Google Summer of Code 2008 projects assigned
As mentioned a few weeks ago, I had submitted two entries as possible topics for this year's version of the Google Summer of Code. And lo and behold, the response was very, very good and both applications were slotted!

For the topic 'create a PostgreSQL package for R that uses the standard DBI interface', a number of interested students contacted me, and a total of three applications were submitted. And while the R Foundation was only able to allocate four topics among a number of really good applications, Sameer Prayaga was our pick for this topic. It would be nice to fill this gap among the existing database connection methods for R, and I feel that Sameer can pull this off.

For the second topic of 'create a cran2deb tool for converting CRAN sources into Debian package' which I had submitted within Debian, Charles Blundell wrote an excellent application. In a way, this topic is a '2.0' version of our previous attempts of a 'top-down' set of tools in the pkg-bioc project on Alioth. This time, we will try something smaller, maybe more modular and lighter and see how far we get there if we try it 'bottom-up'.

And as we are currently in the community bonding phase, say Hi to Sameer or Charles when you come across them these days.

Lastly, I'd like to thank everybody who submitted an entry at Debian or R, or who contacted me about one of the topics I posted. The respone was very humbling, many of you were imminently qualified and seemingly very motivated -- but even Google's pockets can only pay for a finite number of projects. Sorry if yours did not get picked.

/computers/misc | permanent link

Google Summer of Code 2008 projects are up
For the past few years, Google has been running their Summer of Code events where Google offers $5000 for college students who are asked to code for a summer for the benefit of various Open Source efforts.

And just like in 2006 and 2007, I put up proposals and offered to act as a mentor. The first one is up at both Debian and R: an opportunity to help with the ongoing efforts of 'turning more CRAN package into Debian packages'. The second one is only at the R page: a proposal to fill the missing link of DBI database interface modules with a matching one for PostgreSQL. More details for either idea are at the respective pages. Anybody interested should ping me by email.

/computers/misc | permanent link

Dead disks, and lvm woes
As posted earlier on the rather recently announced CRANberries feed (that is generated and hosted on my box) covering CRAN package updates, my main server bit the dust. The hard disk no longer wants to talk to any of its lvm partitions, leaving me without /usr, /var/, /var/local/, /home, /srv. Fortunately, most of this was backed-up but now I have to go through reconfiguring the replacement machine I already set up. Not fun.

If anybody has tips on recovering the lvm partitions, I'm all ears. /etc/lvm/ seems fine if that helps as a starting point.

/computers/misc | permanent link

Patch to build palm-db-tools_0.3.6 with recent g++ versions
A freshly downloaded version of palm-db-tools (using the most recent version 0.3.6 from June 2003) will not compile with g++ 4.0.3 and its pickier interpretation of C++.

A simple patch which removes trailing semicolons after class definitions, and adds virtual destructors for a few classes, is below. The mailing list archives show one other patch for a different (yet probably relevant :) problem, and its from November 2003.

By the way, would be nice if someone added the package to Debian. The Makefile's make clean target isn't quite right, and make install isn't exactly correct either. Plus, I seem to be building this by hand every few years, and it's so much easier to just apt-get. And no, my plate is already too full.

diff -ru palm-db-tools-0.3.6.orig/libpalm/Block.h palm-db-tools-0.3.6/libpalm/Block.h
--- palm-db-tools-0.3.6.orig/libpalm/Block.h	2003-06-19 18:37:47.000000000 -0500
+++ palm-db-tools-0.3.6/libpalm/Block.h	2006-07-29 15:04:19.000000000 -0500
@@ -176,7 +176,7 @@
 	size_type m_size;
     };
 
-};
+}
 
 bool operator == (const PalmLib::Block& lhs, const PalmLib::Block& rhs);
 
diff -ru palm-db-tools-0.3.6.orig/libpalm/File.h palm-db-tools-0.3.6/libpalm/File.h
--- palm-db-tools-0.3.6.orig/libpalm/File.h	2003-06-19 18:37:47.000000000 -0500
+++ palm-db-tools-0.3.6/libpalm/File.h	2006-07-29 15:04:42.000000000 -0500
@@ -89,6 +89,6 @@
 	uid_map_t m_uid_map;
     };
 
-};
+}
 
 #endif
diff -ru palm-db-tools-0.3.6.orig/libsupport/infofile.h palm-db-tools-0.3.6/libsupport/infofile.h
--- palm-db-tools-0.3.6.orig/libsupport/infofile.h	2003-06-19 18:37:47.000000000 -0500
+++ palm-db-tools-0.3.6/libsupport/infofile.h	2006-07-29 15:07:08.000000000 -0500
@@ -33,6 +33,7 @@
         {
         public:
             virtual void parse(int linenum, std::vector< std::string> array) = 0;
+	  virtual ~Parser() {};
         };
         class ConfigParser: public Parser
         {
@@ -40,6 +41,7 @@
                 ConfigParser(DataFile::CSVConfig& state)
                     : m_Config(state)
                     {}
+	        virtual ~ConfigParser() {};
                 virtual void parse(int linenum, std::vector< std::string> array);
             private:
                 DataFile::CSVConfig& m_Config;
@@ -50,6 +52,7 @@
                 DatabaseParser(PalmLib::FlatFile::Database& db)
                     : m_DB(db)
                     {}
+	        virtual ~DatabaseParser() {};
                 virtual void parse(int linenum, std::vector< std::string> array);
             private:
                 PalmLib::FlatFile::Database& m_DB;
@@ -60,6 +63,7 @@
                 TypeParser(std::string& p_Type)
                     : m_Type(p_Type)
                     {}
+	        virtual ~TypeParser() {};
                 virtual void parse(int linenum, std::vector< std::string> array);
             private:
                 std::string& m_Type;

/computers/misc | permanent link

Undeleting from ext3
Kudos to Paul Wise who suggested late last night to try magicrescue to recover an OpenOffice file with meeting notes I had mistakenly deleted from the laptop before I even got to editing these very notes, or backing them up.

And it worked -- despite the dire warnings from the ext3 FAQ about the near impossibility of undeleting from ext3 partitions. But a few things worked in my favour here: OpenOffice files are zip files 'under the hood', and magicrescue knows how to deal with certain file formats via its collection of 'recipes' (which one can extend), and zip is among the shipped recipes. Also, I still had the 'ls -l' session in one konsole tab so I knew the exact file size I was looking for. And I wasn't in a hurry. So this morning, after magicrescue had faithfully restored 4479 files in over four hours, its companion magicsort then filtered these into a handful of directories, one of which was 'OpenDocument Text' -- which contained a few files, including two versions of the desired file as well as copies of the version from the previous meeting. Nice. And OpenOffice gladly opened the file. Lastly, it cetainly helped that I happened to have a lurking debian-devel irc session open where --- where Paul not only caught my remark, but almost immediately suggested to try magicrescue. So here goes a well-earned Thank You to Paul!

/computers/misc | permanent link

Mail broken
Comcast, in their infinite wisdom, decided to RBL block (at least one of) Debian's mailhost(s), master.debian.org. As essentially all my mail is forwarded from Debian to Comcast, mail traffic was affected.

At first, I noticed dropped posts from mailing list subscriptions relative to the list web archives. I posted the suggested noticed to the Comcast RBL admins, so far to no avail other than a to yield a more complete stop. The mail forwarding has been disabled for now, and I am dealing with this more manually.

If you tried to contact me in the last few days and have not gotten a response, please resend your mail. I should now be in a position to receive it. Sorry for any inconveniences.

Offers of better mail hosting would be gladly accepted, of course.

/computers/misc | permanent link

Smokes, that ain't pretty
From the headers of a mail I just got:

Received: from master.debian.org ([146.82.138.7])
   by sccrmxc11.comcast.net (sccrmxc11) with ESMTP
   id <20051105044942s1100j9crge>; Sat, 5 Nov 2005 04:49:42 +0000
X-Originating-IP: [146.82.138.7]
Received: from wproxy.gmail.com [64.233.184.204]
   by master.debian.org with esmtp (Exim 3.35 1 (Debian))
   id 1E7EfR-0004zq-00; Mon, 22 Aug 2005 10:56:58 -0500
Received: by wproxy.gmail.com with SMTP id i34so340646wra
   for <edd©debian.org>; Mon, 22 Aug 2005 08:56:47 -0700 (PDT)


So if you, anonymous reader, happened to have emailed me lately and are still awaiting a reply ... please consider the possibility that I may not have received your mail yet.

I should add that the underlying problem has been rectified at Debian's end as one of our hard-working admins stated yesterday.

/computers/misc | permanent link

Quite right
The widely-read and rather influential Walt Mossberg was reviewing Windows security in today's column and concluded

Bottom line: If you use Windows, you're asking for trouble.

As they say, truer words have never been spoken... Other than recommending OS X in no uncertain terms, he listed a host of required add-ons to make that one dominant OS cope with its own lack of security.

/computers/misc | permanent link

Compiling afio under Cywgin
Here is a simple patch against the current afio-2.5 sources, derived mostly from an older patch from Japan against 2.4.7. This allows compilation of afio under Cygwin by simply calling make, no further config needed.

I sent it upstream to Koen, maybe it'll show up in a future versiom.

 diff -ru afio-2.5.orig/afio.c afio-2.5/afio.c ---
afio-2.5.orig/afio.c 2003-12-20 16:16:13.000000000 -0600 +++ afio-2.5/afio.c
2004-09-13 17:12:50.548515800 -0500 @@ -184,7 +184,11 @@
 #include 
 #include 
 #include 
+#ifdef __CYGWIN32__
+#include 
+#else
 #include 
+#endif
 #include 
 #include 
 #include 
Only in afio-2.5: afio.exe
diff -ru afio-2.5.orig/afio.h afio-2.5/afio.h
--- afio-2.5.orig/afio.h	2003-12-20 07:59:42.000000000 -0600
+++ afio-2.5/afio.h	2004-09-13 15:17:51.700744200 -0500
@@ -477,7 +477,7 @@
 #ifndef MKDIR
 int rmdir (char *);
 #endif
-#if !defined (linux) && !defined(__FreeBSD__) && !defined(sun)
+#if !defined (linux) && !defined(__FreeBSD__) && !defined(sun) && !defined(__CYGWIN32__)
 VOIDFN (*signal ())();
 #endif
      int fswrite (int, char*, uint);
diff -ru afio-2.5.orig/compfile.c afio-2.5/compfile.c
--- afio-2.5.orig/compfile.c	2003-06-24 16:32:20.000000000 -0500
+++ afio-2.5/compfile.c	2004-09-13 15:03:44.532576200 -0500
@@ -210,7 +210,7 @@
  * version;
  */
 
-#if ( defined(sun) && defined(__svr4__) )
+#if ( defined(sun) && defined(__svr4__) ) || defined(__CYGWIN32__)
 #include 
 #else
 #include 

/computers/misc | permanent link

That was fast
Ordered a new box to replace our dual-amd, with which we continue to have random locks every couple of days, on Wednesday evening just before one of these Dell special deals expired -- it's their entry level server which has a nice Unofficial Dell PowerEdge 400SC FAQ.

Shipment was supposedly to be in three days from now ... yet the box arrived today! It boots Knoppix as well as my Quantian just fine. A pIV 2.8 GHz and a mobo with sata support, gigabit lan, graphics, sounds, whathaveyou all integrated along with a puny little disk and a laughable amount of Ram (order for a gb from crucial is on its way), it all came to just over $500 of which $100 should come back via a mail-in rebate.

/computers/misc | permanent link

ATX power supplies suck
Grr. Power went out on Thursday, and one of our computers didn't come back on. Took two days to figure that the stupid connector from the power switch to the motherboard was loose so that the power supply was able to operate. Is it just me, or does anybody else think that AT power supplied were simpler? Power on whne pressed, and off otherwise. Clean. Simple.

/computers/misc | permanent link

Compiling a2ps under Cywgin and adding R / S support
For those of use with fingers and brains hardwired to Unix, Cygwin is a godsend. One package I was always missing from Cygwin is a2ps -- which is really nice for pretty-printing just about anything, which would include source code. Thanks to a rather useful support 'style sheet' for the S language (i.e. GNU R and its commercial sibbling S-Plus), you can typeset S code as well. The patch is once again part of the Debian package and can also be found on CRAN.

I simply grabbed the most recent Debian tarball and diff.gz, unpacked the tarball and applied the patch. You then need to run the appropriate debian/patches patch from the a2ps sources directory as per

sh debian/patches/10_s_support.dpatch -patch

After that, it's just a matter of adding a two-line patch in /usr/include/string.h to comment out two lines

#ifndef __CYGWIN__
_PTR	 _EXFUN(memccpy,(_PTR, const _PTR, int, size_t));
_PTR	 _EXFUN(mempcpy,(_PTR, const _PTR, size_t));
#endif

configure --medium=letter; make; make install

/computers/misc | permanent link