PackagesWithIssues.txt

   1 debian-i386
   2
   3 Package         Needs                   License         Other
   4 =================================================================================
   5
   6 RESOLVED
   7 ---------------------------------------------------------------------------------
   8 matlab                                  Rice U          added
   9 rwt             matlab                  Rice U
  10 arrayImpute     matlab
  11 rtiff                                   tiff + gpl      added
  12 sendplot        rtiff
  13 BARD                                    AGPL            added
  14 DierckxSpline                                           new version builds
  15 FAiR                                    AGPL            added
  16 StatFingerprints tcltk2                                 now builds
  17 WriteXLS                                                (many) sysreq ignore added
  18 mlbench                                 added
  19 adabag          mlbench
  20 ipred           mlbench
  21 gWidgetsWWW     Rpad, rebuilt
  22 rgrs            xclip                   added alias_run,sysreq
  23 scagnostics                             scagnostics license -- added
  24 seewave         flac                                    added alias_run,sysreq
  25 snpXpert        tcltk2                                  now builds
  26 tlnise                                  tlnise license added
  27 tsModel         tlnise                                  now builds
  28 qAnalyst        SuppDists
  29 survcomp        SuppDists
  30 BayesTree                                               added one-line C++ patch
  31 HAPim                                                   added one-char DESCRIPTION patch
  32 MatchIt                                                 added one-line patch
  33 race                                                    remove debian/ from source tarball -- fixed in cran2deb
  34 RJaCGH                                                  contains zlib, added patch to remove it
  35 seqinr                                                  contains zlib, added patch to remove it
  36 rSymPy                                                  small patch for python path
  37 svSocket                                                small patch re tcl path
  38 rgrs                                                    xclip sysreq/force added
  39 RLadyBug                                                added patch, now works
  40 dlmap                                                   now works
  41 TSpadi                                                  now works
  42 ash                                     statlib ?
  43 alphahull                                               now works
  44 sgeostat                                                now works
  45
  46 BLACKLISTED
  47 ---------------------------------------------------------------------------------
  48 ADaCGH          tilingArray (BioC)
  49 DAAGbio         limma (BioC ?)
  50 metaMA          limma (BioC ?)
  51 GFMaps          affy (BioC)
  52 GOSim           GO.db (BioC)
  53 Metabonomic     PROcess (BioC ?)
  54 PhViD           LBE (BioC)
  55 SNPMaP          affxparser, SNPMaP.cdm (BioC)
  56 SubpathwayMiner KEGG.db (BioC)
  57 gene2pathway    KEGG.db (BioC)
  58 bayesCGH        snapCGH (BioC ?)
  59 classGraph      Rgraphviz (BioC ?)
  60 gcExplorer      Rgraphviz (BioC ?)
  61 logilasso       Rgraphviz (BioC ?)
  62 pcalg           Rgraphviz (BioC ?)
  63 qdg             pcalg -> Rgraphviz
  64 celsius         BioBase (BioC ?)
  65 multtest        BioBase (BioC ?)
  66 hopach          BioBase (BioC ?)
  67 GExMap          multtest (BioC)
  68 LMGene          multtest (BioC)
  69 PCS             multtest (BioC)
  70 crosshybDetector marray (disappread ?)
  71 lsa             Rstem
  72 mpm             geneplotter (BioC ?)
  73 sisus           annotate, Biobase (BioC ?)
  74
  75 REJECTED
  76 ---------------------------------------------------------------------------------------------
  77 gpclib                                  non-commercial
  78 AIGIS           gpclib                  non-commercial
  79 RSurvey         gpclib                  non-commercial
  80 aspace          gpclib
  81 tossm           gpclib
  82 spatstat        gpclib
  83 DSpat           spatstat -> gpclib      non-commercial
  84 SGCS            spatstat -> gpclib
  85 arrayMissPattern spatstat -> gpclib
  86 ecespa          spatstat -> gpclib
  87 spatclus        spatstat -> gpclib
  88 CoCo                                    not-for-profit
  89 gmvalid         CoCo                    not-for-profit
  90 ConCalendar                             non-commercial
  91 mclust                                  non-free
  92 EMCC            mclust
  93 StatDA          mclust
  94 chemometrics    mclust
  95 clValid         mclust
  96 latentnetHRT    mclust
  97 sdcMicro        mclust
  98 vabayelMix      mclust
  99 mclust02                                non-free
 100 clustTool       mclust02
 101 clustvarsel     mclust02
 102 mapproj                                 non-commercial
 103 Geneland        mapproj                 non-commercial
 104 PTAk                                    non-commercial
 105 SDDA                                    non-commercial  CSIRO license
 106 optmatch                                non-commercial
 107 SpectralGEM     optmatch                non-commercial
 108 realized                                non-commercial
 109 asypow                                  acm non-commercial
 110 caMassClass                             non-commercial
 111 mapproj                                 non-commercial
 112 rankreg                                 non-profit
 113 rngwell19937                            non-commercial
 114 spatialkernel                           gpc library in non-commercial
 115
 116
 117 CANNOT BUILD
 118 ----------------------------------------------------------------------------------------------
 119 CarbonEL                                                Mac OS X only
 120 ROracle                                                 requires Oracle libs
 121 RScaLAPAPCK     licese is free                          MPI, Blacs, ScaLAPACK, ...
 122 Rcplex                                                  CPLEX library
 123 Rlsf                                                    LSF required
 124 Rsge                                                    SGE required
 125 VhayuR                                                  Vhauy required
 126 gputools                                                nvcc (>= 2.1)
 127 klar                                                    svmlight (non-commercial)
 128 rimage                                                  C++ needs g++ 4.* update
 129 sabreR                                                  contains binary, lintian override ?
 130 svGUI                                                   komodo
 131 wgaim                                                   asreml-r
 132 xgobi                                                   Xgobi
 133
 134 TODO:
 135 ---------------------------------------------------------------------------------
 136 aroma.apd                                               requires aroma.light from BioC
 137 aroma.core                                              requires aroma.light from BioC
 138 IDPmisc                                                 broken R file (!!)
 139 Rsymphony                                               build bombs, patch ?, Debian build exists
 140 SuppDists                                               build bombs, DESCRIPTION needs space, patch added
 141 cmprskContin                                            fortan95 compiler wants memory model
 142 mvgraph         statDA ?                                need pkg-config ?