X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=PackagesWithIssues.txt;h=6bfd60dd121b8059af289b6b5ad837836820c4a2;hb=ff5fa2262544332700761a420bc4ceca9a11c7a2;hp=de207d4db5cd30103621daaf8ee7a8d5e747d2bb;hpb=c0ff50def0d1797562bcc443ea1c49614fb74736;p=cran2deb.git

diff --git a/PackagesWithIssues.txt b/PackagesWithIssues.txt
index de207d4..6bfd60d 100644
--- a/PackagesWithIssues.txt
+++ b/PackagesWithIssues.txt
@@ -5,50 +5,100 @@ Package		Needs			License		Other
 
 RESOLVED
 ---------------------------------------------------------------------------------
-BARD					AGPL -- added
-DierckxSpline						new version built
-FAiR					AGPL -- added
-StatFingerprints					now builds
-WriteXLS						(lots of) sysreq ignore added
+matlab					Rice U		added					
+rwt		matlab			Rice U		
+arrayImpute	matlab
+rtiff					tiff + gpl	added
+sendplot	rtiff			
+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
+tsModel		tlnise					now builds					
+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)
-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
-HAPim							odd build failure
-MatchIt							need small patch
 Metabonomic	PROcess (BioC ?)
-PhViD 		LBE ????
-RJaCGH							contains zli, may need patch
-RLadyBug						needs small patch
-Rsymphony						build bombs, patch ?, Debian build
+PhViD 		LBE (BioC)
 SNPMaP		affxparser, SNPMaP.cdm (BioC)						
 SubpathwayMiner KEGG.db (BioC)
-SuppDists						build bombs, unclear why
-TSpaid							build bombs, wild linking ?
-alphahull	removed ?
-												
+gene2pathway    KEGG.db (BioC)
+bayesCGH	snapCGH (BioC ?)
+classGraph	Rgraphviz (BioC ?)			
+gcExplorer	Rgraphviz (BioC ?)											
+logilasso	Rgraphviz (BioC ?)
+pcalg		Rgraphviz (BioC ?)
+qdg		pcalg -> Rgraphviz 
+celsius		BioBase (BioC ?)
+multtest	BioBase (BioC ?)
+hopach		BioBase (BioC ?)
+GExMap		multtest (BioC)
+LMGene		multtest (BioC)
+PCS		multtest (BioC)
+crosshybDetector marray (disappread ?)
+lsa		Rstem 
+mpm		geneplotter (BioC ?)
+sisus		annotate, Biobase (BioC ?)
+
 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
@@ -56,6 +106,13 @@ 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
 ----------------------------------------------------------------------------------------------
@@ -66,13 +123,20 @@ Rcplex							CPLEX library
 Rlsf							LSF required
 Rsge							SGE required
 VhayuR							Vhauy required
-
+gputools						nvcc (>= 2.1)						
+klar							svmlight (non-commercial)
+rimage							C++ needs g++ 4.* update
+sabreR							contains binary, lintian override ?
+svGUI							komodo
+wgaim							asreml-r
+xgobi							Xgobi
 
 TODO:
-alphahull,arrayImpute,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
+---------------------------------------------------------------------------------
+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 ?