[pkg-bioc] bioconductor source packages

[David Vernazobres]

Dear all,
I just subscribe to this pkg-bioc-devel list as I am also interested in
some bioc/cran package.
I got a quick look and try to the bioc packaging part.

I started browsing the archive, and as I was not able to make
bioc_update downloading package working, so I just patch it. 
I just attach a patch for bioc_update.sh to make it working on my
system. 
The first hunk is just a typo syntax, I think.

For the second part of the patch, we mainly need to download the source
archive (.tar.gz) if they are not present in the "sources" directory,
isn't it ?
Is this implementation too short, and I am missing something ? Or is it
enough for the need of packaging ?

Sorry for this jump in, without asking.
david 

-- 
David VERNAZOBRES, PhD student                     | dv at uni-muenster.de
Division of Bioinformatics, University of Muenster | Schlossplatz 4
(+49)(251)8321635                                  | D48149 Muenster
http://www.uni-muenster.de/Evolution.ebb/          | Germany
-------------- next part --------------
Index: bioc_update.sh
===================================================================
RCS file: /cvsroot/pkg-bioc/tools/bioc_update.sh,v
retrieving revision 1.6
diff -u -r1.6 bioc_update.sh
--- bioc_update.sh	18 Feb 2007 22:56:41 -0000	1.6
+++ bioc_update.sh	21 Feb 2007 14:13:36 -0000
@@ -43,7 +43,7 @@
 	fi
 done
 
-if [ ! -r "patches" ] || [ ! -r "cran2deb.pl" ] || [ -r "CRAN2DEB.pm" ]; then
+if [ ! -r "patches" ] || [ ! -r "cran2deb.pl" ] || [ ! -r "CRAN2DEB.pm" ]; then
 	echo "The patches directory, cran2deb.pl and CRAN2DEB.pm should all be linked symbolically to this folder."
 fi
 
@@ -77,7 +77,6 @@
 
 	biocdownload.allPkgs <- function(destdir="sources")
 	{
-		packs<-NULL
 		for (contriburl in  c(
 			"http://bioconductor.org/packages/1.9/bioc/src/contrib",
 			"http://bioconductor.org/packages/1.9/data/annotation/src/contrib",
@@ -91,35 +90,18 @@
 						".tar.gz", sep="")
 				e<-file.exists(fname)
 				cat(fname,":",e,"\n")
+				if( !e ) { 
+				  urlname<-paste(contriburl,"/",
+				        X["Package"],"_",X["Version"],
+						".tar.gz", sep="")
+				  print ( urlname )
+                  download.file(url=urlname , destfile=fname, method="wget")
+				}
 				return(e)
 			})
-			packs<-c(packs,ap[!ee, "Package"])
 		}
 	}
-
-	biocdownload <- function()
-	{
-	    pkgs <- biocdownload.allPkgs()
-	    cat("Will install the following packages:\n")
-	    print(pkgs)
-	    cat("Please wait...\n\n")
-
-	    ## CRAN-style Repositories where we'll look for packages
-	    repos <- c(
-		"bioc",
-		"data/annotation",
-		"data/experiment",
-		"omegahat",
-		"monograph"
-	    )
-	    repos <- paste("http://bioconductor.org/packages/1.9", repos, sep="/")
-	    # Temporary only (H. 11/10/2006)
-	    #repos <- c(repos, "http://cran.us.r-project.org")
-	    #repos <- c(repos, "http://cran.fhcrc.org")
-
-	    #download.packages(pkgs=pkgs, repos=repos, destdir="sources",method="wget", type=type, ...)
-	}
-	biocdownload()
+	biocdownload.allPkgs()
 EORSCRIPT
 
 fi