Filed under: Coding Gammu Wammu 1 comments

Projects 2010 As in 2008 and 2009, the R Project has again participated in the Google Summer of Code during 2010. Based on ideas collected and disussed on the R Wiki, the projects and students listed below (and sorted alphabetically by student) were selected for participation and have been sponsored by Google during the summer 2010. The finished projects are available via the R / GSoC 2010 repository at Google Code, and in several cases also via their individual repos (see below). Informal updates and final summaries on the work was also provided via the GSoC 2010 R group blog.

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rdx - Automatic Differentiation in R Chidambaram Annamalai, mentored by John Nash. Proposal: radx is a package to compute derivatives (of any order) of native R code for multivariate functions with vector outputs, f:R^m -> R^n, through Automatic Differentiation (AD). Numerical evaluation of derivatives has widespread uses in many fields. rdx will implement two modes for the computation of derivatives, the Forward and Reverse modes of AD, combining which we can efficiently compute Jacobians and Hessians. Higher order derivatives will be evaluated through Univariate Taylor Propagation. Delivered: Two packages radx: forward automatic differentiation in R and tada: templated automatic differentiation in C++ were created; see this blog post for details.

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A GUI for Graphics using ggplot and Deducer by Ian Fellows, mentored by Hadley Wickham. Proposal: R puts the latest statistical techniques at one's fingertips through thousands of add-on packages available on the CRAN download servers. The price for all of this power is complexity. Deducer is a cross-platform cross-console graphical user interface built on top of R designed to reduce this complexity. This project proposes to extend the scope of Deducer by creating an innovative yet intuitive system for generating statistical graphics based on the ggplot2 package. Delivered: All of the major features have been implemented, and are outlined in the video links in this blog post.

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rgeos - an R wrapper for GEOS by Colin Rundel, mentored by Roger Bivand. Proposal: At present there does not exist a robust geometry engine available to R, the tools that are available tend to be limited in scope and do not easily integrate with existing spatial analysis tools. GEOS is a powerful open source geometry engine written in C++ that implements spatial functions and operators from the OpenGIS Simple Features for SQL specification. rgeos will make these tools available within R and will integrate with existing spatial data tools through the sp package. Delivered: The rgeos project on R-Forge; see the final update blog post.

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Social Relations Analyses in R by Felix Schoenbrodt, mentored by Stefan Schmukle. Proposal: Social Relations Analyses (SRAs; Kenny, 1994) are a hot topic both in personality and in social psychology. While more and more research groups adopt the methodology, software solutions are lacking far behind - the main software for calculating SRAs are two DOS programs from 1995, which have a lot of restrictions. My GSOC project will extend the functionality of these existing programs and bring the power of SRAs into the R Environment for Statistical Computing as a state-of-the-art package. Delivered: The TripleR package is now on CRAN and hosted on RForge.Net; see this blog post for updates.

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NoSQL Interface for R by Yasuhisa Yoshida, mentored by Dirk Eddelbuettel. Proposal: So-called NoSQL databases are becoming increasingly popular. They generally provide very efficient lookup of key/value pairs. I'll provide several implementation of NoSQL interface for R. Beyond a sample interface package, I'll try to support generic interface similar to what the DBI package does for SQL backends Status: An initial prototype is available via RTokyoCabinet on Github. No updates were made since June; no communication occurred with anybody related to the GSoC project since June and the project earned a fail.

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Last modified: Wed Sep 22 19:39:43 CDT 2010

As I already wrote too many times, I've started to use Gnus 6 months ago, and never looked back. At that time, I joined the ding mailing list in order to ask some dumb questions and, once, send a patch. There were very low activity on that list. Until Lars, the original Gnus author, came back. Three weeks ago, he started to wrote a new wash function to render HTML mails properly, with pictures. It's named gnus-html', and is (for now) based on w3m (but not on emacs-w3m, which is not part of Emacs). Last week, I've sent a set of patches to replace the usage of curl by the standard url-retrieve' function to fetch images, plus various enhancement. It seems that my work was good enough that Lars offered me write access to the git repository. I can therefore mess up the Gnus entirely. Hurrah! I've continued to work on gnus-html' and recently merged a set of patches improving image retrieval (which is now done in parallel) and starting to use url-cache' to cache image for a defined period of time. Of course, I found a bunch of tiny bug and special case while reading RSS feeds and various HTML mails, and fixed them all along. Lars added a libxml binding for Emacs 24, providing the html-parse-string' function. His future plan seems to be the abandon of w3m in favor of a native parsing via libxml to render HTML, and therefore, HTML mails. I should also mention the new nnimap' back-end; Gnus has been designed to read NNTP newsgroups, and not mails. Consequently, it had a very poor behaviour when used with a back-end such has IMAP. Lars took a week to rewrite entirely our dear nnimap' back-end, and make it act in a more expected way. There's still a bunch of bug and code to write, but it is at least usable and seems faster than the old code. Last thing I did was to rewrite the icon support in the group buffer. When I started to use Gnus, I was curious and tried to configure this. I never managed to make it work, and now know and understand why it was broken. So I ended rewriting entirely, and now it works. I never though I would understand, fix, and commit this code when reading the Gnus documentation this winter, but hell yeah, I did. Now I've still several little project to improve things in all sort of area. We'll see what I'll do next. :-)

Thank you for your message. This is an automated reply.
I am on sabbatical leave and unable to reply to my email. For all matters concerning the __________________________ Department of __________ Contact ____________ .
Thank you for your patience,
Professor

Thank you for your message. This is an automated reply. I am on sabbatical leave and while I am able to reply to my email, in fact, I have a heck of a lot more time compared to when I teach, it is customary to write a message like this and claim otherwise. However, being on leave does relieve you of (most) all department responsibilities. And given the grueling pace of academic jobs and the contemporary burden of email avalanches we all suffer from, I am taking the license (the sabbatical license) to say: 1) I may never get back to you 2) I may but it may take longer than usual 3) honestly I suffer from MEAD (Massive Email Anxiety Disorder) and hate it when people don t respond to me, so I will likely get back to you but don t you get MEAD if I fail to do so. Thanks for your patience,
Gabriella Coleman
On leave 2010-2011

Thank you for your message. This is an automated reply.
I am on sabbatical leave and unable to reply to my email. For all matters concerning the __________________________ Department of __________ Contact ____________ .
Thank you for your patience,
Professor

Thank you for your message. This is an automated reply. I am on sabbatical leave and while I am able to reply to my email, in fact, I have a heck of a lot more time compared to when I teach, it is customary to write a message like this and claim otherwise. However, being on leave does relieve you of (most) all department responsibilities. And given the grueling pace of academic jobs and the contemporary burden of email avalanches we all suffer from, I am taking the license (the sabbatical license) to say: 1) I may never get back to you 2) I may but it may take longer than usual 3) honestly I suffer from MEAD (Massive Email Anxiety Disorder) and hate it when people don t respond to me, so I will likely get back to you but don t you get MEAD if I fail to do so. Thanks for your patience,
Gabriella Coleman
On leave 2010-2011

post-up ip addr add 192.168.100.2/31 dev extern0   true

#!/bin/sh
# Copyright (c) 2010 Bernd Zeimetz <bzed@debian.org>
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
PATH=/bin:/sbin:/usr/bin:/usr/sbin
export PATH
if [ "$1" = "config" ]; then
        echo graph_title cable modem signal to noise ratio
        echo 'graph_args --base 1000'
        echo 'graph_vlabel dB'
        echo 'graph_category network'
        echo 'graph_info This graph shows the signal to noise ratio of the Scientific-Atlanta cable modem.'
        echo "signalnoise.label ratio"
        echo "signalnoise.info Signal to noise ratio"
        echo 'signalnoise.draw LINE2'
        echo 'signalnoise.type GAUGE'
        exit 0
fi
wget -q -O - http://192.168.100.1/system.asp  \
     grep 'Signal to Noise'   \
     sed 's,.* ,signalnoise.value ,;s, dB.*,,'

#!/bin/sh
# Copyright (c) 2010 Bernd Zeimetz <bzed@debian.org>
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE
PATH=/bin:/sbin:/usr/bin:/usr/sbin
export PATH
if [ "$1" = "config" ]; then
        echo graph_title cable modem power level
        echo 'graph_args --base 1000'
        echo 'graph_vlabel dBmV'
        echo 'graph_category network'
        echo 'graph_info This graph shows receive and transmit power levels of the Scientific-Atlanta cable modem.'
        echo "receive.label receive"
        echo "receive.info Receive power level"
        echo 'receive.draw LINE2'
        echo 'receive.type GAUGE'
        echo "transmit.label transmit"
        echo "transmit.info Transmit power level"
        echo "transmit.draw LINE2"
        echo "transmit.type GAUGE"
        exit 0
fi
wget -q -O - http://192.168.100.1/system.asp   grep dBmV   \
    sed -e 's,.* ,,;s, dBmV.*,,' \
        -e '1s/^/receive.value /' \
        -e '2s/^/transmit.value /'

-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: A revocation certificate should follow
iHIEIBEIADIFAkyaOZwrHQJBIGNvbXB1dGVyIGNvbnRhaW5pbmcgdGhpcyBrZXkg
d2FzIHN0b2xlbgAKCRDYDvNai7UnrzWAAKC34eF76JQjxrZqSjNwcC0dU/5VbACg
gMIMmYg91Sl3y8KsZXdGj/rV7UE=
=rdlT
-----END PGP PUBLIC KEY BLOCK-----

$ OLDKEY=xyHywJuHD3nsfLh03G1TqUEBKSj6NlzMfB1T759haoAQ
$ for host in $(cat .ssh/known_hosts   cut -f 1 -d \  cut -f 1 -d ,  
                sort   uniq); do 
    echo == $host
    ssh-copy-id -i .ssh/id_rsa.new.pub $host && 
    ssh $host "perl -n -i -e 'next if /$OLDKEY/;print' .ssh/authorized_keys"
done

• .ssh/known_hosts' lines start with the server's name (or names, if more than one, comma-separated), followed by the key algorithm and the key fingerprint (space-separated). That's the reason for the double cut It could probably be better using a regex-enabled thingy understanding /[, ]/, but... I didn't think of that. Besides, the savings would be just for academic purposes ;-)
• I thought about not having the ssh line conditionally depend on ssh-copy-id. But OTOH, this makes sure I only try to remove the old key from the servers it is present on, and that I don't start sending my new key everywhere just for the sake of it.
• my $OLDKEY (declared in Shell, and only literally interpolated in the Perl one-liner below) contains the final bits of my old key. It is long enough for me not to think I'm risking collision with any other key. Why did I choose that particular length? Oh, it was a mouse motion.
• perl -n -i -e is one of my favorite ways to invoke perl. -i means in-line editing, it allows me to modify a file on the fly. This line just skips (removes) any keys containing $OLDKEY; -n tells it to loop all the lines over the provided program (and very similarly, -p would add a print at the end Which in this particular ocassion, I prefer not to have). It is a sed lookalike, if you wish, but with a full Perl behind.

• This assumes you have set HashKnownHosts: no in your .ssh/config. It is a tradeoff, after all I use a lot tab-expansion (via bash_completion) for hostnames, so I do have the fully parseable list of hosts I have used on each of my computers.
• I have always requested my account names to be gwolf. If you use more than one username... well, you will have to probably do more than one run of it connecting to foo@$host instead.
• Although most multiuser servers stick to the usual port 22, many people change the ports (me included) either because they perceive concealing them gives extra security, or (as in my case) because they are fed up with random connection attempts. Those hosts are stored as [hostname]:port (i.e. [foo.gwolf.org]:22000). Of course, a little refinement takes care of it all.,/li>
• Oh, I am not storing results... I should, so for successive runs I won't try to connect to a system I already did, or that already denied me access. Why would I want to? Because some computers are not currently turned on. So I'll run this script at least a couple of times.

The event been also attended by some members of the Debian Women and Ubuntu Women teams (whose goal is to promote women participation in both projects), who organized a round-table debate taking the Italian panorama as a study case. The discussion embraced different topics, ranging from the wide difference in numbers, to the deep causes of this phenomenon and how to improve the situation. With the help of the hacklab staff (hosting the debate), an audio/video streaming has been made available in real-time, and many remote participants joined us with comments and questions. This new kind of collaboration between our communities was found to be really positive and more events has already been drafted for the next year, including a translation sprint and a contributors meeting. We encourage worldwide local communities to try and engage in a similar experiment: organizing and joining a DUCC event will be pure fun. A detailed report of the conference will be soon available, completed by photos, participants comments, video records and slides for the talks.
We d really like to thank the Math Department of University of Perugia, the Projectz On Island hacklab, FSUG Italia, the Ubuntu-it community and everyone who contribute to this event.

Transport Layer Security support -

this successor to SSL means that your connection will be encrypted. You want this so that your email and your login details aren t being intercepted. Unless you trust everything between you and your mailserver completely, this is pretty much a minimum requirement.

A good login method, probably either CRAM-MD5 or APOP -

you want this so that you aren t simply sending your password over the network. Your connection might be encrypted, but this is a belt-and-braces approach.

IMAP rather than POP -

Internet Message Access Protocol usually offers many more features than the antiquated Post Office Protocol. POP usually shoves all your email through your virtual letterbox, junk or not, and dumps it on your computer. IMAP is more like telling a postman which email to deliver where and when. You can create folders on the server (as well as on your local computer), you can delete junk mail before you download its bodies and it s easier to access your email from multiple locations like your desktop and your phone. QMUL has a longer comparison but nearly everyone would be better off with IMAP.

Sieve configuration -

Now I m getting really optimistic. A Sieve file is an instruction file of standardised mail filtering rules. They re a little harder to write, but should be much easier to move between Sieve-compatible mailservers.

• Attendees are supposed to put the amounts they can't afford to pay themselves, but we have no way of checking this (and probably wouldn't want to pry so much to be able to...)
• Historically, money has been budgeted for travel sponsorship last, thus travel sponsorship usually isn't confirmed until late in the process. This means that flight prices have constantly gone up, and some people may be unable to attend DebConf due to uncertainty over travel sponsorship.
• Attendees have a dilemma: They are supposed to enter only the amount they cannot fund themselves. But if there is a chance of fares being reimbursed at less the requested amount, then entering the amount absolutely required to attend results in a disadvantage.
• Invariably, people get confuse "amount I am unable to afford" as "amount I am able to afford"
• For some years, entering too high a requested sponsorship amount could result in a lower priority - instead of the selection team adjusting the amount downward. Thus, attendees have another dilemma about what to request.

• Why are we publishing our hardware architectures from our browsers anyway? This seems like unncessary leakage, and not all browsers do it. For example, Arora doesn't leak this info (despite a poorly-argued request to do so). Browsers are already too identifiable by servers. This information should not be leaked by default.
• Why does live.com insist on sending ppc users to the crappy "mobile" version? Are they trying to encourage the treadmill of hardware upgrades that proprietary vendors benefit from? Is there some less insidious explanation? Are there actually more powerpc-based mobile devices than desktops?
• why is there no simple way to tell Firefox/Iceweasel to override or suppress the architecture information? Having to override the useragent string entirely means that when iceweasel does eventually get upgraded, it's going to report the wrong version unless i can remember to update the override myself (i can't reasonably expect a non-techie client who never heard of user agents before today to remember how to do this correctly).

Configuration file  /etc/bash.bashrc'
 ==> Modified (by you or by a script) since installation.
 ==> Package distributor has shipped an updated version.
   What would you like to do about it ?  Your options are:
    Y or I  : install the package maintainer's version
    N or O  : keep your currently-installed version
      D     : show the differences between the versions
      Z     : start a shell to examine the situation
 The default action is to keep your current version.
*** bash.bashrc (Y/I/N/O/D/Z) [default=N] ?

$ dpkg --status bash
[...]
Conffiles:
 /etc/skel/.profile ecb6d3479ac3823f1da7f314d871989b
 /etc/skel/.bashrc 2afdd6c53990f2387a7ef9989af0bc07
 /etc/skel/.bash_logout 22bfb8c1dd94b5f3813a2b25da67463f
 /etc/bash.bashrc 5b3c3bc73d236e4e1b6f9b6c1ed5964e
[...]

• --force-confold: do not modify the current configuration file, the new version is installed with a .dpkg-dist suffix. With this option alone, even configuration files that you have not modified are left untouched. You need to combine it with --force-confdef to let dpkg overwrite configuration files that you have not modified.
• --force-confnew: always install the new version of the configuration file, the current version is kept in a file with the .dpkg-old suffix.
• --force-confdef: ask dpkg to decide alone when it can and prompt otherwise. This is the default behavior of dpkg and this option is mainly useful in combination with --force-confold.
• --force-confmiss: ask dpkg to install the configuration file if it s currently missing (for example because you have removed the file by mistake).

$ apt-get -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" dist-upgrade

Dpkg::Options  
   "--force-confdef";
   "--force-confold";
 

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