the source only builds do not care about the R dependencies

[cran2deb.git] / PackagesWithIssues.txt

diff --git a/PackagesWithIssues.txt b/PackagesWithIssues.txt
index 5ba7aa5d29c7cb2d7e07346c2f74b2a1146883eb..6bfd60dd121b8059af289b6b5ad837836820c4a2 100644 (file)
--- a/PackagesWithIssues.txt
+++ b/PackagesWithIssues.txt
@@ -25,19 +25,25 @@ 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                         
+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 ?)
@@ -45,17 +51,12 @@ metaMA              limma (BioC ?)
 GFMaps         affy (BioC)
 GOSim          GO.db (BioC)
 Metabonomic    PROcess (BioC ?)
-PhViD          LBE ????
-RLadyBug                                               added small patch, still fails ??
-Rsymphony                                              build bombs, patch ?, Debian build exists
+PhViD          LBE (BioC)
 SNPMaP         affxparser, SNPMaP.cdm (BioC)                                           
 SubpathwayMiner KEGG.db (BioC)
 gene2pathway    KEGG.db (BioC)
-TSpadi                                                 build bombs on i386 but not amd64, wild linking ?
-alphahull      removed ?
-ash                                    statlib ?
 bayesCGH       snapCGH (BioC ?)
-classGraoh     Rgraphviz (BioC ?)                      
+classGraph     Rgraphviz (BioC ?)                      
 gcExplorer     Rgraphviz (BioC ?)                                                                                      
 logilasso      Rgraphviz (BioC ?)
 pcalg          Rgraphviz (BioC ?)
@@ -63,18 +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 ?)
-fPortfolio     RSymphony (which will be in Debian)
-lsa            Rstem ?
+lsa            Rstem 
 mpm            geneplotter (BioC ?)
-mvgraph                statDA ?
-sabreR                                                 contains binary, lintian override ?
-sgeostat       license ? package `5gone ?
 sisus          annotate, Biobase (BioC ?)
-dlmap                                                  empty DESCRIPTION, added patch, still fails ?
 
 REJECTED
 ---------------------------------------------------------------------------------------------
@@ -117,6 +113,7 @@ rankreg                                     non-profit
 rngwell19937                           non-commercial
 spatialkernel                          gpc library in non-commercial
 
+
 CANNOT BUILD
 ----------------------------------------------------------------------------------------------
 CarbonEL                                               Mac OS X only
@@ -128,10 +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 ?