                                      
 logilasso      Rgraphviz (BioC ?)
 pcalg          Rgraphviz (BioC ?)
@@ -60,22 +64,13 @@ qdg         pcalg -> Rgraphviz
 celsius                BioBase (BioC ?)
 multtest       BioBase (BioC ?)
 hopach         BioBase (BioC ?)
-multtest       BioBase (BioC ?)
 GExMap         multtest (BioC)
 LMGene         multtest (BioC)
+PCS            multtest (BioC)
 crosshybDetector marray (disappread ?)
-dlmap          empty DESCRIPTION ?
-fPortfolio     RSymphony (which will be in Debian)
-lsa            Rstem ?
+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
 ---------------------------------------------------------------------------------------------
@@ -118,6 +113,7 @@ rankreg                                     non-profit
 rngwell19937                           non-commercial
 spatialkernel                          gpc library in non-commercial
 
+
 CANNOT BUILD
 ----------------------------------------------------------------------------------------------
 CarbonEL                                               Mac OS X only
@@ -129,10 +125,18 @@ Rsge                                                      SGE required
 VhayuR                                                 Vhauy required
 gputools                                               nvcc (>= 2.1)                                           
 klar                                                   svmlight (non-commercial)
-rgrs                                                   xclip
 rimage                                                 C++ needs g++ 4.* update
+sabreR                                                 contains binary, lintian override ?
 svGUI                                                  komodo
 wgaim                                                  asreml-r
 xgobi                                                  Xgobi
 
 TODO:
+---------------------------------------------------------------------------------
+aroma.apd                                              requires aroma.light from BioC
+aroma.core                                             requires aroma.light from BioC
+IDPmisc                                                        broken R file (!!)
+Rsymphony                                              build bombs, patch ?, Debian build exists
+SuppDists                                              build bombs, DESCRIPTION needs space, patch added
+cmprskContin                                           fortan95 compiler wants memory model
+mvgraph                statDA ?                                need pkg-config ?