From: blundellc <blundellc@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Sat, 13 Sep 2008 13:16:48 +0000 (+0000)
Subject: cran2deb: make into an R package.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=86055c81b378b4629c33aa1c588deb5637e32975;p=cran2deb.git

cran2deb: make into an R package.

not complete.  mostly seems to work, but certain parts are broken: e.g.,
updating the availability lists.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@47 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---

diff --git a/pkg/trunk/DESCRIPTION b/pkg/trunk/DESCRIPTION
new file mode 100644
index 0000000..1bfa413
--- /dev/null
+++ b/pkg/trunk/DESCRIPTION
@@ -0,0 +1,10 @@
+Package: cran2deb
+Version: 0.0
+Date: 2008-07-14
+Title: Convert CRAN packages into Debian packages
+Author: Charles Blundell <blundellc@gmail.com>, with assistance from Dirk Eddelbuettel <>
+Maintainer: Charles Blundell <blundellc@gmail.com>
+Depends: ctv, utils
+Description: Convert CRAN packages into Debian packages, mostly unassisted, easily
+ subverting the R package system.
+License: GPL-3
diff --git a/pkg/trunk/R/debcontrol.R b/pkg/trunk/R/debcontrol.R
new file mode 100644
index 0000000..ea25962
--- /dev/null
+++ b/pkg/trunk/R/debcontrol.R
@@ -0,0 +1,100 @@
+get.dependencies <- function(pkg,extra_deps) {
+    if ('SystemRequirements' %in% colnames(pkg$description)) {
+        stop(paste('Unsupported SystemRequirements:',pkg$description[1,'SystemRequirements']))
+    }
+
+    # determine dependencies
+    dependencies <- r.dependencies.of(description=pkg$description)
+    depends <- list()
+    # these are used for generating the Depends fields
+    as.deb <- function(r,binary) {
+        return(pkgname.as.debian(paste(dependencies[r,]$name)
+                                ,version=dependencies[r,]$version
+                                ,repopref=pkg$repo
+                                ,binary=binary))
+    }
+    depends$bin <- lapply(rownames(dependencies), as.deb, binary=T)
+    depends$build <- lapply(rownames(dependencies), as.deb, binary=F)
+    # add the command line dependencies
+    depends$bin = c(extra_deps$deb,depends$bin)
+    depends$build = c(extra_deps$deb,depends$build)
+
+    # make sure we depend upon R in some way...
+    if (!length(grep('^r-base',depends$build))) {
+        depends$build = c(depends$build,pkgname.as.debian('R',version='>= 2.7.0',binary=F))
+        depends$bin   = c(depends$bin,  pkgname.as.debian('R',version='>= 2.7.0',binary=T))
+    }
+    # also include stuff to allow tcltk to build (suggested by Dirk)
+    depends$build = c(depends$build,'xvfb','xauth','xfont-base')
+
+    # remove duplicates
+    depends <- lapply(depends,unique)
+
+    # append the Debian dependencies
+    depends$build=c(depends$build,'debhelper (>> 4.1.0)','cdbs')
+    if (pkg$archdep) {
+        depends$bin=c(depends$bin,'${shlibs:Depends}')
+    }
+
+    # the names of dependent source packages (to find the .changes file to
+    # upload via dput). these can be found recursively.
+    depends$r = lapply(r.dependency.closure(dependencies)
+                      ,tolower)
+    # append command line dependencies
+    depends$r = c(extra_deps$r, depends$r)
+    return(depends)
+}
+
+generate.control <- function(pkg) {
+    # construct control file
+    control = data.frame()
+    control[1,'Source'] = pkg$srcname
+    control[1,'Section'] = 'math'
+    control[1,'Priority'] = 'optional'
+    control[1,'Maintainer'] = maintainer
+    control[1,'Build-Depends'] = paste(pkg$depends$build,collapse=', ')
+    control[1,'Standards-Version'] = '3.8.0'
+
+    control[2,'Package'] = pkg$debname
+    control[2,'Architecture'] = 'all'
+    if (pkg$archdep) {
+        control[2,'Architecture'] = 'any'
+    }
+    control[2,'Depends'] = paste(pkg$depends$bin,collapse=', ')
+
+    # bundles provide virtual packages of their contents
+    if (pkg$is_bundle) {
+        control[2,'Provides'] = paste(
+                    lapply(r.bundle.contains(pkg$name)
+                          ,function(name) return(pkgname.as.debian(paste(name)
+                                                                  ,repopref=pkg$repo
+                                                                  ,binary=T)))
+                          ,collapse=', ')
+    }
+
+    # generate the description
+    descr = 'GNU R package "'
+    if ('Title' %in% colnames(pkg$description)) {
+        descr = paste(descr,pkg$description[1,'Title'],sep='')
+    } else {
+        descr = paste(descr,pkg$name,sep='')
+    }
+    if (pkg$is_bundle) {
+        long_descr <- pkg$description[1,'BundleDescription']
+    } else {
+        long_descr <- pkg$description[1,'Description']
+    }
+    # using \n\n.\n\n is not very nice, but is necessary to make sure
+    # the longer description does not begin on the synopsis line --- R's
+    # write.dcf does not appear to have a nicer way of doing this.
+    descr = paste(descr,'"\n\n', long_descr, sep='')
+    if ('URL' %in% colnames(pkg$description)) {
+        descr = paste(descr,'\n\nURL: ',pkg$description[1,'URL'],sep='')
+    }
+    control[2,'Description'] = descr
+
+    # Debian policy says 72 char width; indent minimally
+    write.dcf(control,file=pkg$debfile('control.in'),indent=1,width=72)
+    write.dcf(control,indent=1,width=72)
+}
+
diff --git a/pkg/trunk/R/debiannaming.R b/pkg/trunk/R/debiannaming.R
new file mode 100644
index 0000000..08c3f84
--- /dev/null
+++ b/pkg/trunk/R/debiannaming.R
@@ -0,0 +1,49 @@
+# sudo pbuilder --execute r -e 'rownames(installed.packages())'
+# XXX: has to be a better way of doing this
+base_pkgs=c('base',   'datasets','grDevices','graphics','grid', 'methods'
+           ,'splines','stats',   'stats4',   'tcltk',   'tools','utils')
+# found in R source directory:
+# 'profile', 'datasets'
+
+repourl.as.debian <- function(url) {
+    # map the url to a repository onto its name in debian package naming
+    if (length(grep('cran',url))) {
+        return('cran')
+    }
+    if (length(grep('bioc',url))) {
+        return('bioc')
+    }
+    stop(paste('unknown repository',url))
+}
+
+pkgname.as.debian <- function(name,repopref=NULL,version=NULL,binary=T) {
+    # generate the debian package name corresponding to the R package name
+    if (name %in% base_pkgs) {
+        name = 'R'
+    }
+    if (name == 'R') {
+        # R is special.
+        if (binary) {
+            debname='r-base-core'
+        } else {
+            debname='r-base-dev'
+        }
+    } else {
+        # XXX: data.frame rownames are unique, so always override repopref for
+        #      now.
+        if (!(name %in% rownames(available))) {
+            bundle <- r.bundle.of(name)
+            if (is.na(bundle)) {
+                stop(paste('package',name,'is not available'))
+            }
+            name <- bundle
+        }
+        repopref <- repourl.as.debian(available[name,'Repository'])
+        debname = paste('r',tolower(repopref),tolower(name),sep='-')
+    }
+    if (!is.null(version) && length(version) > 1) {
+        debname = paste(debname,' (',version,')',sep='')
+    }
+    return(debname)
+}
+
diff --git a/pkg/trunk/R/debianpkg.R b/pkg/trunk/R/debianpkg.R
new file mode 100644
index 0000000..3b9ca62
--- /dev/null
+++ b/pkg/trunk/R/debianpkg.R
@@ -0,0 +1,153 @@
+generate.changelog <- function(pkg) {
+    # construct a dummy changelog
+    # TODO: ``Writing R extensions'' mentions that a package may also have
+    # {NEWS,ChangeLog} files.
+    cat(paste(paste(pkg$srcname,' (',pkg$debversion,') unstable; urgency=low',sep='')
+             ,'' ,'  * Initial release.',''
+             ,paste(' --',maintainer,'',format(Sys.time(),'%a, %d %b %Y %H:%M:%S %z'))
+             ,'',sep='\n'),file=pkg$debfile('changelog.in'))
+}
+
+generate.rules <- function(pkg) {
+    cat(paste('#!/usr/bin/make -f'
+             ,paste('debRreposname :=',pkg$repo)
+             ,'include /usr/share/R/debian/r-cran.mk'
+             ,'',sep='\n')
+       ,file=pkg$debfile('rules'))
+    Sys.chmod(pkg$debfile('rules'),'0700')
+}
+
+generate.copyright <- function(pkg) {
+    # generate copyright file; we trust DESCRIPTION
+    writeLines(strwrap(
+        paste('This Debian package of the GNU R package',pkg$name
+             ,'was generated automatically using cran2deb by'
+             ,paste(maintainer,'.',sep='')
+             ,''
+             ,'The original GNU R package is Copyright (C) '
+             # TODO: copyright start date, true copyright date
+             ,format(Sys.time(),'%Y')
+             ,pkg$description[1,'Author']
+             ,'and possibly others.'
+             ,''
+             ,'The original GNU R package is maintained by'
+             ,pkg$description[1,'Maintainer'],'and was obtained from:'
+             ,''
+             ,pkg$repoURL
+             ,''
+             ,''
+             ,'The GNU R package DESCRIPTION offers a'
+             ,'Copyright licenses under the terms of the',pkg$license
+             ,'license.  On a Debian GNU/Linux system, common'
+             ,'licenses are included in the directory'
+             ,'/usr/share/common-licenses/.'
+             ,''
+             ,'The DESCRIPTION file for the original GNU R package '
+             ,'can be found in '
+             ,file.path('/usr/lib/R/site-library'
+                   ,pkg$debname
+                   ,'DESCRIPTION'
+                   )
+             ,sep='\n'), width=72), con=pkg$debfile('copyright.in'))
+}
+
+prepare.new.debian <- function(pkg,extra_deps) {
+    # generate Debian version and name
+    pkg$repo = repourl.as.debian(pkg$repoURL)
+    pkg$debversion = version.new(pkg$version)
+    if (!length(grep('^[A-Za-z0-9][A-Za-z0-9+.-]+$',pkg$name))) {
+        stop(paste('Cannot convert package name into a Debian name',pkg$name))
+    }
+    pkg$srcname = tolower(pkg$name)
+    pkg$debname = pkgname.as.debian(pkg$name,repo=pkg$repo)
+
+    if (!length(grep('\\.tar\\.gz',pkg$archive))) {
+        stop('archive is not tarball')
+    }
+
+    # re-pack into a Debian-named archive with a Debian-named directory.
+    debpath = file.path(dirname(pkg$archive)
+                   ,paste(pkg$srcname,'-'
+                         ,pkg$version
+                         ,sep=''))
+    file.rename(pkg$path, debpath)
+    pkg$path = debpath
+    debarchive = file.path(dirname(pkg$archive)
+                          ,paste(pkg$srcname,'_'
+                                ,pkg$version,'.orig.tar.gz'
+                                ,sep=''))
+    wd <- getwd()
+    setwd(dirname(pkg$path))
+    # remove them pesky +x files
+    system(paste('find',shQuote(basename(pkg$path))
+                ,'-type f -exec chmod -x {} \\;'))
+    # tar it all back up
+    system(paste('tar -czf',shQuote(debarchive),shQuote(basename(pkg$path))))
+    setwd(wd)
+    file.remove(pkg$archive)
+    pkg$archive = debarchive
+
+    # make the debian/ directory
+    debdir <- file.path(pkg$path,'debian')
+    pkg$debfile <- function(x) { file.path(debdir,x) }
+    unlink(debdir,recursive=T)
+    dir.create(debdir)
+
+    # see if this is an architecture-dependent package.
+    # heuristic: if /src/ exists in pkg$path, then this is an
+    #            architecture-dependent package.
+    # CRAN2DEB.pm is a bit fancier about this but ``Writing R extensions''
+    # says: ``The sources and headers for the compiled code are in src, plus
+    # optionally file Makevars or Makefile.'' It seems unlikely that
+    # architecture independent code would end up here.
+    if (pkg$is_bundle) {
+        # if it's a bundle, check each of the packages
+        pkg$archdep = F
+        for (pkgname in r.bundle.contains(pkg$name)) {
+            pkg$archdep = file.exists(file.path(pkg$path,pkgname,'src'))
+            if (pkg$archdep) {
+                break
+            }
+        }
+    } else {
+        pkg$archdep = file.exists(file.path(pkg$path,'src'))
+    }
+    pkg$arch <- 'all'
+    if (pkg$archdep) {
+        pkg$arch <- host.arch()
+    }
+
+    pkg$license <- accept.license(pkg)
+    pkg$depends <- get.dependencies(pkg,extra_deps)
+    generate.changelog(pkg)
+    generate.rules(pkg)
+    generate.copyright(pkg)
+    generate.control(pkg)
+
+    # TODO: debian/watch from pkg$repoURL
+
+    # convert text to utf8 (who knows what the original character set is --
+    # let's hope iconv DTRT).
+    for (file in c('control','changelog','copyright')) {
+        system(paste('iconv -o ',shQuote(pkg$debfile(file))
+                    ,' -t utf8 '
+                    ,shQuote(pkg$debfile(paste(file,'in',sep='.')))))
+        file.remove(pkg$debfile(paste(file,'in',sep='.')))
+    }
+    return(pkg)
+}
+
+build.debian <- function(pkg) {
+    wd <- getwd()
+    setwd(pkg$path)
+    message(paste('N: building Debian package'
+                 ,pkg$debname
+                 ,paste('(',pkg$debversion,')',sep='')
+                 ,'...'))
+    ret = system(paste('pdebuild --configfile',pbuilder_config))
+    setwd(wd)
+    if (ret != 0) {
+        stop('Failed to build package.')
+    }
+}
+
diff --git a/pkg/trunk/R/getrpkg.R b/pkg/trunk/R/getrpkg.R
new file mode 100644
index 0000000..45fbe6d
--- /dev/null
+++ b/pkg/trunk/R/getrpkg.R
@@ -0,0 +1,68 @@
+
+setup <- function() {
+    # set up the working directory
+    tmp <- tempfile('cran2deb')
+    dir.create(tmp)
+    return (tmp)
+}
+
+cleanup <- function(dir) {
+    # remove the working directory
+    unlink(dir,recursive=T)
+    invisible()
+}
+
+prepare.pkg <- function(dir, pkgname) {
+    # download and extract an R package named pkgname
+    # OR the bundle containing pkgname
+
+    # based loosely on library/utils/R/packages2.R::install.packages
+    # should do nothing Debian specific
+
+    # first a little trick; change pkgname if pkgname is contained in a bundle
+    if (!(pkgname %in% rownames(available))) {
+        bundle <- r.bundle.of(pkgname)
+        if (is.na(bundle)) {
+            stop(paste('package',pkgname,'is unavailable'))
+        }
+        pkgname <- bundle
+    }
+    archive <- download.packages(pkgname, dir, available=available, repos='', type="source")[1,2]
+    if (length(grep('\\.\\.',archive)) || normalizePath(archive) != archive) {
+        stop(paste('funny looking path',archive))
+    }
+    wd <- getwd()
+    setwd(dir)
+    if (length(grep('\\.zip$',archive))) {
+        cmd = paste('unzip',shQuote(archive))
+    } else if (length(grep('\\.tar\\.gz$',archive))) {
+        cmd = paste('tar','xzf',shQuote(archive))
+    } else {
+        stop(paste('Type of archive',archive,'is unknown.'))
+    }
+    ret = system(cmd)
+    setwd(wd)
+    if (ret != 0) {
+        stop(paste('Extraction of archive',archive,'failed.'))
+    }
+    pkg <- pairlist()
+    pkg$name = pkgname
+    pkg$archive = archive
+    pkg$path = sub("_\\.(zip|tar\\.gz)", ""
+                  ,gsub(.standard_regexps()$valid_package_version, ""
+                  ,archive))
+    if (!file.info(pkg$path)[,'isdir']) {
+        stop(paste(pkg$path,'is not a directory and should be.'))
+    }
+    pkg$description = read.dcf(file.path(pkg$path,'DESCRIPTION'))
+    pkg$repoURL = available[pkgname,'Repository']
+    pkg$version = pkg$description[1,'Version']
+    pkg$is_bundle = 'Bundle' %in% names(pkg$description[1,])
+    # note subtly of short circuit operators (no absorption)
+    if ((!pkg$is_bundle && pkg$description[1,'Package'] != pkg$name) ||
+        ( pkg$is_bundle && pkg$description[1,'Bundle'] != pkg$name)) {
+        stop(paste('package name mismatch'))
+    }
+    return(pkg)
+}
+
diff --git a/pkg/trunk/R/license.R b/pkg/trunk/R/license.R
new file mode 100644
index 0000000..7112572
--- /dev/null
+++ b/pkg/trunk/R/license.R
@@ -0,0 +1,77 @@
+debian_ok_licenses=c('GPL','LGPL','AGPL','ARTISTIC' #,'UNLIMITED'
+                    ,'BSD','MIT','APACHE','X11','MPL')
+
+is_acceptable_license <- function(license) {
+    # determine if license is acceptable
+
+    # compress spaces into a single space
+    license = gsub('[[:blank:]]+',' ',license)
+    # make all characters upper case
+    license = toupper(license)
+    # don't care about versions of licenses
+    license = chomp(sub('\\( ?[<=>!]+ ?[0-9.-]+ ?\\)',''
+                    ,sub('-[0-9.-]+','',license)))
+    if (license %in% debian_ok_licenses) {
+        return(T)
+    }
+    # uninteresting urls
+    license = gsub('HTTP://WWW.GNU.ORG/[A-Z/._-]*','',license)
+    license = gsub('HTTP://WWW.X.ORG/[A-Z/._-]*','',license)
+    license = gsub('HTTP://WWW.OPENSOURCE.ORG/[A-Z/._-]*','',license)
+    # remove all punctuation
+    license = gsub('[[:punct:]]+','',license)
+    # remove any extra space introduced
+    license = chomp(gsub('[[:space:]]+',' ',license))
+    # redundant
+    license = gsub('THE','',license)
+    license = gsub('SEE','',license)
+    license = gsub('STANDARD','',license)
+    license = gsub('LICEN[SC]E','',license)
+    license = gsub('(GNU )?(GPL|GENERAL PUBLIC)','GPL',license)
+    license = gsub('(MOZILLA )?(MPL|MOZILLA PUBLIC)','MPL',license)
+    # remove any extra space introduced
+    license = chomp(gsub('[[:space:]]+',' ',license))
+    if (license %in% debian_ok_licenses) {
+        message(paste('W: Accepted wild license as',license,'. FIX THE PACKAGE!'))
+        return(T)
+    }
+    # remove everything that looks like a version specification
+    license = gsub('(VER?SION|V)? *[0-9.-]+ *(OR *(HIGHER|LATER|NEWER|GREATER|ABOVE))?',''
+                   ,license)
+    # remove any extra space introduced
+    license = chomp(gsub('[[:space:]]+',' ',license))
+    if (license %in% debian_ok_licenses) {
+        message(paste('W: Accepted wild license as',license,'. FIX THE PACKAGE!'))
+        return(T)
+    }
+    # TODO: put debian_ok_licenses in DB
+    # TODO: file {LICENSE,LICENCE} (+ maybe COPYING?)
+    message(paste('E: Wild license',license,'did not match'))
+    return(F)
+}
+
+accept.license <- function(pkg) {
+    # check the license
+    if (!('License' %in% names(pkg$description[1,]))) {
+        stop('package has no License: field in description!')
+    }
+    accept=NULL
+    for (license in strsplit(chomp(pkg$description[1,'License'])
+                            ,'[[:space:]]*\\|[[:space:]]*')[[1]]) {
+        if (is_acceptable_license(license)) {
+            accept=license
+            break
+        }
+    }
+    if (is.null(accept)) {
+        stop(paste('No acceptable license:',pkg$description[1,'License']))
+    } else {
+        message(paste('N: Auto-accepted license',accept))
+    }
+    if (accept == 'Unlimited') {
+        # definition of Unlimited from ``Writing R extensions''
+        accept=paste('Unlimited (no restrictions on distribution or'
+                    ,'use other than those imposed by relevant laws)')
+    }
+    return(accept)
+}
diff --git a/pkg/trunk/R/rdep.R b/pkg/trunk/R/rdep.R
new file mode 100644
index 0000000..0af9451
--- /dev/null
+++ b/pkg/trunk/R/rdep.R
@@ -0,0 +1,152 @@
+
+r.bundle.of <- function(pkgname) {
+    # returns the bundle containing pkgname or NA
+    bundles <- names(available[!is.na(available[, 'Bundle']), 'Contains'])
+    # use the first bundle
+    for (bundle in bundles) {
+        if (pkgname %in% r.bundle.contains(bundle)) {
+            return(bundle)
+        }
+    }
+    return(NA)
+}
+
+r.bundle.contains <- function(bundlename) {
+    return(strsplit(available[bundlename,'Contains'],'[[:space:]]+')[[1]])
+}
+
+r.requiring <- function(names) {
+    for (name in names) {
+        if (!(name %in% base_pkgs) && !(name %in% rownames(available))) {
+            bundle <- r.bundle.of(name)
+            if (is.na(bundle)) {
+                stop(paste('package',name,'is not available'))
+            }
+            names <- c(names,r.bundle.contains(bundle))
+        }
+    }
+    # approximately prune first into a smaller availability
+    candidates <- available[sapply(rownames(available)
+                                  ,function(name)
+                                      length(grep(paste(names,sep='|')
+                                                 ,available[name,r_depend_fields])) > 0)
+                           ,r_depend_fields
+                           ,drop=F]
+    if (length(candidates) == 0) {
+        return(c())
+    }
+    # find a logical index into available of every package/bundle
+    # whose dependency field contains at least one element of names.
+    # (this is not particularly easy to read---sorry---but is much faster than
+    # the alternatives i could think of)
+    prereq=c()
+    dep_matches <- function(dep) chomp(gsub('\\([^\\)]+\\)','',dep)) %in% names
+    any_dep_matches <- function(name,field=NA)
+                any(sapply(strsplit(chomp(candidates[name,field])
+                                   ,'[[:space:]]*,[[:space:]]*')
+                          ,dep_matches))
+
+    for (field in r_depend_fields) {
+        matches = sapply(rownames(candidates), any_dep_matches, field=field)
+        if (length(matches) > 0) {
+            prereq = c(prereq,rownames(candidates[matches,]))
+        }
+    }
+    return(unique(prereq))
+}
+
+r.dependencies.of <- function(name=NULL,description=NULL) {
+    # find the immediate dependencies (children in the dependency graph) of an
+    # R package
+    if (!is.null(name) && (name == 'R' || name %in% base_pkgs)) {
+        return(data.frame())
+    }
+    if (is.null(description) && is.null(name)) {
+        stop('must specify either a description or a name.')
+    }
+    if (is.null(description)) {
+        if (!(name %in% rownames(available))) {
+            bundle <- r.bundle.of(name)
+            if (is.na(bundle)) {
+                stop(paste('package',name,'is not available'))
+            }
+            name <- bundle
+        }
+        description <- data.frame()
+        # keep only the interesting fields
+        for (field in r_depend_fields) {
+            if (!(field %in% names(available[name,]))) {
+                next
+            }
+            description[1,field] = available[name,field]
+        }
+    }
+    # extract the dependencies from the description
+    deps <- data.frame()
+    for (field in r_depend_fields) {
+        if (!(field %in% names(description[1,]))) {
+            next
+        }
+        new_deps <- lapply(strsplit(chomp(description[1,field])
+                                   ,'[[:space:]]*,[[:space:]]*')[[1]]
+                          ,r.parse.dep.field)
+        deps <- iterate(lapply(new_deps[!is.na(new_deps)],rbind),deps,rbind)
+    }
+    return (deps)
+}
+
+r.parse.dep.field <- function(dep) {
+    if (is.na(dep)) {
+        return(NA)
+    }
+    # remove other comments
+    dep = gsub('(\\(\\)|\\([[:space:]]*[^<=>!].*\\))','',dep)
+    # squish spaces
+    dep = chomp(gsub('[[:space:]]+',' ',dep))
+    # parse version
+    pat = '^([^ ()]+) ?(\\( ?([<=>!]+ ?[0-9.-]+) ?\\))?$'
+    if (!length(grep(pat,dep))) {
+        stop(paste('R dependency',dep,'does not appear to be well-formed'))
+    }
+    version = sub(pat,'\\3',dep)
+    dep = sub(pat,'\\1',dep)
+    if (!(dep %in% rownames(available))) {
+        depb <- r.bundle.of(dep)
+        if (!is.na(depb)) {
+            dep <- depb
+        }
+    }
+    return(list(name=dep,version=version))
+}
+
+r.dependency.closure <- function(fringe, forward_arcs=T) {
+    # find the transitive closure of the dependencies/prerequisites of some R
+    # packages
+    closure <- list()
+    if (is.data.frame(fringe)) {
+        fringe <- levels(fringe$name)
+    }
+    fun = function(x) levels(r.dependencies.of(name=x)$name)
+    if (!forward_arcs) {
+        fun = r.requiring
+    }
+    while(length(fringe) > 0) {
+        # pop off the top
+        top <- fringe[[1]]
+        if (length(fringe) > 1) {
+            fringe <- fringe[2:length(fringe)]
+        } else {
+            fringe <- list()
+        }
+        src <- pkgname.as.debian(top,binary=F)
+        if (!length(grep('^r-',src)) || length(grep('^r-base',src))) {
+            next
+        }
+        newdeps <- fun(top)
+        closure=c(closure,top)
+        fringe=c(fringe,newdeps)
+    }
+    # build order
+    return(rev(unique(closure,fromLast=T)))
+}
+
diff --git a/pkg/trunk/R/util.R b/pkg/trunk/R/util.R
new file mode 100644
index 0000000..35f6413
--- /dev/null
+++ b/pkg/trunk/R/util.R
@@ -0,0 +1,17 @@
+iterate <- function(xs,z,fun) {
+    y <- z
+    for (x in xs)
+        y <- fun(y,x)
+    return(y)
+}
+
+chomp <- function(x) {
+    # remove leading and trailing spaces
+    return(sub('^[[:space:]]+','',sub('[[:space:]]+$','',x)))
+}
+
+host.arch <- function() {
+    # return the host system architecture
+    system('dpkg-architecture -qDEB_HOST_ARCH',intern=T)
+}
+
diff --git a/pkg/trunk/R/version.R b/pkg/trunk/R/version.R
new file mode 100644
index 0000000..29c8c0e
--- /dev/null
+++ b/pkg/trunk/R/version.R
@@ -0,0 +1,70 @@
+version.new <- function(rver,debian_revision=1, debian_epoch=0) {
+    # generate a string representation of the Debian version of an
+    # R version of a package
+    pkgver = rver
+
+    # ``Writing R extensions'' says that the version consists of at least two
+    # non-negative integers, separated by . or -
+    if (!length(grep('^([0-9]+[.-])+[0-9]+$',rver))) {
+        stop(paste('Not a valid R package version',rver))
+    }
+
+    # Debian policy says that an upstream version should start with a digit and
+    # may only contain ASCII alphanumerics and '.+-:~'
+    if (!length(grep('^[0-9][A-Za-z0-9.+:~-]*$',rver))) {
+        stop(paste('R package version',rver
+                  ,'does not obviously translate into a valid Debian version.'))
+    }
+
+    # if rver contains a : then the Debian version must also have a colon
+    if (debian_epoch == 0 && length(grep(':',pkgver)))
+        debian_epoch = 1
+
+    # if the epoch is non-zero then include it
+    if (debian_epoch != 0)
+        pkgver = paste(debian_epoch,':',pkgver,sep='')
+
+    # always add the '-1' Debian release; nothing is lost and rarely will R
+    # packages be Debian packages without modification.
+    return(paste(pkgver,'-',debian_revision,sep=''))
+}
+
+version.epoch <- function(pkgver) {
+    # return the Debian epoch of a Debian package version
+    if (!length(grep(':',pkgver)))
+        return(0)
+    return(as.integer(sub('^([0-9]+):.*','\\1',pkgver)))
+}
+# version.epoch . version.new(x,y) = id
+# version.epoch(version.new(x,y)) = 0
+
+version.revision <- function(pkgver) {
+    # return the Debian revision of a Debian package version
+    return(as.integer(sub('.*-([0-9]+)$','\\1',pkgver)))
+}
+# version.revision . version.new(x) = id
+# version.revision(version.new(x)) = 1
+
+version.upstream <- function(pkgver) {
+    # return the upstream version of a Debian package version
+    return(sub('-[0-9]+$','',sub('^[0-9]+:','',pkgver)))
+}
+# version.upstream . version.new = id
+
+version.update <- function(rver, prev_pkgver) {
+    # return the next debian package version
+    prev_rver <- version.upstream(prev_pkgver)
+    if (prev_rver == rver) {
+        # increment the Debian revision
+        return(version.new(rver
+                          ,debian_revision = version.revision(prev_pkgver)+1
+                          ,debian_epoch    = version.epoch(prev_pkgver)
+                          ))
+    }
+    # new release
+    # TODO: implement Debian ordering over version and then autoincrement
+    #       Debian epoch when upstream version does not increment.
+    return(version.new(rver
+                      ,debian_epoch = version.epoch(prev_pkgver)
+                      ))
+}
diff --git a/pkg/trunk/R/zzz.R b/pkg/trunk/R/zzz.R
new file mode 100644
index 0000000..a57cc3a
--- /dev/null
+++ b/pkg/trunk/R/zzz.R
@@ -0,0 +1,20 @@
+
+changesfile <- function(srcname,version='*') {
+    return(file.path(pbuilder_results
+                    ,paste(srcname,'_',version,'_'
+                          ,host.arch(),'.changes',sep='')))
+}
+
+maintainer <- 'cran2deb buildbot <cran2deb@example.org>'
+root <- system.file('')
+pbuilder_results <- file.path(root,'var/results')
+pbuilder_config  <- file.path(root,'etc/pbuilderrc')
+dput_config      <- file.path(root,'etc/dput.cf')
+dinstall_config  <- file.path(root,'etc/mini-dinstall.conf')
+dinstall_archive <- file.path(root,'var/archive')
+r_depend_fields  <- c('Depends','Imports') # Suggests, Enhances
+
+# we cache the list of available packages
+# should be pulled in already
+#load(file.path(root,'var/cache/available.cache.Rd'))
+
diff --git a/pkg/trunk/build_ctv b/pkg/trunk/build_ctv
deleted file mode 100755
index 754dd58..0000000
--- a/pkg/trunk/build_ctv
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env rc
-
-for (ctv in `{./cranpkgs query}) {
-    echo task view $ctv...
-    if (![ -e ctv/$ctv ]) {
-        ./build_some $ctv
-        mkdir -p ctv/$ctv
-        mv warn fail ctv/$ctv
-    }
-}
-
diff --git a/pkg/trunk/build_some b/pkg/trunk/build_some
deleted file mode 100755
index dd12c2d..0000000
--- a/pkg/trunk/build_some
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/rc
-
-mkdir -p warn fail
-./cranpkgs $* >all_pkgs
-for (pkg in `{cat all_pkgs}) {
-    if (~ $pkg *..* */*) {
-        echo bad name $pkg >>fail/ERROR
-    } else {
-        echo .. package $pkg
-        fail=0
-        ./cran2deb $pkg >fail/$pkg >[2=1] || fail=1
-        if (~ $fail 0) {
-            grep '^[WE]:' fail/$pkg >warn/$pkg
-            if (~ `{stat -c '%s' warn/$pkg} 0) {
-                rm -f warn/$pkg
-            }
-            rm -f fail/$pkg
-        }
-    }
-}
diff --git a/pkg/trunk/copy_find b/pkg/trunk/copy_find
deleted file mode 100755
index fe3d619..0000000
--- a/pkg/trunk/copy_find
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/rc
-kwords='copyright|warranty|redistribution|modification|patent|trademark|licen[cs]e|permission'
-nl=`` () {printf '\n'}
-ifs=$nl {
-    files=`{find $1 ! -path '*debian*' -type f}
-    lines=()
-    for (file in $files) {
-        notices=`{grep -H '(C)' $file}
-        notices=($notices `{grep -HEi $kwords $file})
-        lines=($lines `{{for (notice in $notices) echo $notice} | sort -u})
-    }
-    # let's hope no file has a : in it
-    ifs=() { seen_files=`{{for (line in $lines) echo $line} | cut -d: -f1} }
-    missing_copyright=()
-    for (file in $files) {
-        if (echo -n $seen_files | grep -q '^'^$file^'$') {
-        } else {
-            missing_copyright=($missing_copyright $file)
-        }
-    }
-    echo 'Suspect copyright notices:'
-    for (line in $lines) echo '    '$line
-    echo 'Files without *suspect* copyright notices:'
-    for (missing in $missing_copyright) {
-        echo '    '$missing
-        echo '       type: '`{file $missing}
-        echo '      chars: '`{wc -c $missing | awk '{print $1}'}
-        echo '      lines: '`{wc -l $missing | awk '{print $1}'}
-    }
-}
diff --git a/pkg/trunk/cran2deb b/pkg/trunk/cran2deb
deleted file mode 100755
index 821d8a6..0000000
--- a/pkg/trunk/cran2deb
+++ /dev/null
@@ -1,798 +0,0 @@
-#!/usr/bin/env r
-
-maintainer <- 'cran2deb buildbot <cran2deb@example.org>'
-root <- '/home/cb/work/gsoc/cran2deb'
-pbuilder_results <- file.path(root,'var/results')
-pbuilder_config  <- file.path(root,'etc/pbuilderrc')
-dput_config      <- file.path(root,'etc/dput.cf')
-dinstall_config  <- file.path(root,'etc/mini-dinstall.conf')
-dinstall_archive <- file.path(root,'var/archive')
-r_depend_fields  <- c('Depends','Imports') # Suggests, Enhances
-
-# we cache the list of available packages
-load(file.path(root,'var/cache/available.cache.Rd'))
-
-version.new <- function(rver,debian_revision=1, debian_epoch=0) {
-    # generate a string representation of the Debian version of an
-    # R version of a package
-    pkgver = rver
-
-    # ``Writing R extensions'' says that the version consists of at least two
-    # non-negative integers, separated by . or -
-    if (!length(grep('^([0-9]+[.-])+[0-9]+$',rver))) {
-        stop(paste('Not a valid R package version',rver))
-    }
-
-    # Debian policy says that an upstream version should start with a digit and
-    # may only contain ASCII alphanumerics and '.+-:~'
-    if (!length(grep('^[0-9][A-Za-z0-9.+:~-]*$',rver))) {
-        stop(paste('R package version',rver
-                  ,'does not obviously translate into a valid Debian version.'))
-    }
-
-    # if rver contains a : then the Debian version must also have a colon
-    if (debian_epoch == 0 && length(grep(':',pkgver)))
-        debian_epoch = 1
-
-    # if the epoch is non-zero then include it
-    if (debian_epoch != 0)
-        pkgver = paste(debian_epoch,':',pkgver,sep='')
-
-    # always add the '-1' Debian release; nothing is lost and rarely will R
-    # packages be Debian packages without modification.
-    return(paste(pkgver,'-',debian_revision,sep=''))
-}
-
-version.epoch <- function(pkgver) {
-    # return the Debian epoch of a Debian package version
-    if (!length(grep(':',pkgver)))
-        return(0)
-    return(as.integer(sub('^([0-9]+):.*','\\1',pkgver)))
-}
-# version.epoch . version.new(x,y) = id
-# version.epoch(version.new(x,y)) = 0
-
-version.revision <- function(pkgver) {
-    # return the Debian revision of a Debian package version
-    return(as.integer(sub('.*-([0-9]+)$','\\1',pkgver)))
-}
-# version.revision . version.new(x) = id
-# version.revision(version.new(x)) = 1
-
-version.upstream <- function(pkgver) {
-    # return the upstream version of a Debian package version
-    return(sub('-[0-9]+$','',sub('^[0-9]+:','',pkgver)))
-}
-# version.upstream . version.new = id
-
-version.update <- function(rver, prev_pkgver) {
-    # return the next debian package version
-    prev_rver <- version.upstream(prev_pkgver)
-    if (prev_rver == rver) {
-        # increment the Debian revision
-        return(version.new(rver
-                          ,debian_revision = version.revision(prev_pkgver)+1
-                          ,debian_epoch    = version.epoch(prev_pkgver)
-                          ))
-    }
-    # new release
-    # TODO: implement Debian ordering over version and then autoincrement
-    #       Debian epoch when upstream version does not increment.
-    return(version.new(rver
-                      ,debian_epoch = version.epoch(prev_pkgver)
-                      ))
-}
-
-# sudo pbuilder --execute r -e 'rownames(installed.packages())'
-# XXX: has to be a better way of doing this
-base_pkgs=c('base',   'datasets','grDevices','graphics','grid', 'methods'
-           ,'splines','stats',   'stats4',   'tcltk',   'tools','utils')
-# found in R source directory:
-# 'profile', 'datasets'
-
-repourl.as.debian <- function(url) {
-    # map the url to a repository onto its name in debian package naming
-    if (length(grep('cran',url))) {
-        return('cran')
-    }
-    if (length(grep('bioc',url))) {
-        return('bioc')
-    }
-    stop(paste('unknown repository',url))
-}
-
-pkgname.as.debian <- function(name,repopref=NULL,version=NULL,binary=T) {
-    # generate the debian package name corresponding to the R package name
-    if (name %in% base_pkgs) {
-        name = 'R'
-    }
-    if (name == 'R') {
-        # R is special.
-        if (binary) {
-            debname='r-base-core'
-        } else {
-            debname='r-base-dev'
-        }
-    } else {
-        # XXX: data.frame rownames are unique, so always override repopref for
-        #      now.
-        if (!(name %in% rownames(available))) {
-            bundle <- r.bundle.of(name)
-            if (is.na(bundle)) {
-                stop(paste('package',name,'is not available'))
-            }
-            name <- bundle
-        }
-        repopref <- repourl.as.debian(available[name,'Repository'])
-        debname = paste('r',tolower(repopref),tolower(name),sep='-')
-    }
-    if (!is.null(version) && length(version) > 1) {
-        debname = paste(debname,' (',version,')',sep='')
-    }
-    return(debname)
-}
-
-setup <- function() {
-    # set up the working directory
-    tmp <- tempfile('cran2deb')
-    dir.create(tmp)
-    return (tmp)
-}
-
-cleanup <- function(dir) {
-    # remove the working directory
-    unlink(dir,recursive=T)
-    invisible()
-}
-
-r.bundle.of <- function(pkgname) {
-    # returns the bundle containing pkgname or NA
-    bundles <- names(available[!is.na(available[, 'Bundle']), 'Contains'])
-    # use the first bundle
-    for (bundle in bundles) {
-        if (pkgname %in% r.bundle.contains(bundle)) {
-            return(bundle)
-        }
-    }
-    return(NA)
-}
-
-r.bundle.contains <- function(bundlename) {
-    return(strsplit(available[bundlename,'Contains'],'[[:space:]]+')[[1]])
-}
-
-prepare.pkg <- function(dir, pkgname) {
-    # download and extract an R package named pkgname
-    # OR the bundle containing pkgname
-
-    # based loosely on library/utils/R/packages2.R::install.packages
-    # should do nothing Debian specific
-
-    # first a little trick; change pkgname if pkgname is contained in a bundle
-    if (!(pkgname %in% rownames(available))) {
-        bundle <- r.bundle.of(pkgname)
-        if (is.na(bundle)) {
-            stop(paste('package',pkgname,'is unavailable'))
-        }
-        pkgname <- bundle
-    }
-    archive <- download.packages(pkgname, dir, available=available, repos='', type="source")[1,2]
-    if (length(grep('\\.\\.',archive)) || normalizePath(archive) != archive) {
-        stop(paste('funny looking path',archive))
-    }
-    wd <- getwd()
-    setwd(dir)
-    if (length(grep('\\.zip$',archive))) {
-        cmd = paste('unzip',shQuote(archive))
-    } else if (length(grep('\\.tar\\.gz$',archive))) {
-        cmd = paste('tar','xzf',shQuote(archive))
-    } else {
-        stop(paste('Type of archive',archive,'is unknown.'))
-    }
-    ret = system(cmd)
-    setwd(wd)
-    if (ret != 0) {
-        stop(paste('Extraction of archive',archive,'failed.'))
-    }
-    pkg <- pairlist()
-    pkg$name = pkgname
-    pkg$archive = archive
-    pkg$path = sub("_\\.(zip|tar\\.gz)", ""
-                  ,gsub(.standard_regexps()$valid_package_version, ""
-                  ,archive))
-    if (!file.info(pkg$path)[,'isdir']) {
-        stop(paste(pkg$path,'is not a directory and should be.'))
-    }
-    pkg$description = read.dcf(file.path(pkg$path,'DESCRIPTION'))
-    pkg$repoURL = available[pkgname,'Repository']
-    pkg$version = pkg$description[1,'Version']
-    pkg$is_bundle = 'Bundle' %in% names(pkg$description[1,])
-    # note subtly of short circuit operators (no absorption)
-    if ((!pkg$is_bundle && pkg$description[1,'Package'] != pkg$name) ||
-        ( pkg$is_bundle && pkg$description[1,'Bundle'] != pkg$name)) {
-        stop(paste('package name mismatch'))
-    }
-    return(pkg)
-}
-
-debian_ok_licenses=c('GPL','LGPL','AGPL','ARTISTIC' #,'UNLIMITED'
-                    ,'BSD','MIT','APACHE','X11','MPL')
-
-is_acceptable_license <- function(license) {
-    # determine if license is acceptable
-
-    # compress spaces into a single space
-    license = gsub('[[:blank:]]+',' ',license)
-    # make all characters upper case
-    license = toupper(license)
-    # don't care about versions of licenses
-    license = chomp(sub('\\( ?[<=>!]+ ?[0-9.-]+ ?\\)',''
-                    ,sub('-[0-9.-]+','',license)))
-    if (license %in% debian_ok_licenses) {
-        return(T)
-    }
-    # uninteresting urls
-    license = gsub('HTTP://WWW.GNU.ORG/[A-Z/._-]*','',license)
-    license = gsub('HTTP://WWW.X.ORG/[A-Z/._-]*','',license)
-    license = gsub('HTTP://WWW.OPENSOURCE.ORG/[A-Z/._-]*','',license)
-    # remove all punctuation
-    license = gsub('[[:punct:]]+','',license)
-    # remove any extra space introduced
-    license = chomp(gsub('[[:space:]]+',' ',license))
-    # redundant
-    license = gsub('THE','',license)
-    license = gsub('SEE','',license)
-    license = gsub('STANDARD','',license)
-    license = gsub('LICEN[SC]E','',license)
-    license = gsub('(GNU )?(GPL|GENERAL PUBLIC)','GPL',license)
-    license = gsub('(MOZILLA )?(MPL|MOZILLA PUBLIC)','MPL',license)
-    # remove any extra space introduced
-    license = chomp(gsub('[[:space:]]+',' ',license))
-    if (license %in% debian_ok_licenses) {
-        message(paste('W: Accepted wild license as',license,'. FIX THE PACKAGE!'))
-        return(T)
-    }
-    # remove everything that looks like a version specification
-    license = gsub('(VER?SION|V)? *[0-9.-]+ *(OR *(HIGHER|LATER|NEWER|GREATER|ABOVE))?',''
-                   ,license)
-    # remove any extra space introduced
-    license = chomp(gsub('[[:space:]]+',' ',license))
-    if (license %in% debian_ok_licenses) {
-        message(paste('W: Accepted wild license as',license,'. FIX THE PACKAGE!'))
-        return(T)
-    }
-    # TODO: put debian_ok_licenses in DB
-    # TODO: file {LICENSE,LICENCE} (+ maybe COPYING?)
-    message(paste('E: Wild license',license,'did not match'))
-    return(F)
-}
-
-iterate <- function(xs,z,fun) {
-    y <- z
-    for (x in xs)
-        y <- fun(y,x)
-    return(y)
-}
-
-chomp <- function(x) {
-    # remove leading and trailing spaces
-    return(sub('^[[:space:]]+','',sub('[[:space:]]+$','',x)))
-}
-
-host.arch <- function() {
-    # return the host system architecture
-    system('dpkg-architecture -qDEB_HOST_ARCH',intern=T)
-}
-
-r.requiring <- function(names) {
-    for (name in names) {
-        if (!(name %in% base_pkgs) && !(name %in% rownames(available))) {
-            bundle <- r.bundle.of(name)
-            if (is.na(bundle)) {
-                stop(paste('package',name,'is not available'))
-            }
-            names <- c(names,r.bundle.contains(bundle))
-        }
-    }
-    # approximately prune first into a smaller availability
-    candidates <- available[sapply(rownames(available)
-                                  ,function(name)
-                                      length(grep(paste(names,sep='|')
-                                                 ,available[name,r_depend_fields])) > 0)
-                           ,r_depend_fields
-                           ,drop=F]
-    if (length(candidates) == 0) {
-        return(c())
-    }
-    # find a logical index into available of every package/bundle
-    # whose dependency field contains at least one element of names.
-    # (this is not particularly easy to read---sorry---but is much faster than
-    # the alternatives i could think of)
-    prereq=c()
-    dep_matches <- function(dep) chomp(gsub('\\([^\\)]+\\)','',dep)) %in% names
-    any_dep_matches <- function(name,field=NA)
-                any(sapply(strsplit(chomp(candidates[name,field])
-                                   ,'[[:space:]]*,[[:space:]]*')
-                          ,dep_matches))
-
-    for (field in r_depend_fields) {
-        matches = sapply(rownames(candidates), any_dep_matches, field=field)
-        if (length(matches) > 0) {
-            prereq = c(prereq,rownames(candidates[matches,]))
-        }
-    }
-    return(unique(prereq))
-}
-
-r.dependencies.of <- function(name=NULL,description=NULL) {
-    # find the immediate dependencies (children in the dependency graph) of an
-    # R package
-    if (!is.null(name) && (name == 'R' || name %in% base_pkgs)) {
-        return(data.frame())
-    }
-    if (is.null(description) && is.null(name)) {
-        stop('must specify either a description or a name.')
-    }
-    if (is.null(description)) {
-        if (!(name %in% rownames(available))) {
-            bundle <- r.bundle.of(name)
-            if (is.na(bundle)) {
-                stop(paste('package',name,'is not available'))
-            }
-            name <- bundle
-        }
-        description <- data.frame()
-        # keep only the interesting fields
-        for (field in r_depend_fields) {
-            if (!(field %in% names(available[name,]))) {
-                next
-            }
-            description[1,field] = available[name,field]
-        }
-    }
-    # extract the dependencies from the description
-    deps <- data.frame()
-    for (field in r_depend_fields) {
-        if (!(field %in% names(description[1,]))) {
-            next
-        }
-        new_deps <- lapply(strsplit(chomp(description[1,field])
-                                   ,'[[:space:]]*,[[:space:]]*')[[1]]
-                          ,r.parse.dep.field)
-        deps <- iterate(lapply(new_deps[!is.na(new_deps)],rbind),deps,rbind)
-    }
-    return (deps)
-}
-
-r.parse.dep.field <- function(dep) {
-    if (is.na(dep)) {
-        return(NA)
-    }
-    # remove other comments
-    dep = gsub('(\\(\\)|\\([[:space:]]*[^<=>!].*\\))','',dep)
-    # squish spaces
-    dep = chomp(gsub('[[:space:]]+',' ',dep))
-    # parse version
-    pat = '^([^ ()]+) ?(\\( ?([<=>!]+ ?[0-9.-]+) ?\\))?$'
-    if (!length(grep(pat,dep))) {
-        stop(paste('R dependency',dep,'does not appear to be well-formed'))
-    }
-    version = sub(pat,'\\3',dep)
-    dep = sub(pat,'\\1',dep)
-    if (!(dep %in% rownames(available))) {
-        depb <- r.bundle.of(dep)
-        if (!is.na(depb)) {
-            dep <- depb
-        }
-    }
-    return(list(name=dep,version=version))
-}
-
-r.dependency.closure <- function(fringe, forward_arcs=T) {
-    # find the transitive closure of the dependencies/prerequisites of some R
-    # packages
-    closure <- list()
-    if (is.data.frame(fringe)) {
-        fringe <- levels(fringe$name)
-    }
-    fun = function(x) levels(r.dependencies.of(name=x)$name)
-    if (!forward_arcs) {
-        fun = r.requiring
-    }
-    while(length(fringe) > 0) {
-        # pop off the top
-        top <- fringe[[1]]
-        if (length(fringe) > 1) {
-            fringe <- fringe[2:length(fringe)]
-        } else {
-            fringe <- list()
-        }
-        src <- pkgname.as.debian(top,binary=F)
-        if (!length(grep('^r-',src)) || length(grep('^r-base',src))) {
-            next
-        }
-        newdeps <- fun(top)
-        closure=c(closure,top)
-        fringe=c(fringe,newdeps)
-    }
-    # build order
-    return(rev(unique(closure,fromLast=T)))
-}
-
-accept.license <- function(pkg) {
-    # check the license
-    if (!('License' %in% names(pkg$description[1,]))) {
-        stop('package has no License: field in description!')
-    }
-    accept=NULL
-    for (license in strsplit(chomp(pkg$description[1,'License'])
-                            ,'[[:space:]]*\\|[[:space:]]*')[[1]]) {
-        if (is_acceptable_license(license)) {
-            accept=license
-            break
-        }
-    }
-    if (is.null(accept)) {
-        stop(paste('No acceptable license:',pkg$description[1,'License']))
-    } else {
-        message(paste('N: Auto-accepted license',accept))
-    }
-    if (accept == 'Unlimited') {
-        # definition of Unlimited from ``Writing R extensions''
-        accept=paste('Unlimited (no restrictions on distribution or'
-                    ,'use other than those imposed by relevant laws)')
-    }
-    return(accept)
-}
-
-get.dependencies <- function(pkg,extra_deps) {
-    if ('SystemRequirements' %in% colnames(pkg$description)) {
-        stop(paste('Unsupported SystemRequirements:',pkg$description[1,'SystemRequirements']))
-    }
-
-    # determine dependencies
-    dependencies <- r.dependencies.of(description=pkg$description)
-    depends <- list()
-    # these are used for generating the Depends fields
-    as.deb <- function(r,binary) {
-        return(pkgname.as.debian(paste(dependencies[r,]$name)
-                                ,version=dependencies[r,]$version
-                                ,repopref=pkg$repo
-                                ,binary=binary))
-    }
-    depends$bin <- lapply(rownames(dependencies), as.deb, binary=T)
-    depends$build <- lapply(rownames(dependencies), as.deb, binary=F)
-    # add the command line dependencies
-    depends$bin = c(extra_deps$deb,depends$bin)
-    depends$build = c(extra_deps$deb,depends$build)
-
-    # make sure we depend upon R in some way...
-    if (!length(grep('^r-base',depends$build))) {
-        depends$build = c(depends$build,pkgname.as.debian('R',version='>= 2.7.0',binary=F))
-        depends$bin   = c(depends$bin,  pkgname.as.debian('R',version='>= 2.7.0',binary=T))
-    }
-    # also include stuff to allow tcltk to build (suggested by Dirk)
-    depends$build = c(depends$build,'xvfb','xauth','xfont-base')
-
-    # remove duplicates
-    depends <- lapply(depends,unique)
-
-    # append the Debian dependencies
-    depends$build=c(depends$build,'debhelper (>> 4.1.0)','cdbs')
-    if (pkg$archdep) {
-        depends$bin=c(depends$bin,'${shlibs:Depends}')
-    }
-
-    # the names of dependent source packages (to find the .changes file to
-    # upload via dput). these can be found recursively.
-    depends$r = lapply(r.dependency.closure(dependencies)
-                      ,tolower)
-    # append command line dependencies
-    depends$r = c(extra_deps$r, depends$r)
-    return(depends)
-}
-
-generate.changelog <- function(pkg) {
-    # construct a dummy changelog
-    # TODO: ``Writing R extensions'' mentions that a package may also have
-    # {NEWS,ChangeLog} files.
-    cat(paste(paste(pkg$srcname,' (',pkg$debversion,') unstable; urgency=low',sep='')
-             ,'' ,'  * Initial release.',''
-             ,paste(' --',maintainer,'',format(Sys.time(),'%a, %d %b %Y %H:%M:%S %z'))
-             ,'',sep='\n'),file=pkg$debfile('changelog.in'))
-}
-
-generate.rules <- function(pkg) {
-    cat(paste('#!/usr/bin/make -f'
-             ,paste('debRreposname :=',pkg$repo)
-             ,'include /usr/share/R/debian/r-cran.mk'
-             ,'',sep='\n')
-       ,file=pkg$debfile('rules'))
-    Sys.chmod(pkg$debfile('rules'),'0700')
-}
-
-generate.copyright <- function(pkg) {
-    # generate copyright file; we trust DESCRIPTION
-    writeLines(strwrap(
-        paste('This Debian package of the GNU R package',pkg$name
-             ,'was generated automatically using cran2deb by'
-             ,paste(maintainer,'.',sep='')
-             ,''
-             ,'The original GNU R package is Copyright (C) '
-             # TODO: copyright start date, true copyright date
-             ,format(Sys.time(),'%Y')
-             ,pkg$description[1,'Author']
-             ,'and possibly others.'
-             ,''
-             ,'The original GNU R package is maintained by'
-             ,pkg$description[1,'Maintainer'],'and was obtained from:'
-             ,''
-             ,pkg$repoURL
-             ,''
-             ,''
-             ,'The GNU R package DESCRIPTION offers a'
-             ,'Copyright licenses under the terms of the',pkg$license
-             ,'license.  On a Debian GNU/Linux system, common'
-             ,'licenses are included in the directory'
-             ,'/usr/share/common-licenses/.'
-             ,''
-             ,'The DESCRIPTION file for the original GNU R package '
-             ,'can be found in '
-             ,file.path('/usr/lib/R/site-library'
-                   ,pkg$debname
-                   ,'DESCRIPTION'
-                   )
-             ,sep='\n'), width=72), con=pkg$debfile('copyright.in'))
-}
-
-generate.control <- function(pkg) {
-    # construct control file
-    control = data.frame()
-    control[1,'Source'] = pkg$srcname
-    control[1,'Section'] = 'math'
-    control[1,'Priority'] = 'optional'
-    control[1,'Maintainer'] = maintainer
-    control[1,'Build-Depends'] = paste(pkg$depends$build,collapse=', ')
-    control[1,'Standards-Version'] = '3.8.0'
-
-    control[2,'Package'] = pkg$debname
-    control[2,'Architecture'] = 'all'
-    if (pkg$archdep) {
-        control[2,'Architecture'] = 'any'
-    }
-    control[2,'Depends'] = paste(pkg$depends$bin,collapse=', ')
-
-    # bundles provide virtual packages of their contents
-    if (pkg$is_bundle) {
-        control[2,'Provides'] = paste(
-                    lapply(r.bundle.contains(pkg$name)
-                          ,function(name) return(pkgname.as.debian(paste(name)
-                                                                  ,repopref=pkg$repo
-                                                                  ,binary=T)))
-                          ,collapse=', ')
-    }
-
-    # generate the description
-    descr = 'GNU R package "'
-    if ('Title' %in% colnames(pkg$description)) {
-        descr = paste(descr,pkg$description[1,'Title'],sep='')
-    } else {
-        descr = paste(descr,pkg$name,sep='')
-    }
-    if (pkg$is_bundle) {
-        long_descr <- pkg$description[1,'BundleDescription']
-    } else {
-        long_descr <- pkg$description[1,'Description']
-    }
-    # using \n\n.\n\n is not very nice, but is necessary to make sure
-    # the longer description does not begin on the synopsis line --- R's
-    # write.dcf does not appear to have a nicer way of doing this.
-    descr = paste(descr,'"\n\n', long_descr, sep='')
-    if ('URL' %in% colnames(pkg$description)) {
-        descr = paste(descr,'\n\nURL: ',pkg$description[1,'URL'],sep='')
-    }
-    control[2,'Description'] = descr
-
-    # Debian policy says 72 char width; indent minimally
-    write.dcf(control,file=pkg$debfile('control.in'),indent=1,width=72)
-    write.dcf(control,indent=1,width=72)
-}
-
-prepare.new.debian <- function(pkg,extra_deps) {
-    # generate Debian version and name
-    pkg$repo = repourl.as.debian(pkg$repoURL)
-    pkg$debversion = version.new(pkg$version)
-    if (!length(grep('^[A-Za-z0-9][A-Za-z0-9+.-]+$',pkg$name))) {
-        stop(paste('Cannot convert package name into a Debian name',pkg$name))
-    }
-    pkg$srcname = tolower(pkg$name)
-    pkg$debname = pkgname.as.debian(pkg$name,repo=pkg$repo)
-
-    if (!length(grep('\\.tar\\.gz',pkg$archive))) {
-        stop('archive is not tarball')
-    }
-
-    # re-pack into a Debian-named archive with a Debian-named directory.
-    debpath = file.path(dirname(pkg$archive)
-                   ,paste(pkg$srcname,'-'
-                         ,pkg$version
-                         ,sep=''))
-    file.rename(pkg$path, debpath)
-    pkg$path = debpath
-    debarchive = file.path(dirname(pkg$archive)
-                          ,paste(pkg$srcname,'_'
-                                ,pkg$version,'.orig.tar.gz'
-                                ,sep=''))
-    wd <- getwd()
-    setwd(dirname(pkg$path))
-    # remove them pesky +x files
-    system(paste('find',shQuote(basename(pkg$path))
-                ,'-type f -exec chmod -x {} \\;'))
-    # tar it all back up
-    system(paste('tar -czf',shQuote(debarchive),shQuote(basename(pkg$path))))
-    setwd(wd)
-    file.remove(pkg$archive)
-    pkg$archive = debarchive
-
-    # make the debian/ directory
-    debdir <- file.path(pkg$path,'debian')
-    pkg$debfile <- function(x) { file.path(debdir,x) }
-    unlink(debdir,recursive=T)
-    dir.create(debdir)
-
-    # see if this is an architecture-dependent package.
-    # heuristic: if /src/ exists in pkg$path, then this is an
-    #            architecture-dependent package.
-    # CRAN2DEB.pm is a bit fancier about this but ``Writing R extensions''
-    # says: ``The sources and headers for the compiled code are in src, plus
-    # optionally file Makevars or Makefile.'' It seems unlikely that
-    # architecture independent code would end up here.
-    if (pkg$is_bundle) {
-        # if it's a bundle, check each of the packages
-        pkg$archdep = F
-        for (pkgname in r.bundle.contains(pkg$name)) {
-            pkg$archdep = file.exists(file.path(pkg$path,pkgname,'src'))
-            if (pkg$archdep) {
-                break
-            }
-        }
-    } else {
-        pkg$archdep = file.exists(file.path(pkg$path,'src'))
-    }
-    pkg$arch <- 'all'
-    if (pkg$archdep) {
-        pkg$arch <- host.arch()
-    }
-
-    pkg$license <- accept.license(pkg)
-    pkg$depends <- get.dependencies(pkg,extra_deps)
-    generate.changelog(pkg)
-    generate.rules(pkg)
-    generate.copyright(pkg)
-    generate.control(pkg)
-
-    # TODO: debian/watch from pkg$repoURL
-
-    # convert text to utf8 (who knows what the original character set is --
-    # let's hope iconv DTRT).
-    for (file in c('control','changelog','copyright')) {
-        system(paste('iconv -o ',shQuote(pkg$debfile(file))
-                    ,' -t utf8 '
-                    ,shQuote(pkg$debfile(paste(file,'in',sep='.')))))
-        file.remove(pkg$debfile(paste(file,'in',sep='.')))
-    }
-    return(pkg)
-}
-
-build.debian <- function(pkg) {
-    wd <- getwd()
-    setwd(pkg$path)
-    message(paste('N: building Debian package'
-                 ,pkg$debname
-                 ,paste('(',pkg$debversion,')',sep='')
-                 ,'...'))
-    ret = system(paste('pdebuild --configfile',pbuilder_config))
-    setwd(wd)
-    if (ret != 0) {
-        stop('Failed to build package.')
-    }
-}
-
-changesfile <- function(srcname,version='*') {
-    return(file.path(pbuilder_results
-                    ,paste(srcname,'_',version,'_'
-                          ,host.arch(),'.changes',sep='')))
-}
-
-go <- function(name,extra_deps) {
-    dir <- setup()
-    pkg <- try((function() {
-        pkg <- prepare.new.debian(prepare.pkg(dir,name),extra_deps)
-        if (file.exists(changesfile(pkg$srcname,pkg$debversion))) {
-            message(paste('N: already built',pkg$srcname,'version',pkg$debversion))
-            return(pkg)
-        }
-
-        # delete the current archive (XXX: assumes mini-dinstall)
-        for (subdir in c('mini-dinstall','unstable')) {
-            path = file.path(dinstall_archive,subdir)
-            if (file.exists(path)) {
-                unlink(path,recursive=T)
-            }
-        }
-
-        # delete notes of upload
-        file.remove(Sys.glob(file.path(pbuilder_results,'*.upload')))
-
-        # make mini-dinstall generate the skeleton of the archive
-        ret = system(paste('umask 022;mini-dinstall --batch -c',dinstall_config))
-        if (ret != 0) {
-            stop('failed to create archive')
-        }
-
-        # pull in all the R dependencies
-        message(paste('N: dependencies:',paste(pkg$depends$r,collapse=', ')))
-        for (dep in pkg$depends$r) {
-            message(paste('N: uploading',dep))
-            ret = system(paste('umask 022;dput','-c',shQuote(dput_config),'local'
-                        ,changesfile(dep)))
-            if (ret != 0) {
-                stop('upload of dependency failed! maybe you did not build it first?')
-            }
-        }
-        build.debian(pkg)
-
-        # upload the package
-        ret = system(paste('umask 022;dput','-c',shQuote(dput_config),'local'
-                    ,changesfile(pkg$srcname,pkg$debversion)))
-        if (ret != 0) {
-            stop('upload failed!')
-        }
-
-        return(pkg)
-    })())
-    cleanup(dir)
-    if (inherits(pkg,'try-error')) {
-        stop(call.=F)
-    }
-    return(pkg)
-}
-
-if (exists('argv')) { # check for littler
-    argc <- length(argv)
-    extra_deps = list()
-    extra_deps$deb = c()
-    extra_deps$r = c()
-    opts = c('-D','-R')
-    for (i in 1:argc) {
-        if (!(argv[i] %in% opts)) {
-            if (argc >= i) {
-                argv <- argv[i:argc]
-            } else {
-                argv <- list()
-            }
-            argc = argc - i + 1
-            break
-        }
-        if (i == argc) {
-            message('E: missing argument')
-            q(save='no')
-        }
-        if (argv[i] == '-D') {
-            extra_deps$deb = c(extra_deps$deb,strsplit(chomp(argv[i+1]),',')[[1]])
-        }
-        if (argv[i] == '-R') {
-            extra_deps$r = c(extra_deps$r,strsplit(chomp(argv[i+1]),',')[[1]])
-            extra_deps$deb = c(extra_deps$deb,lapply(extra_deps$r,pkgname.as.debian))
-        }
-    }
-    if (argc == 0) {
-        message('E: usage: cran2deb [-D extra_dep1,extra_dep2,...] package package ...')
-        q(save='no')
-    }
-    build_order <- r.dependency.closure(c(extra_deps$r,argv))
-    message(paste('N: build order',paste(build_order,collapse=', ')))
-    for (pkg in build_order) {
-        go(pkg,extra_deps)
-    }
-}
diff --git a/pkg/trunk/cranpkgs b/pkg/trunk/cranpkgs
deleted file mode 100755
index 8fbe81f..0000000
--- a/pkg/trunk/cranpkgs
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env r
-
-root <- '/home/cb/work/gsoc/cran2deb'
-# we cache the list of available packages
-load(file.path(root,'var/cache/available.cache.Rd'))
-
-if (length(argv) == 0) {
-    writeLines(sample(dimnames(available)[[1]],800))
-    #writeLines(dimnames(available)[[1]])
-} else {
-    if (argv[1] == 'query') {
-        for (ctv in ctv.available) {
-            writeLines(ctv$name)
-        }
-        q(save='no')
-    }
-    # list of task lists
-    for (ctv in ctv.available) {
-        if (ctv$name %in% argv) {
-            writeLines(ctv$packagelist$name)
-        }
-    }
-}
diff --git a/pkg/trunk/diagnose b/pkg/trunk/diagnose
deleted file mode 100755
index 5f303e7..0000000
--- a/pkg/trunk/diagnose
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/rc
-
-#success=`{ls var/results/*.deb | wc -l}
-#echo $success successful packages
-#total=$success
-total=0
-
-fn count_dup { sort | uniq -c | sort -n}# | awk '$1 > 1{print}' }
-fn collapse { a=`{echo $^* | sed -e 's/ | /|/g'}; echo $^a }
-echo 'warnings:'
-{for (x in (warn/* /dev/null)) cut -d: -f3- <$x | sort -u} | awk '{print $1}' | count_dup
-echo
-
-faildep=('^Error: package ''.*'' could not be loaded'
-     '|' '^ERROR: lazy loading failed for package ''.*'''
-     '|' '^[[:space:]]*package .* is not available'
-     '|' 'there is no package called ''.*''')
-faildeb='Unsupported SystemRequirements:'
-faillic=('No acceptable license: ')
-failspc=': No space left on device'
-failhdr='error: .*\.hp?p?: No such file or directory'
-faildep=`{collapse $faildep}
-faildep=$^faildep
-faillic=`{collapse $faillic}
-faillic=$^faillic
-other=''
-
-nfaildep=`{grep -El $faildep fail/* /dev/null | wc -l}
-echo $nfaildep failed R dependencies.
-grep -Eh $faildep fail/* | count_dup
-other=$faildep
-#total=$total+$nfaildep
-echo
-
-nfaillic=`{grep -El $faillic `{grep -EL $other fail/*} /dev/null | wc -l}
-echo $nfaillic failed licenses.
-grep -Eh $faillic `{grep -EL $other fail/*} | count_dup
-other=$other^'|'^$faillic
-total=$total+$nfaillic
-echo
-
-nfailspc=`{grep -El $failspc `{grep -EL $other fail/*} /dev/null | wc -l}
-echo $nfailspc out of space
-other=$other^'|'^$failspc
-total=$total+$nfailspc
-echo
-
-nfailhdr=`{grep -El $failhdr `{grep -EL $other fail/*} /dev/null | wc -l}
-echo $nfailhdr missing C header
-grep -Eh $failhdr `{grep -EL $other fail/* /dev/null} | count_dup
-other=$other^'|'^$failhdr
-total=$total+$nfailhdr
-echo
-
-nfaildeb=`{grep -El $faildeb `{grep -EL $other fail/*} /dev/null | wc -l}
-echo $nfaildeb system requirement failures.
-grep -Eh $faildeb `{grep -EL $other fail/* /dev/null} | count_dup
-other=$other^'|'^$faildeb
-total=$total+$nfaildeb
-echo
-
-nfailother=`{hoc -e `{grep -EL $other fail/* /dev/null | wc -l}^-1}
-echo $nfailother other failures.
-
-#total=`{hoc -e $total}
-#succrate=`{hoc -e $success/'('$total')*100'}
-#echo $succrate% success rate '('$total' total)'
-#total=`{hoc -e $total-$nfaillic-$nfailspc-$nfailhdr}
-#succrate=`{hoc -e $success/'('$total')*100'}
-#echo $succrate% success rate without licensing, space and Debian deps issues '('$total' total)'
-grep -EL $other fail/* /dev/null | xargs tail -n 20
-
diff --git a/pkg/trunk/diagnose_ctv b/pkg/trunk/diagnose_ctv
deleted file mode 100755
index 665ff8c..0000000
--- a/pkg/trunk/diagnose_ctv
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/usr/bin/env rc
-{for (x in ctv/*) {echo;echo;echo $x: ; cd $x && ../../diagnose && cd ../..}} >ctv.results
diff --git a/pkg/trunk/etc/dput.cf.in b/pkg/trunk/etc/dput.cf.in
deleted file mode 100644
index 7d6b8d2..0000000
--- a/pkg/trunk/etc/dput.cf.in
+++ /dev/null
@@ -1,8 +0,0 @@
-[local]
-method = local
-incoming = @ROOT@/var/archive/mini-dinstall/incoming
-allow_non-us_software = 1
-run_dinstall = 0
-run_lintian = 1
-post_upload_command = /usr/bin/mini-dinstall --batch -c @ROOT@/etc/mini-dinstall.conf
-allow_unsigned_uploads = 1
diff --git a/pkg/trunk/etc/hook/B90lintian b/pkg/trunk/etc/hook/B90lintian
deleted file mode 100755
index 57fcfc4..0000000
--- a/pkg/trunk/etc/hook/B90lintian
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-# example file to be used with --hookdir
-#
-# run lintian on generated deb files
-apt-get install -y --force-yes lintian
-lintian /tmp/buildd/*.deb
diff --git a/pkg/trunk/etc/hook/B91dpkg-i b/pkg/trunk/etc/hook/B91dpkg-i
deleted file mode 100755
index ee031bb..0000000
--- a/pkg/trunk/etc/hook/B91dpkg-i
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-# example file to be used with --hookdir
-#
-# try to install the resulting debs.
-
-echo "Trying to install resulting packages and test upgrades"
-set -ex
-
-
-PKGNAMES=$(cd /tmp/buildd && ls -1 *.deb | sed 's/_.*$//' )
-
-# install-remove check
-dpkg -i /tmp/buildd/*.deb
-dpkg --remove $PKGNAMES
-
-# install-purge check
-dpkg -i /tmp/buildd/*.deb
-dpkg --purge $PKGNAMES
-
-# upgrade-remove check
-apt-get install -y --force-yes  $PKGNAMES || true
-dpkg -i /tmp/buildd/*.deb
-dpkg --remove $PKGNAMES
-
-# upgrade-purge check
-apt-get install -y --force-yes $PKGNAMES || true
-dpkg -i /tmp/buildd/*.deb
-dpkg --purge $PKGNAMES
diff --git a/pkg/trunk/etc/hook/B92test-pkg b/pkg/trunk/etc/hook/B92test-pkg
deleted file mode 100755
index 7372ca0..0000000
--- a/pkg/trunk/etc/hook/B92test-pkg
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/bin/bash
-# example file to be used with --hookdir
-#
-# run tests. Current directory is top of source-code.
-#
-# 2005, 2007 Junichi Uekawa
-# 
-set -e 
-
-echo "Installing the prerequisites"
-for PKG in $(ls /tmp/buildd/*.deb | sed -e's,.*/,,;s,_.*,,' ); do
-    apt-get install -y --force-yes "$PKG" || true 
-    apt-get remove -y "$PKG" || true 
-done
-# ignore the failures since they are not the prime interest
-
-dpkg -i /tmp/buildd/*.deb
-
-if chmod a+x /tmp/buildd/*/debian/pbuilder-test/*; then
-    :
-else
-    echo "W: no pbuilder-test script found, skipping"
-    exit 0
-fi
-
-SUCCESS=0
-COUNT=0
-unset FAIL || true
-NOFAIL=1
-
-# The current directory is the top of the source-tree.
-cd /tmp/buildd/*/debian/..
-
-for SCRIPT in $(run-parts --test /tmp/buildd/*/debian/pbuilder-test) ; do
-    echo "--- BEGIN test: ${SCRIPT##*/}"
-    if "${SCRIPT}"; then
-    	echo SUCCESS
-	((SUCCESS=SUCCESS+1))
-    else
-    	echo FAIL
-	FAIL[${#FAIL[@]}]="${SCRIPT##*/}"
-	NOFAIL=0
-    fi
-    echo "--- END test: ${SCRIPT##*/}"
-    ((COUNT=COUNT+1))
-done
-
-echo "Summary:"
-echo "=== $SUCCESS out of $COUNT tests passed"
-echo "${FAIL[@]/#/ failed }"
-echo "-- end of testsuite."
-
diff --git a/pkg/trunk/etc/hook/D70aptupdate b/pkg/trunk/etc/hook/D70aptupdate
deleted file mode 100755
index 4d42b3d..0000000
--- a/pkg/trunk/etc/hook/D70aptupdate
+++ /dev/null
@@ -1 +0,0 @@
-/usr/bin/apt-get update
diff --git a/pkg/trunk/etc/mini-dinstall.conf.in b/pkg/trunk/etc/mini-dinstall.conf.in
deleted file mode 100644
index b75f1d7..0000000
--- a/pkg/trunk/etc/mini-dinstall.conf.in
+++ /dev/null
@@ -1,12 +0,0 @@
-[DEFAULT]
-architectures = all, i386
-use_dnotify = 0
-verify_sigs = 0
-mail_on_success = 0
-archive_style = simple-subdir
-mail_log_level = NONE
-archivedir = @ROOT@/var/archive
-logfile = @ROOT@/var/mini-dinstall.log
-
-[unstable]
-
diff --git a/pkg/trunk/etc/pbuilderrc.in b/pkg/trunk/etc/pbuilderrc.in
deleted file mode 100644
index 1f99b77..0000000
--- a/pkg/trunk/etc/pbuilderrc.in
+++ /dev/null
@@ -1,8 +0,0 @@
-HOOKDIR=@ROOT@/etc/hook
-BUILDRESULT=@ROOT@/var/results
-EXTRAPACKAGES='debhelper r-base-dev cdbs r-base-core lintian xauth xfont-base xvfb'
-DISTRIBUTION=lenny
-OTHERMIRROR='deb http://localhost/users/cb/cran2deb/ unstable/$(ARCH)/ | deb http://localhost/users/cb/cran2deb/ unstable/all/'
-MIRRORSITE='http://ftp.debian.org/debian/'
-APTCACHE=''
-PBUILDERSATISFYDEPENDSCMD='/usr/lib/pbuilder/pbuilder-satisfydepends-classic'
diff --git a/pkg/trunk/exec/build_ctv b/pkg/trunk/exec/build_ctv
new file mode 100755
index 0000000..754dd58
--- /dev/null
+++ b/pkg/trunk/exec/build_ctv
@@ -0,0 +1,11 @@
+#!/usr/bin/env rc
+
+for (ctv in `{./cranpkgs query}) {
+    echo task view $ctv...
+    if (![ -e ctv/$ctv ]) {
+        ./build_some $ctv
+        mkdir -p ctv/$ctv
+        mv warn fail ctv/$ctv
+    }
+}
+
diff --git a/pkg/trunk/exec/build_some b/pkg/trunk/exec/build_some
new file mode 100755
index 0000000..dd12c2d
--- /dev/null
+++ b/pkg/trunk/exec/build_some
@@ -0,0 +1,20 @@
+#!/usr/bin/rc
+
+mkdir -p warn fail
+./cranpkgs $* >all_pkgs
+for (pkg in `{cat all_pkgs}) {
+    if (~ $pkg *..* */*) {
+        echo bad name $pkg >>fail/ERROR
+    } else {
+        echo .. package $pkg
+        fail=0
+        ./cran2deb $pkg >fail/$pkg >[2=1] || fail=1
+        if (~ $fail 0) {
+            grep '^[WE]:' fail/$pkg >warn/$pkg
+            if (~ `{stat -c '%s' warn/$pkg} 0) {
+                rm -f warn/$pkg
+            }
+            rm -f fail/$pkg
+        }
+    }
+}
diff --git a/pkg/trunk/exec/copy_find b/pkg/trunk/exec/copy_find
new file mode 100755
index 0000000..fe3d619
--- /dev/null
+++ b/pkg/trunk/exec/copy_find
@@ -0,0 +1,30 @@
+#!/usr/bin/rc
+kwords='copyright|warranty|redistribution|modification|patent|trademark|licen[cs]e|permission'
+nl=`` () {printf '\n'}
+ifs=$nl {
+    files=`{find $1 ! -path '*debian*' -type f}
+    lines=()
+    for (file in $files) {
+        notices=`{grep -H '(C)' $file}
+        notices=($notices `{grep -HEi $kwords $file})
+        lines=($lines `{{for (notice in $notices) echo $notice} | sort -u})
+    }
+    # let's hope no file has a : in it
+    ifs=() { seen_files=`{{for (line in $lines) echo $line} | cut -d: -f1} }
+    missing_copyright=()
+    for (file in $files) {
+        if (echo -n $seen_files | grep -q '^'^$file^'$') {
+        } else {
+            missing_copyright=($missing_copyright $file)
+        }
+    }
+    echo 'Suspect copyright notices:'
+    for (line in $lines) echo '    '$line
+    echo 'Files without *suspect* copyright notices:'
+    for (missing in $missing_copyright) {
+        echo '    '$missing
+        echo '       type: '`{file $missing}
+        echo '      chars: '`{wc -c $missing | awk '{print $1}'}
+        echo '      lines: '`{wc -l $missing | awk '{print $1}'}
+    }
+}
diff --git a/pkg/trunk/exec/cran2deb b/pkg/trunk/exec/cran2deb
new file mode 100755
index 0000000..fc6c45c
--- /dev/null
+++ b/pkg/trunk/exec/cran2deb
@@ -0,0 +1,94 @@
+#!/usr/bin/env r
+library(cran2deb)
+go <- function(name,extra_deps) {
+    dir <- setup()
+    pkg <- try((function() {
+        pkg <- prepare.new.debian(prepare.pkg(dir,name),extra_deps)
+        if (file.exists(changesfile(pkg$srcname,pkg$debversion))) {
+            message(paste('N: already built',pkg$srcname,'version',pkg$debversion))
+            return(pkg)
+        }
+
+        # delete the current archive (XXX: assumes mini-dinstall)
+        for (subdir in c('mini-dinstall','unstable')) {
+            path = file.path(dinstall_archive,subdir)
+            if (file.exists(path)) {
+                unlink(path,recursive=T)
+            }
+        }
+
+        # delete notes of upload
+        file.remove(Sys.glob(file.path(pbuilder_results,'*.upload')))
+
+        # make mini-dinstall generate the skeleton of the archive
+        ret = system(paste('umask 022;mini-dinstall --batch -c',dinstall_config))
+        if (ret != 0) {
+            stop('failed to create archive')
+        }
+
+        # pull in all the R dependencies
+        message(paste('N: dependencies:',paste(pkg$depends$r,collapse=', ')))
+        for (dep in pkg$depends$r) {
+            message(paste('N: uploading',dep))
+            ret = system(paste('umask 022;dput','-c',shQuote(dput_config),'local'
+                        ,changesfile(dep)))
+            if (ret != 0) {
+                stop('upload of dependency failed! maybe you did not build it first?')
+            }
+        }
+        build.debian(pkg)
+
+        # upload the package
+        ret = system(paste('umask 022;dput','-c',shQuote(dput_config),'local'
+                    ,changesfile(pkg$srcname,pkg$debversion)))
+        if (ret != 0) {
+            stop('upload failed!')
+        }
+
+        return(pkg)
+    })())
+    cleanup(dir)
+    if (inherits(pkg,'try-error')) {
+        stop(call.=F)
+    }
+    return(pkg)
+}
+
+if (exists('argv')) { # check for littler
+    argc <- length(argv)
+    extra_deps = list()
+    extra_deps$deb = c()
+    extra_deps$r = c()
+    opts = c('-D','-R')
+    for (i in 1:argc) {
+        if (!(argv[i] %in% opts)) {
+            if (argc >= i) {
+                argv <- argv[i:argc]
+            } else {
+                argv <- list()
+            }
+            argc = argc - i + 1
+            break
+        }
+        if (i == argc) {
+            message('E: missing argument')
+            q(save='no')
+        }
+        if (argv[i] == '-D') {
+            extra_deps$deb = c(extra_deps$deb,strsplit(chomp(argv[i+1]),',')[[1]])
+        }
+        if (argv[i] == '-R') {
+            extra_deps$r = c(extra_deps$r,strsplit(chomp(argv[i+1]),',')[[1]])
+            extra_deps$deb = c(extra_deps$deb,lapply(extra_deps$r,pkgname.as.debian))
+        }
+    }
+    if (argc == 0) {
+        message('E: usage: cran2deb [-D extra_dep1,extra_dep2,...] package package ...')
+        q(save='no')
+    }
+    build_order <- r.dependency.closure(c(extra_deps$r,argv))
+    message(paste('N: build order',paste(build_order,collapse=', ')))
+    for (pkg in build_order) {
+        go(pkg,extra_deps)
+    }
+}
diff --git a/pkg/trunk/exec/cranpkgs b/pkg/trunk/exec/cranpkgs
new file mode 100755
index 0000000..ba9e727
--- /dev/null
+++ b/pkg/trunk/exec/cranpkgs
@@ -0,0 +1,21 @@
+#!/usr/bin/env r
+
+library(cran2deb)
+
+if (length(argv) == 0) {
+    writeLines(sample(dimnames(available)[[1]],800))
+    #writeLines(dimnames(available)[[1]])
+} else {
+    if (argv[1] == 'query') {
+        for (ctv in ctv.available) {
+            writeLines(ctv$name)
+        }
+        q(save='no')
+    }
+    # list of task lists
+    for (ctv in ctv.available) {
+        if (ctv$name %in% argv) {
+            writeLines(ctv$packagelist$name)
+        }
+    }
+}
diff --git a/pkg/trunk/exec/diagnose b/pkg/trunk/exec/diagnose
new file mode 100755
index 0000000..5f303e7
--- /dev/null
+++ b/pkg/trunk/exec/diagnose
@@ -0,0 +1,72 @@
+#!/usr/bin/rc
+
+#success=`{ls var/results/*.deb | wc -l}
+#echo $success successful packages
+#total=$success
+total=0
+
+fn count_dup { sort | uniq -c | sort -n}# | awk '$1 > 1{print}' }
+fn collapse { a=`{echo $^* | sed -e 's/ | /|/g'}; echo $^a }
+echo 'warnings:'
+{for (x in (warn/* /dev/null)) cut -d: -f3- <$x | sort -u} | awk '{print $1}' | count_dup
+echo
+
+faildep=('^Error: package ''.*'' could not be loaded'
+     '|' '^ERROR: lazy loading failed for package ''.*'''
+     '|' '^[[:space:]]*package .* is not available'
+     '|' 'there is no package called ''.*''')
+faildeb='Unsupported SystemRequirements:'
+faillic=('No acceptable license: ')
+failspc=': No space left on device'
+failhdr='error: .*\.hp?p?: No such file or directory'
+faildep=`{collapse $faildep}
+faildep=$^faildep
+faillic=`{collapse $faillic}
+faillic=$^faillic
+other=''
+
+nfaildep=`{grep -El $faildep fail/* /dev/null | wc -l}
+echo $nfaildep failed R dependencies.
+grep -Eh $faildep fail/* | count_dup
+other=$faildep
+#total=$total+$nfaildep
+echo
+
+nfaillic=`{grep -El $faillic `{grep -EL $other fail/*} /dev/null | wc -l}
+echo $nfaillic failed licenses.
+grep -Eh $faillic `{grep -EL $other fail/*} | count_dup
+other=$other^'|'^$faillic
+total=$total+$nfaillic
+echo
+
+nfailspc=`{grep -El $failspc `{grep -EL $other fail/*} /dev/null | wc -l}
+echo $nfailspc out of space
+other=$other^'|'^$failspc
+total=$total+$nfailspc
+echo
+
+nfailhdr=`{grep -El $failhdr `{grep -EL $other fail/*} /dev/null | wc -l}
+echo $nfailhdr missing C header
+grep -Eh $failhdr `{grep -EL $other fail/* /dev/null} | count_dup
+other=$other^'|'^$failhdr
+total=$total+$nfailhdr
+echo
+
+nfaildeb=`{grep -El $faildeb `{grep -EL $other fail/*} /dev/null | wc -l}
+echo $nfaildeb system requirement failures.
+grep -Eh $faildeb `{grep -EL $other fail/* /dev/null} | count_dup
+other=$other^'|'^$faildeb
+total=$total+$nfaildeb
+echo
+
+nfailother=`{hoc -e `{grep -EL $other fail/* /dev/null | wc -l}^-1}
+echo $nfailother other failures.
+
+#total=`{hoc -e $total}
+#succrate=`{hoc -e $success/'('$total')*100'}
+#echo $succrate% success rate '('$total' total)'
+#total=`{hoc -e $total-$nfaillic-$nfailspc-$nfailhdr}
+#succrate=`{hoc -e $success/'('$total')*100'}
+#echo $succrate% success rate without licensing, space and Debian deps issues '('$total' total)'
+grep -EL $other fail/* /dev/null | xargs tail -n 20
+
diff --git a/pkg/trunk/exec/diagnose_ctv b/pkg/trunk/exec/diagnose_ctv
new file mode 100755
index 0000000..665ff8c
--- /dev/null
+++ b/pkg/trunk/exec/diagnose_ctv
@@ -0,0 +1,2 @@
+#!/usr/bin/env rc
+{for (x in ctv/*) {echo;echo;echo $x: ; cd $x && ../../diagnose && cd ../..}} >ctv.results
diff --git a/pkg/trunk/exec/setup b/pkg/trunk/exec/setup
new file mode 100755
index 0000000..011bd12
--- /dev/null
+++ b/pkg/trunk/exec/setup
@@ -0,0 +1,19 @@
+#!/usr/bin/rc
+umask 022
+root=`{r -e 'library(cran2deb);cat(system.file('''',package=''cran2deb''),file=stdout())'}
+for (x in `{find etc -type f -name '*.in'}) {
+    y=`{echo $x | sed -e 's,.in$,,'}
+    sed -e 's:@ROOT@:'^$root^':g' <$x >$y
+}
+mkdir -p var/results
+if ([ ! -e var/archive ]) {
+    # I symbolically link this into /var/www/
+    mkdir var/archive
+}
+mini-dinstall --batch -c $root/etc/mini-dinstall.conf || exit 1
+mode=create
+if ([ -e /var/cache/pbuilder/base.tgz ]) {
+    mode=update
+}
+sudo pbuilder $mode --override-config --configfile $root/etc/pbuilderrc
+./update_available
diff --git a/pkg/trunk/exec/update_available b/pkg/trunk/exec/update_available
new file mode 100755
index 0000000..11df8b0
--- /dev/null
+++ b/pkg/trunk/exec/update_available
@@ -0,0 +1,11 @@
+#!/usr/bin/env r
+#mirror <- 'http://cran.uk.r-project.org/'
+mirror <- 'http://cran.r-project.org/'
+message('updating list of available R packages...')
+available <- available.packages(contrib.url(mirror))
+available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
+message('updating list of available R task views...')
+library(ctv)
+ctv.available <- available.views(repo=mirror)
+library(cran2deb)
+save(available, ctv.available, file=system.file('R/sysdata.rda',package='cran2deb'),eval.promises=T)
diff --git a/pkg/trunk/inst/etc/dput.cf.in b/pkg/trunk/inst/etc/dput.cf.in
new file mode 100644
index 0000000..7d6b8d2
--- /dev/null
+++ b/pkg/trunk/inst/etc/dput.cf.in
@@ -0,0 +1,8 @@
+[local]
+method = local
+incoming = @ROOT@/var/archive/mini-dinstall/incoming
+allow_non-us_software = 1
+run_dinstall = 0
+run_lintian = 1
+post_upload_command = /usr/bin/mini-dinstall --batch -c @ROOT@/etc/mini-dinstall.conf
+allow_unsigned_uploads = 1
diff --git a/pkg/trunk/inst/etc/hook/B90lintian b/pkg/trunk/inst/etc/hook/B90lintian
new file mode 100755
index 0000000..57fcfc4
--- /dev/null
+++ b/pkg/trunk/inst/etc/hook/B90lintian
@@ -0,0 +1,6 @@
+#!/bin/bash
+# example file to be used with --hookdir
+#
+# run lintian on generated deb files
+apt-get install -y --force-yes lintian
+lintian /tmp/buildd/*.deb
diff --git a/pkg/trunk/inst/etc/hook/B91dpkg-i b/pkg/trunk/inst/etc/hook/B91dpkg-i
new file mode 100755
index 0000000..ee031bb
--- /dev/null
+++ b/pkg/trunk/inst/etc/hook/B91dpkg-i
@@ -0,0 +1,28 @@
+#!/bin/bash
+# example file to be used with --hookdir
+#
+# try to install the resulting debs.
+
+echo "Trying to install resulting packages and test upgrades"
+set -ex
+
+
+PKGNAMES=$(cd /tmp/buildd && ls -1 *.deb | sed 's/_.*$//' )
+
+# install-remove check
+dpkg -i /tmp/buildd/*.deb
+dpkg --remove $PKGNAMES
+
+# install-purge check
+dpkg -i /tmp/buildd/*.deb
+dpkg --purge $PKGNAMES
+
+# upgrade-remove check
+apt-get install -y --force-yes  $PKGNAMES || true
+dpkg -i /tmp/buildd/*.deb
+dpkg --remove $PKGNAMES
+
+# upgrade-purge check
+apt-get install -y --force-yes $PKGNAMES || true
+dpkg -i /tmp/buildd/*.deb
+dpkg --purge $PKGNAMES
diff --git a/pkg/trunk/inst/etc/hook/B92test-pkg b/pkg/trunk/inst/etc/hook/B92test-pkg
new file mode 100755
index 0000000..7372ca0
--- /dev/null
+++ b/pkg/trunk/inst/etc/hook/B92test-pkg
@@ -0,0 +1,52 @@
+#!/bin/bash
+# example file to be used with --hookdir
+#
+# run tests. Current directory is top of source-code.
+#
+# 2005, 2007 Junichi Uekawa
+# 
+set -e 
+
+echo "Installing the prerequisites"
+for PKG in $(ls /tmp/buildd/*.deb | sed -e's,.*/,,;s,_.*,,' ); do
+    apt-get install -y --force-yes "$PKG" || true 
+    apt-get remove -y "$PKG" || true 
+done
+# ignore the failures since they are not the prime interest
+
+dpkg -i /tmp/buildd/*.deb
+
+if chmod a+x /tmp/buildd/*/debian/pbuilder-test/*; then
+    :
+else
+    echo "W: no pbuilder-test script found, skipping"
+    exit 0
+fi
+
+SUCCESS=0
+COUNT=0
+unset FAIL || true
+NOFAIL=1
+
+# The current directory is the top of the source-tree.
+cd /tmp/buildd/*/debian/..
+
+for SCRIPT in $(run-parts --test /tmp/buildd/*/debian/pbuilder-test) ; do
+    echo "--- BEGIN test: ${SCRIPT##*/}"
+    if "${SCRIPT}"; then
+    	echo SUCCESS
+	((SUCCESS=SUCCESS+1))
+    else
+    	echo FAIL
+	FAIL[${#FAIL[@]}]="${SCRIPT##*/}"
+	NOFAIL=0
+    fi
+    echo "--- END test: ${SCRIPT##*/}"
+    ((COUNT=COUNT+1))
+done
+
+echo "Summary:"
+echo "=== $SUCCESS out of $COUNT tests passed"
+echo "${FAIL[@]/#/ failed }"
+echo "-- end of testsuite."
+
diff --git a/pkg/trunk/inst/etc/hook/D70aptupdate b/pkg/trunk/inst/etc/hook/D70aptupdate
new file mode 100755
index 0000000..4d42b3d
--- /dev/null
+++ b/pkg/trunk/inst/etc/hook/D70aptupdate
@@ -0,0 +1 @@
+/usr/bin/apt-get update
diff --git a/pkg/trunk/inst/etc/mini-dinstall.conf.in b/pkg/trunk/inst/etc/mini-dinstall.conf.in
new file mode 100644
index 0000000..b75f1d7
--- /dev/null
+++ b/pkg/trunk/inst/etc/mini-dinstall.conf.in
@@ -0,0 +1,12 @@
+[DEFAULT]
+architectures = all, i386
+use_dnotify = 0
+verify_sigs = 0
+mail_on_success = 0
+archive_style = simple-subdir
+mail_log_level = NONE
+archivedir = @ROOT@/var/archive
+logfile = @ROOT@/var/mini-dinstall.log
+
+[unstable]
+
diff --git a/pkg/trunk/inst/etc/pbuilderrc.in b/pkg/trunk/inst/etc/pbuilderrc.in
new file mode 100644
index 0000000..1f99b77
--- /dev/null
+++ b/pkg/trunk/inst/etc/pbuilderrc.in
@@ -0,0 +1,8 @@
+HOOKDIR=@ROOT@/etc/hook
+BUILDRESULT=@ROOT@/var/results
+EXTRAPACKAGES='debhelper r-base-dev cdbs r-base-core lintian xauth xfont-base xvfb'
+DISTRIBUTION=lenny
+OTHERMIRROR='deb http://localhost/users/cb/cran2deb/ unstable/$(ARCH)/ | deb http://localhost/users/cb/cran2deb/ unstable/all/'
+MIRRORSITE='http://ftp.debian.org/debian/'
+APTCACHE=''
+PBUILDERSATISFYDEPENDSCMD='/usr/lib/pbuilder/pbuilder-satisfydepends-classic'
diff --git a/pkg/trunk/setup b/pkg/trunk/setup
deleted file mode 100755
index 03e441e..0000000
--- a/pkg/trunk/setup
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/rc
-umask 022
-root=`pwd
-for (x in `{find etc -type f -name '*.in'}) {
-    y=`{echo $x | sed -e 's,.in$,,'}
-    sed -e 's:@ROOT@:'^$root^':g' <$x >$y
-}
-mkdir -p var/results
-if ([ ! -e var/archive ]) {
-    # I symbolically link this into /var/www/
-    mkdir var/archive
-}
-mini-dinstall --batch -c $root/etc/mini-dinstall.conf || exit 1
-mode=create
-if ([ -e /var/cache/pbuilder/base.tgz ]) {
-    mode=update
-}
-sudo pbuilder $mode --override-config --configfile $root/etc/pbuilderrc
-./update_available
diff --git a/pkg/trunk/update_available b/pkg/trunk/update_available
deleted file mode 100755
index cc99376..0000000
--- a/pkg/trunk/update_available
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env r
-#mirror <- 'http://cran.uk.r-project.org/'
-mirror <- 'http://cran.r-project.org/'
-message('updating list of available R packages...')
-available <- available.packages(contrib.url(mirror))
-available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
-message('updating list of available R task views...')
-library(ctv)
-ctv.available <- available.views(repo=mirror)
-save(available, ctv.available, file='var/cache/available.cache.Rd',eval.promises=T)