cran2deb: bundles considered functional but need more testing.

Add a few comments describing some of the functions and what they do.

Make dependencies on bundles work by translating dependencies on
packages up into their potential bundle where no individual package is
available.

Add the repository name to debian/rules. This should allow bioc packages
to be build and included via cross-repo dependencies.

Bundle packages have Provides: fields --- these aren't actually used but
do no harm.

Bundle packages have a Description: field of just the BundleDescription
--- otherwise it may become too long.

Look in the package subdirectories of bundles for 'src' to determine if
a package is architecture independent or not.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@37 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

diff --git a/pkg/trunk/cran2deb b/pkg/trunk/cran2deb
index b995ca19444556a29b94fb459a97bc8961433dca..801cba698c95857bf7adb967a7bc1f3e3410b769 100755 (executable)
--- a/pkg/trunk/cran2deb
+++ b/pkg/trunk/cran2deb
@@ -66,6 +66,7 @@ version.upstream <- function(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
@@ -90,6 +91,7 @@ base_pkgs=c('base',   'datasets','grDevices','graphics','grid', 'methods'
 # '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')
     }
@@ -100,6 +102,7 @@ repourl.as.debian <- function(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'
     }
@@ -130,29 +133,38 @@ pkgname.as.debian <- function(name,repopref=NULL,version=NULL,binary=T) {
 }
 
 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) {
-    bundles <- available[!is.na(available[, "Bundle"]), "Contains"]
+    # returns the bundle containing pkgname or NA
+    bundles <- names(available[!is.na(available[, 'Bundle']), 'Contains'])
     # use the first bundle
-    for (bundle in names(bundles)) {
-        content <- strsplit(bundles[[bundle]],'[[:space:]]+')[[1]]
-        if (pkgname %in% content) {
+    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
 
@@ -207,6 +219,8 @@ 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
@@ -218,8 +232,8 @@ is_acceptable_license <- function(license) {
         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.GNU.ORG/[A-Z/._-]*','',license)
+    license = gsub('HTTP://WWW.X.ORG/[A-Z/._-]*','',license)
     # remove all punctuation
     license = gsub('[[:punct:]]+','',license)
     # remove any extra space introduced
@@ -252,14 +266,17 @@ is_acceptable_license <- function(license) {
 }
 
 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.dependencies.of <- function(name=NULL,description=NULL) {
+    # find the immediate dependencies of an R package
     if (!is.null(name) && (name == 'R' || name %in% base_pkgs)) {
         return(data.frame())
     }
@@ -307,6 +324,12 @@ r.dependencies.of <- function(name=NULL,description=NULL) {
             }
             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
+                }
+            }
             deps <- rbind(deps,data.frame(list(name=dep
                                               ,version=version)))
         }
@@ -315,6 +338,7 @@ r.dependencies.of <- function(name=NULL,description=NULL) {
 }
 
 r.dependency.closure <- function(fringe) {
+    # find the transitive closure of the dependencies of some R packages
     closure <- list()
     if (is.data.frame(fringe)) {
         fringe <- levels(fringe$name)
@@ -413,6 +437,7 @@ generate.changelog <- function(pkg) {
 
 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'))
@@ -461,7 +486,7 @@ generate.control <- function(pkg) {
     control[1,'Priority'] = 'optional'
     control[1,'Maintainer'] = maintainer
     control[1,'Build-Depends'] = paste(pkg$depends$build,collapse=', ')
-    control[1,'Standards-Version'] = '3.7.3.0'
+    control[1,'Standards-Version'] = '3.8.0'
 
     control[2,'Package'] = pkg$debname
     control[2,'Architecture'] = 'all'
@@ -469,31 +494,44 @@ generate.control <- function(pkg) {
         control[2,'Architecture'] = 'any'
     }
     control[2,'Depends'] = paste(pkg$depends$bin,collapse=', ')
+
+    # bundles provide virtual packages of their contents
+    if (pkg$is_bundle) {
+        control[2,'Provides'] = paste(
+                    lapply(r.bundle.contains(pkg$name)
+                          ,function(name) return(pkgname.as.debian(name
+                                                                  ,repopref=pkg$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', pkg$description[1,'Description'], sep='')
+    descr = paste(descr,'"\n\n', long_descr, sep='')
     if ('URL' %in% colnames(pkg$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) {
-    # XXX: TODO: bundles do not work.
-    if ('Bundle' %in% names(pkg$description[1,])) {
-        stop('E: TODO: bundles')
-    }
-
     # generate Debian version and name
     pkg$repo = repourl.as.debian(pkg$repoURL)
     pkg$debversion = version.new(pkg$version)
@@ -542,7 +580,18 @@ prepare.new.debian <- function(pkg) {
     # says: ``The sources and headers for the compiled code are in src, plus
     # optionally file Makevars or Makefile.'' It seems unlikely that
     # architecture independent code would end up here.
-    pkg$archdep = file.exists(file.path(pkg$path,'src'))
+    if (pkg$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()