To install:
-$ cd ..
-$ R CMD INSTALL cran2deb
+Please install a series of packages that you will need to
+run cran2deb successfully:
-copy cran2deb/exec/cran2deb into somewhere in your executable path (e.g.,
-/usr/local/bin, $home/bin)
+ sudo apt-get install pbuilder python-gpgme gnupg-agent
+You may install cran2deb manually
+
+ $ cd ..
+ $ R CMD INSTALL cran2deb
+
+ copy cran2deb/exec/cran2deb into somewhere in your executable path (e.g.,
+ /usr/local/bin, $home/bin)
+
+or prepare a Debian package for it
+
+ fakeroot debian/rules binary
+ sudo dpkg -i ../r-*cran2deb*.deb
To configure:
Let ROOT be the value returned by running: cran2deb root
Let SYS be the system you wish to build for (e.g., debian-amd64)
+Create user "c2d" who shall have write permissions to the archive.
2. create /etc/cran2deb
a. copy ROOT/etc/* into /etc/cran2deb/
$ ln -s /var/www/cran2deb/ /etc/cran2deb/archive
$ mkdir /var/www/cran2deb/SYS
- d. modify OTHERMIRROR of /etc/cran2deb/sys/SYS/pbuilderrc.in to point to your webserver
+ d. modify OTHERMIRROR of /etc/cran2deb/sys/SYS/pbuilderrc.in to point to your webserver.
+ As long as the packages on debian.cran.r-project.org are not signed with a
+ current key, just rebuild also the architecture-dependent packages or find
+ a way for pbuilder to ignore the failing gpg signature check.
+
+ Example:
+ OTHERMIRROR='deb http://master.dermacloud.uni-luebeck.de/cran2deb/rep testing main'
+
+ The above URL works for the reprepro tool. For mini-dinstall the URL
+ may be slightly different. Please check after the first packages have been
+ built that do not depend on other packages external to Debian.
+
e. run: cran2deb repopulate
3. cran2deb needs a persistent cache outside of R's control. therefore, create
/var/cache/cran2deb, writable by whichever user(s) will run cran2deb.
+
4. add to /etc/rc.local:
# one mini-dinstall daemon for each apt repo
for sys in debian-i386 debian-amd64
done
and execute.
-5. run: cran2deb update
-6. Try building a simple package: cran2deb build zoo
+5. manual change - allow cran2deb user to execute pdebuild as root via sudo
+ c2d ALL=(ALL) SETENV: NOPASSWD: /usr/sbin/pdebuild
+ The "SETENV:" is important.
+
+6. run: cran2deb update
+ This will also create the pbuilder environment if not already existing.
+
+7. manual changes - create a gpg key for your packages
+
+ gpg --genkey
+
+ and read through 'man gpg-agent' to set it up. Add that key to the
+ pbuilder environment so the packages you signed and uploaded are
+ indeed acceptable to the distribution.
+
+ sudo pbuilder --login --save-after-login \
+ --basetgz /var/cache/pbuilder/base-cran2deb-debian-amd64.tgz
+
+ Once logged in, in a separate shell perform as cran2deb user a
+
+ gpg --export -a
+
+ which should only be one (your) public key. Copy it with the mouse and
+ add it to your pbuilder login shell via
+
+ apt-key add -
+
+ (return) to expect the key from stdin. Paste it, press CTRL-D to end
+ the input. Another CTRL-D or 'exit' to leave the shell and have the
+ base.tgz updated.
+
+ Also, you should allow the arch-independent R packages to be retrieved
+ from the public cran2deb effort. This also requires that key to be
+ available. From a local shell copy again that key
+
+ gpg --recv-key BFAEA5C2
+ gpg --export -a BFAEA5C2
+
+ and use 'apt-key add -' as before.
+
+8. Try building a simple package: cran2deb build zoo
(The result will be in /var/cache/cran2deb/results/SYS)
+9. Check the specification of your pbuilder settings and run
+ 'cran2deb update'. Do not run 'cran2deb update full' which
+ creates a new pbuilder environment and will require the
+ adding of keys again.
+
+10. Educate yourself about the schema of the sqlite3 database,
+ which is likely to reside at ~/cache/cran2deb.db
+ and is directly accessible via calling from the
+ UNIX command line 'sqlite3 ~/cache/cran2deb.db' .
+
+ The sqlite3 shell will directly attach to the database.
+ See the tables first
+
+ sqlite> .tables
+ blacklist_packages debian_dependency license_override
+ builds forced_depends packages
+ database_versions license_hashes sysreq_override
+
+ and then the schema of the one or other table of interest, e.g.
+
+ sqlite> .schema debian_dependency
+ CREATE TABLE debian_dependency (
+ id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ alias TEXT NOT NULL,
+ build INTEGER NOT NULL,
+ debian_pkg TEXT NOT NULL ,
+ UNIQUE (alias,build,debian_pkg) );
+ sqlite> .schema forced_depends
+ CREATE TABLE forced_depends (
+ r_name TEXT NOT NULL,
+ depend_alias TEXT NOT NULL,
+ PRIMARY KEY (r_name,depend_alias) );
+ sqlite> .schema blacklist_packages
+ CREATE TABLE blacklist_packages (
+ package TEXT PRIMARY KEY NOT NULL,
+ nonfree INTEGER NOT NULL DEFAULT 0,
+ obsolete INTEGER NOT NULL DEFAULT 0,
+ broken_dependency INTEGER NOT NULL DEFAULT 0,
+ unsatisfied_dependency INTEGER NOT NULL DEFAULT 0,
+ breaks_cran2deb INTEGER NOT NULL DEFAULT 0,
+ other INTEGER NOT NULL DEFAULT 0,
+ explanation TEXT NOT NULL);
+ sqlite> .schema builds
+ CREATE TABLE builds (
+ id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ system TEXT NOT NULL ,package TEXT NOT NULL,
+ r_version TEXT NOT NULL ,deb_epoch INTEGER NOT NULL,
+ deb_revision INTEGER NOT NULL ,db_version INTEGER NOT NULL,
+ date_stamp TEXT NOT NULL ,time_stamp TEXT NOT NULL,
+ scm_revision TEXT NOT NULL ,success INTEGER NOT NULL,
+ log TEXT,
+ UNIQUE(package,system,r_version,deb_epoch,deb_revision,db_version));
+ sqlite> .schema database_versions
+ CREATE TABLE database_versions (
+ version INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ version_date INTEGER NOT NULL,
+ base_epoch INTEGER NOT NULL );
+ sqlite> .schema license_hashes
+ CREATE TABLE license_hashes (
+ name TEXT NOT NULL,
+ sha1 TEXT PRIMARY KEY NOT NULL );
+ sqlite> .schema license_override
+ CREATE TABLE license_override (
+ name TEXT PRIMARY KEY NOT NULL,
+ accept INT NOT NULL );
+ sqlite> .schema packages
+ CREATE TABLE packages (
+ package TEXT PRIMARY KEY NOT NULL,
+ latest_r_version TEXT );
+ sqlite> .schema sysreq_override
+ CREATE TABLE sysreq_override (
+ depend_alias TEXT NOT NULL,
+ r_pattern TEXT PRIMARY KEY NOT NULL );
+
+ The sqlite3 shell allows to modify all those entries. For a
+ restart with defaults entries distributed via svn, run "cran2deb
+ repopulate". To update the data stored in svn, change to the data
+ directory and run "./pull". Caveat, prior to that, make sure the
+ license data was read in by you. This is not performed automatically in
+ repopulate, a bit to protect us and stress that everyone is reponsible
+ for their own respective interpretation of a license's constraints
+ and the effect on a redistribution of source and/or binary.
+
+11.Add licenses the way you think it is right. The script in
+ 'exec/repopulate' may offer ideas on how to mass-include what
+ you find in the svn. For new entries, you may prefer using
+ 'cran2deb' license that expects to learn from from the command
+ line how to treat individual licenses:
+
+ $ cran2deb license accept akima
+ I: cran2deb svn: 344 building for debian-amd64 at 2011-02-11 18:46:21
+ N: adding akima accept? TRUE
+
+ $ cran2deb license hash_sha1 akima 485316717b03afbd6d20f7810f9123b4445c8660
+ I: cran2deb svn: 344 building for debian-amd64 at 2011-02-11 18:46:37
+ N: adding hash 485316717b03afbd6d20f7810f9123b4445c8660 for akima
+
+ $ cran2deb license ls
+ I: cran2deb svn: 344 building for debian-amd64 at 2011-02-11 18:46:53
+ accept akima
+ hash_sha1 akima 485316717b03afbd6d20f7810f9123b4445c8660
+
+ What happens here is that a license file was read and if that is
+ having the same hash value, then it is mapped to the license 'akima'.
+ The license 'akima' then again is told to be acceptable. It happened
+ here that the license is of the same name as the package that it
+ occurs in.
+
+To think about
+
+1. After several updates of the repository, we have many outdated
+ Debian packages in the pbuilder's archive cache. I prefer removing
+ them with a skriptlet like
+
+ cd /var/cache/apt/archives \
+ && for i in $(ls | cut -f1 -d_ | uniq -c | egrep -v "^ *1 " | sed -e 's/^\s*[0-9]*\s//')
+ do
+ ls -t ${i}_* | tail -n +2 | xargs -r rm
+ done
+
+2. To investigate which packages are already available in your repository
+ and which ones are not, you may add your packages list to your /etc/apt/sources.list
+ and perform
+
+ sudo apt-get update
+ for i in `grep -i net all_pkgs `
+ do
+ a=`echo $i|tr 'A-Z' 'a-z'`
+ echo "$i:$a"
+ apt-cache search r-cran-$a
+ done
+
+3. If running on a separate partition, the place reserved for cran2deb is not unlikely
+ to exceed your expectation, especially when also running BioConductor. You may
+ consider running cran2deb on logical volumes, like by LVM. Together with a file
+ system that allows its extension, the process is rather straight forward:
+
+ # lvextend -L+40G /dev/vg0/cran2deb
+ Extending logical volume cran2deb to 115.04 GiB
+ Logical volume cran2deb successfully resized
+ # xfs_growfs /dev/vg0/cran2deb
+ meta-data=/dev/dm-6 isize=256 agcount=21, agsize=983040 blks
+ = sectsz=512 attr=2
+ data = bsize=4096 blocks=19671040, imaxpct=25
+ = sunit=0 swidth=0 blks
+ naming =version 2 bsize=4096 ascii-ci=0
+ log =internal bsize=4096 blocks=2560, version=2
+ = sectsz=512 sunit=0 blks, lazy-count=1
+ realtime =none extsz=4096 blocks=0, rtextents=0
+ data blocks changed from 19671040 to 30156800
+
+ The directory does not even need to unmounted for that with XFS.
+
+
+To debug:
$ cran2deb help
will display a short summary of help for each cran2deb command.
+The -d option will prevent the cleaning of the unpacked source code.
+
+To improve:
+
+ * The runtime dependencies for Rgraphviz are outdated (there is no libraphviz4
+ any more). To get the package run this was not changed to "alias_run
+ libgraphviz libgraphviz-dev" but this can certainly be optimised
+ towards something less resource-hungry.
+
Concerning data/:
This contains scripts necessary to recreate the database should you lose the
pull that, when run from the data directory will recreate all the files from
the database EXCEPT for the licenses. The licenses cannot be recreated because
licenses can be based on one-way hashes. This process could certainly be
-improved.
+improved. But one gets the hang of it ater a while. So don't despair.
projects / cran2deb.git / blobdiff