Search Results: "cmc"

1 December 2014

NOKUBI Takatsugu: 120th Tokyo area debian seminar

I had attend 120th Tokyo area Debian seminar at Shinjuku. An attendee brought hp Jornada 780 and tried to install Debian, so I helped him. Using a kernel, boot loader and userland from Lenny on j720 page and it worked fine, except PCMCIA NIC. His NIC is Corga PCC-TD is not listed in /etc/pcmcia/*. I didn t have enough time to write it, so I couldn t check it. However, later releases after Lenny don t have arm architecuture, so it should be hard to upgrade it. I don t know recent Linux kernel work on Jornada 780. The configuration and code for jonrnada 780 are still in the kernel, but it wouldn t be tested anyone.

12 October 2014

Iustin Pop: Day trip on the Olympic Peninsula

Day trip on the Olympic Peninsula TL;DR: drove many kilometres on very nice roads, took lots of pictures, saw sunshine and fog and clouds, an angry ocean and a calm one, a quiet lake and lots and lots of trees: a very well spent day. Pictures at http://photos.k1024.org/Daytrips/Olympic-Peninsula-2014/. Sometimes I travel to the US on business, and as such I've been a few times in the Seattle area. Until this summer, when I had my last trip there, I was content to spend any extra days (weekend or such) just visiting Seattle itself, or shopping (I can spend hours in the REI store!), or working on my laptop in the hotel. This summer though, I thought - I should do something a bit different. Not too much, but still - no sense in wasting both days of the weekend. So I thought maybe driving to Mount Rainier, or something like that. On the Wednesday of my first week in Kirkland, as I was preparing my drive to the mountain, I made the mistake of scrolling the map westwards, and I saw for the first time the Olympic Peninsula; furthermore, I was zoomed in enough that I saw there was a small road right up to the north-west corner. Intrigued, I zoomed further and learned about Cape Flattery ( the northwestern-most point of the contiguous United States! ), so after spending a bit time reading about it, I was determined to go there. Easier said than done - from Kirkland, it's a 4h 40m drive (according to Google Maps), so it would be a full day on the road. I was thinking of maybe spending the night somewhere on the peninsula then, in order to actually explore the area a bit, but from Wednesday to Saturday it was a too short notice - all hotels that seemed OK-ish were fully booked. I spent some time trying to find something, even not directly on my way, but I failed to find any room. What I did manage to do though, is to learn a bit about the area, and to realise that there's a nice loop around the whole peninsula - the 104 from Kirkland up to where it meets the 101N on the eastern side, then take the 101 all the way to Port Angeles, Lake Crescent, near Lake Pleasant, then south toward Forks, crossing the Hoh river, down to Ruby Beach, down along the coast, crossing the Queets River, east toward Lake Quinault, south toward Aberdeen, then east towards Olympia and back out of the wilderness, into the highway network and back to Kirkland. This looked like an awesome road trip, but it is as long as it sounds - around 8 hours (continuous) drive, though skipping Cape Flattery. Well, I said to myself, something to keep in mind for a future trip to this area, with a night in between. I was still planning to go just to Cape Flattery and back, without realising at that point that this trip was actually longer (as you drive on smaller, lower-speed roads). Preparing my route, I read about the queues at the Edmonds-Kingston ferry, so I was planning to wake up early on the weekend, go to Cape Flattery, and go right back (maybe stop by Lake Crescent). Saturday comes, I - of course - sleep longer than my trip schedule said, and start the day in a somewhat cloudy weather, driving north from my hotel on Simonds Road, which was quite nicer than the usual East-West or North-South roads in this area. The weather was becoming nicer, however as I was nearing the ferry terminal and the traffic was getting denser, I started suspecting that I'll spend a quite a bit of time waiting to board the ferry. And unfortunately so it was (photo altered to hide some personal information): Waiting for the ferry. The weather at least was nice, so I tried to enjoy it and simply observe the crowd - people were looking forward to a weekend relaxing, so nobody seemed annoyed by the wait. After almost half an hour, time to get on the ferry - my first time on a ferry in US, yay! But it was quite the same as in Europe, just that the ship was much larger. Once I secured the car, I went up deck, and was very surprised to be treated with some excellent views: Harbour view Looking towards the sun   and away from it The crossing was not very short, but it seemed so, because of the view, the sun, the water and the wind. Soon we were nearing the other shore; also, see how well panorama software deals with waves :P! Near the other shore And I was finally on the "real" part of the trip. The road was quite interesting. Taking the 104 North, crossing the "Hood Canal Floating Bridge" (my, what a boring name), then finally joining the 101 North. The environment was quite varied, from bare plains and hills, to wooded areas, to quite dense forests, then into inhabited areas - quite a long stretch of human presence, from the Sequim Bay to Port Angeles. Port Angeles surprised me: it had nice views of the ocean, and an interesting port (a few big ships), but it was much smaller than I expected. The 101 crosses it, and in less than 10 minutes or so it was already over. I expected something nicer, based on the name, but Anyway, onwards! Soon I was at a crossroads and had to decide: I could either follow the 101, crossing the Elwha River and then to Lake Crescent, then go north on the 113/112, or go right off 101 onto 112, and follow it until close to my goal. I took the 112, because on the map it looked "nicer", and closer to the shore. Well, the road itself was nice, but quite narrow and twisty here and there, and there was some annoying traffic, so I didn't enjoy this segment very much. At least it had the very interesting property (to me) that whenever I got closer to the ocean, the sun suddenly disappeared, and I was finding myself in the fog: Foggy road So my plan to drive nicely along the coast failed. At one point, there was even heavy smoke (not fog!), and I wondered for a moment how safe was to drive out there in the wilderness (there were other cars though, so I was not alone). Only quite a bit later, close to Neah Bay, did I finally see the ocean: I saw a small parking spot, stopped, and crossing a small line of trees I found myself in a small cove? bay? In any case, I had the impression I stepped out of the daily life in the city and out into the far far wilderness: Dead trees on the beach Trees growing on a rock Small panorama of the cove There was a couple, sitting on chairs, just enjoying the view. I felt very much intruding, behaving like I did as a tourist: running in, taking pictures, etc., so I tried at least to be quiet . I then quickly moved on, since I still had some road ahead of me. Soon I entered Neah Bay, and was surprised to see once more blue, and even more blue. I'm a sucker for blue, whether sky blue or sea blue , so I took a few more pictures (watch out for the evil fog in the second one): View towards Neah Bay port Sea view from Neah Bay Well, the town had some event, and there were lots of people, so I just drove on, now on the last stretch towards the cape. The road here was also very interesting, yet another environment - I was driving on Cape Flattery Road, which cuts across the tip of the peninsula (quite narrow here) along the Waatch River and through its flooding plains (at least this is how it looked to me). Then it finally starts going up through the dense forest, until it reaches the parking lot, and from there, one goes on foot towards the cape. It's a very easy and nice walk (not a hike), and the sun was shining very nicely through the trees: Sunny forest Sun shinning down Wooden path But as I reached the peak of the walk, and started descending towards the coast, I was surprised, yet again, by fog: Ugly fog again! I realised that probably this means the cape is fully in fog, so I won't have any chance to enjoy the view. Boy, was I wrong! There are three viewpoints on the cape, and at each one I was just "wow" and "aah" at the view. Even thought it was not a sunny summer view, and there was no blue in sight, the combination between the fog (which was hiding the horizon and even the closer islands), the angry ocean which was throwing wave after wave at the shore, making a loud noise, and the fact that even this seemingly inhospitable area was just teeming with life, was both unexpected and awesome. I took here waay to many pictures, here are just a couple inlined: First view at the cape Birds 'enjoying' the weather Foggy shore I spent around half an hour here, just enjoying the rawness of nature. It was so amazing to see life encroaching on each bit of land, even though it was not what I would consider a nice place. Ah, how we see everything through our own eyes! The walk back was through fog again, and at one point it switched over back to sunny. Driving back on the same road was quite different, knowing what lies at its end. On this side, the road had some parking spots, so I managed to stop and take a picture - even though this area was much less wild, it still has that outdoors flavour, at least for me: Waatch River Back in Neah Bay, I stopped to eat. I had a place in mind from TripAdvisor, and indeed - I was able to get a custom order pizza at "Linda's Woodfired Kitchen". Quite good, and I ate without hurry, looking at the people walking outside, as they were coming back from the fair or event that was taking place. While eating, a somewhat disturbing thought was going through my mind. It was still early, around two to half past two, so if I went straight back to Kirkland I would be early at the hotel. But it was also early enough that I could - in theory at least - still do the "big round-trip". I was still rummaging the thought as I left On the drive back I passed once more near Sekiu, Washington, which is a very small place but the map tells me it even has an airport! Fun, and the view was quite nice (a bit of blue before the sea is swallowed by the fog): Sekiu view After passing Sekiu and Clallam Bay, the 112 curves inland and goes on a bit until you are at the crossroads: to the left the 112 continues, back the same way I came; to the right, it's the 113, going south until it meets the 101. I looked left - remembering the not-so-nice road back, I looked south - where a very appealing, early afternoon sun was beckoning - so I said, let's take the long way home! It's just a short stretch on the 113, and then you're on the 101. The 101 is a very nice road, wide enough, and it goes through very very nice areas. Here, west to south-west of the Olympic Mountains, it's a very different atmosphere from the 112/101 that I drove on in the morning; much warmer colours, a bit different tree types (I think), and more flat. I soon passed through Forks, which is one of the places I looked at when searching for hotels. I did so without any knowledge of the town itself (its wikipedia page is quite drab), so imagine my surprise when a month later I learned from a colleague that this is actually a very important place for vampire-book fans. Oh my, and I didn't even stop! This town also had some event, so I just drove on, enjoying the (mostly empty) road. My next planned waypoint was Ruby Beach, and I was looking forward to relaxing a bit under the warm sun - the drive was excellent, weather perfect, so I was watching the distance countdown on my Garmin. At two miles out, the "Near waypoint Ruby Beach" message appeared, and two seconds later the sun went out. What the I was hoping this is something temporary, but as I slowly drove the remaining mile I couldn't believe my eyes that I was, yet again, finding myself in the fog I park the car, thinking that asking for a refund would at least allow me to feel better - but it was I who planned the trip! So I resigned myself, thinking that possibly this beach is another special location that is always in the fog. However, getting near the beach it was clear that it was not so - some people were still in their bathing suits, just getting dressed, so it seems I was just unlucky with regards to timing. However, I the beach itself was nice, even in the fog (I later saw online sunny pictures, and it is quite beautiful), the the lush trees reach almost to the shore, and the way the rocks are sitting on the beach: A lonely dinghy Driftwood  and human construction People on the beach Since the weather was not that nice, I took a few more pictures, then headed back and started driving again. I was soo happy that the weather didn't clear at the 2 mile mark (it was not just Ruby Beach!), but alas - it cleared as soon as the 101 turns left and leaves the shore, as it crosses the Queets river. Driving towards my next planned stop was again a nice drive in the afternoon sun, so I think it simply was not a sunny day on the Pacific shore. Maybe seas and oceans have something to do with fog and clouds ! In Switzerland, I'm very happy when I see fog, since it's a somewhat rare event (and seeing mountains disappearing in the fog is nice, since it gives the impression of a wider space). After this day, I was a bit fed up with fog for a while Along the 101 one reaches Lake Quinault, which seemed pretty nice on the map, and driving a bit along the lake - a local symbol, the "World's largest spruce tree". I don't know what a spruce tree is, but I like trees, so I was planning to go there, weather allowing. And the weather did cooperate, except that the tree was not so imposing as I thought! In any case, I was glad to stretch my legs a bit: Path to largest spruce tree Largest spruce tree, far view Largest spruce tree, closer view Very short path back to the road However, the most interesting thing here in Quinault was not this tree, but rather - the quiet little town and the view on the lake, in the late afternoon sun: Quinault Quinault Lake view The entire town was very very quiet, and the sun shining down on the lake gave an even stronger sense of tranquillity. No wind, not many noises that tell of human presence, just a few, and an overall sense of peace. It was quite the opposite of the Cape Flattery and a very nice way to end the trip. Well, almost end - I still had a bit of driving ahead. Starting from Quinault, driving back and entering the 101, driving down to Aberdeen: Afternoon ride then turning east towards Olympia, and back onto the highways. As to Aberdeen and Olympia, I just drove through, so I couldn't make any impression of them. The old harbour and the rusted things in Aberdeen were a bit interesting, but the day was late so I didn't stop. And since the day shouldn't end without any surprises, during the last profile change between walking and driving in Quinault, my GPS decided to reset its active maps list and I ended up with all maps activated. This usually is not a problem, at least if you follow a pre-calculated route, but I did trigger recalculation as I restarted my driving, so the Montana was trying to decide on which map to route me - between the Garmin North America map and the Open StreeMap one, the result was that it never understood which road I was on. It always said "Drive to I5", even though I was on I5. Anyway, thanks to road signs, and no thanks to "just this evening ramp closures", I was able to arrive safely at my hotel. Overall, a very successful, if long trip: around 725 kilometres, 10h:30m moving, 13h:30m total: Track picture There were many individual good parts, but the overall think about this road trip was that I was able to experience lots of different environments of the peninsula on the same day, and that overall it's a very very nice area. The downside was that I was in a rush, without being able to actually stop and enjoy the locations I visited. And there's still so much to see! A two nights trip sound just about right, with some long hikes in the rain forest, and afternoons spent on a lake somewhere. Another not so optimal part was that I only had my "travel" camera (a Nikon 1 series camera, with a small sensor), which was a bit overwhelmed here and there by the situation. It was fortunate that the light was more or less good, but looking back at the pictures, how I wish that I had my "serious" DSLR So, that means I have two reasons to go back! Not too soon though, since Mount Rainier is also a good location to visit . If the pictures didn't bore you yet, the entire gallery is on my smugmug site. In any case, thanks for reading!

13 April 2014

C.J. Adams-Collier: When was the last time you upgraded from squeeze to wheezy?

Wow. 3G delta. I haven t booted this laptop for a while I think I m finally ready to make the move from gnome2 to gnome3. There are bits that still annoy me, but I think it s off to a good start. Upgrading perl from 5.10 to 5.14.
cjac@calcifer:~$ sudo apt-get dist-upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages will be REMOVED:
  at-spi capplets-data compiz compiz-gnome compiz-gtk defoma deskbar-applet g++-4.3 gcc-4.3 gcj-4.4-base gcj-4.4-jre gcj-4.4-jre-headless gcj-4.4-jre-lib
  gdm3 gir1.0-clutter-1.0 gir1.0-freedesktop gir1.0-glib-2.0 gir1.0-gstreamer-0.10 gir1.0-gtk-2.0 gir1.0-json-glib-1.0 glade-gnome gnome-about
  gnome-accessibility gnome-applets gnome-core gnome-panel gnome-utils-common lib32readline5-dev libbrasero-media0 libclass-mop-perl libdb4.7-java
  libdb4.8-dev libdevhelp-1-1 libdigest-sha1-perl libdirectfb-dev libebook1.2-9 libecal1.2-7 libedata-book1.2-2 libedata-cal1.2-7 libedataserverui1.2-8
  libepc-1.0-2 libepc-ui-1.0-2 libept1 libgcj10 libgcj10-awt libgd2-noxpm libgstfarsight0.10-0 libgtkhtml-editor0 libjpeg62-dev libmetacity-private0
  libmono-accessibility1.0-cil libmono-bytefx0.7.6.1-cil libmono-cairo1.0-cil libmono-cil-dev libmono-corlib1.0-cil libmono-cscompmgd7.0-cil
  libmono-data-tds1.0-cil libmono-data1.0-cil libmono-debugger-soft0.0-cil libmono-getoptions1.0-cil libmono-i18n-west1.0-cil libmono-i18n1.0-cil
  libmono-ldap1.0-cil libmono-microsoft7.0-cil libmono-npgsql1.0-cil libmono-oracle1.0-cil libmono-peapi1.0-cil libmono-posix1.0-cil
  libmono-relaxng1.0-cil libmono-security1.0-cil libmono-sharpzip0.6-cil libmono-sharpzip0.84-cil libmono-sqlite1.0-cil libmono-system-data1.0-cil
  libmono-system-ldap1.0-cil libmono-system-messaging1.0-cil libmono-system-runtime1.0-cil libmono-system-web1.0-cil libmono-system1.0-cil
  libmono-webbrowser0.5-cil libmono-winforms1.0-cil libmono1.0-cil libmtp8 libnautilus-extension1 libpango1.0-common libperl5.10 libpolkit-gtk-1-0
  libpulse-browse0 librpm1 librpmbuild1 libsdl1.2-dev libsdl1.2debian-pulseaudio libseed0 libstdc++6-4.3-dev libtelepathy-farsight0 libupnp3 libvlccore4
  libxmlrpc-c3 linphone-nox linux-headers-2.6.32-5-amd64 linux-sound-base metacity mono-2.0-devel mono-devel mysql-client-5.1 mysql-query-browser
  mysql-server-5.1 mysql-server-core-5.1 openoffice.org-base-core openoffice.org-core openoffice.org-gcj openoffice.org-report-builder-bin
  openoffice.org-style-andromeda php5-suhosin portmap python-beagle python-brasero python-docky python-encutils python-evince python-gnomeapplet
  python-gtop python-mediaprofiles python-metacity python-totem-plparser seahorse-plugins smbfs speedbar totem-coherence tqsllib1c2a unixcw vlc
  xserver-xorg-video-nv
The following NEW packages will be installed:
  accountsservice acl aisleriot apg aptdaemon-data aptitude-common asterisk-core-sounds-en asterisk-modules asterisk-moh-opsound-gsm at-spi2-core
  ax25-node bluez btrfs-tools caribou caribou-antler chromium chromium-inspector colord console-setup console-setup-linux cpp-4.6 cpp-4.7 crda
  cryptsetup-bin cups-filters db-util db5.1-util dconf-gsettings-backend dconf-service dconf-tools distro-info-data docutils-common docutils-doc enchant
  extlinux finger folks-common fonts-cantarell fonts-droid fonts-freefont-ttf fonts-horai-umefont fonts-lg-aboriginal fonts-liberation fonts-lyx
  fonts-opensymbol fonts-sil-gentium fonts-sil-gentium-basic fonts-sipa-arundina fonts-stix fonts-takao fonts-takao-gothic fonts-takao-mincho
  fonts-thai-tlwg fonts-tlwg-garuda fonts-tlwg-kinnari fonts-tlwg-loma fonts-tlwg-mono fonts-tlwg-norasi fonts-tlwg-purisa fonts-tlwg-sawasdee
  fonts-tlwg-typewriter fonts-tlwg-typist fonts-tlwg-typo fonts-tlwg-umpush fonts-tlwg-waree fonts-umeplus fuse g++-4.7 g++-4.7-multilib gcc-4.6
  gcc-4.6-base gcc-4.7 gcc-4.7-base gcc-4.7-multilib gcj-4.7-base gcj-4.7-jre gcj-4.7-jre-headless gcj-4.7-jre-lib gconf-service gcr
  gir1.2-accountsservice-1.0 gir1.2-atk-1.0 gir1.2-atspi-2.0 gir1.2-caribou-1.0 gir1.2-clutter-1.0 gir1.2-clutter-gst-1.0 gir1.2-cogl-1.0
  gir1.2-coglpango-1.0 gir1.2-evince-3.0 gir1.2-folks-0.6 gir1.2-freedesktop gir1.2-gck-1 gir1.2-gconf-2.0 gir1.2-gcr-3 gir1.2-gdesktopenums-3.0
  gir1.2-gdkpixbuf-2.0 gir1.2-gee-1.0 gir1.2-gkbd-3.0 gir1.2-glib-2.0 gir1.2-gmenu-3.0 gir1.2-gnomebluetooth-1.0 gir1.2-gnomekeyring-1.0
  gir1.2-gst-plugins-base-0.10 gir1.2-gstreamer-0.10 gir1.2-gtk-3.0 gir1.2-gtkclutter-1.0 gir1.2-gtksource-3.0 gir1.2-gtop-2.0 gir1.2-gucharmap-2.90
  gir1.2-javascriptcoregtk-3.0 gir1.2-json-1.0 gir1.2-mutter-3.0 gir1.2-networkmanager-1.0 gir1.2-notify-0.7 gir1.2-panelapplet-4.0 gir1.2-pango-1.0
  gir1.2-peas-1.0 gir1.2-polkit-1.0 gir1.2-rb-3.0 gir1.2-soup-2.4 gir1.2-telepathyglib-0.12 gir1.2-telepathylogger-0.2 gir1.2-totem-1.0
  gir1.2-totem-plparser-1.0 gir1.2-upowerglib-1.0 gir1.2-vte-2.90 gir1.2-webkit-3.0 gir1.2-wnck-3.0 gir1.2-xkl-1.0 git-man gjs gkbd-capplet glchess
  glib-networking glib-networking-common glib-networking-services glines gnect gnibbles gnobots2 gnome-bluetooth gnome-contacts gnome-control-center-data
  gnome-desktop3-data gnome-font-viewer gnome-icon-theme-extras gnome-icon-theme-symbolic gnome-online-accounts gnome-packagekit gnome-packagekit-data
  gnome-shell gnome-shell-common gnome-sudoku gnome-sushi gnome-themes-standard gnome-themes-standard-data gnome-user-share gnome-video-effects gnomine
  gnotravex gnotski gnuplot gnuplot-nox grilo-plugins-0.1 groff growisofs gsettings-desktop-schemas gstreamer0.10-gconf gtali guile-2.0-libs gvfs-common
  gvfs-daemons gvfs-libs hardening-includes hwdata iagno ienglish-common imagemagick-common ioquake3 ioquake3-server iputils-tracepath ipxe-qemu iw
  keyutils kmod krb5-locales lib32itm1 lib32quadmath0 lib32tinfo-dev lib32tinfo5 libaacplus2 libaacs0 libabiword-2.9 libaccountsservice0 libamd2.2.0
  libapache-pom-java libapol4 libapt-inst1.5 libapt-pkg4.12 libaqbanking-plugins-libgwenhywfar60 libaqbanking34 libaqbanking34-plugins libaqhbci20
  libaqofxconnect7 libarchive12 libasprintf0c2 libassuan0 libatk-adaptor libatk-adaptor-data libatk-bridge2.0-0 libatkmm-1.6-1 libatkmm-1.6-dev
  libatspi2.0-0 libaudiofile1 libavahi-ui-gtk3-0 libavcodec53 libavcodec54 libavformat53 libavformat54 libavutil51 libbabl-0.1-0 libbind9-80 libbison-dev
  libblas3 libbluray1 libboost-iostreams1.49.0 libboost-program-options1.49.0 libboost-python1.49.0 libboost-serialization1.49.0 libboost-thread1.49.0
  libbrasero-media3-1 libcairo-gobject2 libcairo-script-interpreter2 libcamel-1.2-33 libcanberra-dev libcanberra-gtk3-0 libcanberra-gtk3-module
  libcanberra-pulse libcapi20-3 libcaribou-common libcaribou-gtk-module libcaribou-gtk3-module libcaribou0 libccrtp0 libcdio-cdda1 libcdio-paranoia1
  libcdio13 libcfg4 libchamplain-0.12-0 libchamplain-gtk-0.12-0 libcheese-gtk21 libcheese3 libclass-factory-util-perl libclass-isa-perl libclass-load-perl
  libclass-load-xs-perl libclutter-1.0-common libclutter-gst-1.0-0 libclutter-gtk-1.0-0 libclutter-imcontext-0.1-0 libclutter-imcontext-0.1-bin
  libcluttergesture-0.0.2-0 libcmis-0.2-0 libcogl-common libcogl-pango0 libcogl9 libcolord1 libcommons-parent-java libconfdb4 libcoroipcc4 libcoroipcs4
  libcpg4 libcryptsetup4 libcrystalhd3 libcupsfilters1 libcw3 libdata-alias-perl libdatetime-format-builder-perl libdatetime-format-iso8601-perl
  libdb-java libdb5.1 libdb5.1-dev libdb5.1-java libdb5.1-java-jni libdbus-c++-1-0 libdbus-glib1.0-cil libdbus1.0-cil libdconf0 libdee-1.0-4
  libdevel-partialdump-perl libdevhelp-3-0 libdevmapper-event1.02.1 libdistro-info-perl libdmapsharing-3.0-2 libdns88 libdotconf1.0 libdvbpsi7
  libebackend-1.2-2 libebml3 libebook-1.2-13 libecal-1.2-11 libecore1 libedata-book-1.2-13 libedata-cal-1.2-15 libedataserver-1.2-16
  libedataserverui-3.0-1 libeina1 libemail-valid-perl libencode-locale-perl libepc-1.0-3 libepc-ui-1.0-3 libept1.4.12 libescpr1 libev4
  libeval-closure-perl libevdocument3-4 libevent-2.0-5 libevent-perl libevs4 libevview3-3 libexiv2-12 libexosip2-7 libexporter-lite-perl
  libexttextcat-data libexttextcat0 libfakechroot libfarstream-0.1-0 libfdk-aac0 libfdt1 libfile-basedir-perl libfile-desktopentry-perl
  libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfltk-images1.3 libfltk1.3 libfolks-eds25 libfolks-telepathy25 libfolks25
  libfont-afm-perl libgail-3-0 libgcj13 libgcj13-awt libgck-1-0 libgconf-2-4 libgconf2-doc libgcr-3-1 libgcr-3-common libgd2-xpm libgdata13
  libgdata2.1-cil libgdict-common libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgdk-pixbuf2.0-dev libgegl-0.2-0 libgeocode-glib0 libgettextpo0 libgexiv2-1
  libgirepository-1.0-1 libgjs0b libgkeyfile1.0-cil libgladeui-2-0 libgladeui-common libglapi-mesa libglew1.7 libglib2.0-bin libgmime-2.6-0
  libgmime2.6-cil libgmp10 libgnome-bluetooth10 libgnome-desktop-3-2 libgnome-keyring-common libgnome-media-profiles-3.0-0 libgnome-menu-3-0 libgnomekbd7
  libgnutls-openssl27 libgnutlsxx27 libgoa-1.0-0 libgoa-1.0-common libgphoto2-l10n libgraphite2-2.0.0 libgrilo-0.1-0 libgs9 libgs9-common libgssdp-1.0-3
  libgstreamer-plugins-bad0.10-0 libgtk-3-0 libgtk-3-bin libgtk-3-common libgtk-3-dev libgtk-3-doc libgtk-sharp-beans-cil libgtk-vnc-2.0-0
  libgtkhtml-4.0-0 libgtkhtml-4.0-common libgtkhtml-editor-4.0-0 libgtkmm-3.0-1 libgtksourceview-3.0-0 libgtksourceview-3.0-common libgucharmap-2-90-7
  libgudev1.0-cil libgupnp-1.0-4 libgupnp-av-1.0-2 libgupnp-igd-1.0-4 libgusb2 libgvnc-1.0-0 libgweather-3-0 libgwenhywfar-data libgwenhywfar60 libgxps2
  libhcrypto4-heimdal libheimbase1-heimdal libhtml-form-perl libhtml-format-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
  libhttp-message-perl libhttp-negotiate-perl libhunspell-1.3-0 libicu48 libimobiledevice2 libio-aio-perl libisc84 libisccc80 libisccfg82 libiscsi1
  libiso9660-8 libisoburn1 libitm1 libjavascriptcoregtk-1.0-0 libjavascriptcoregtk-3.0-0 libjbig0 libjs-sphinxdoc libjs-underscore libjson0 libjte1
  libkadm5clnt-mit8 libkadm5srv-mit8 libkarma0 libkdb5-6 libkmod2 libkpathsea6 liblapack3 liblavfile-2.0-0 liblavjpeg-2.0-0 liblavplay-2.0-0 liblcms2-2
  liblensfun-data liblensfun0 liblinear-tools liblinear1 liblinphone4 liblockfile-bin liblogsys4 liblvm2app2.2 liblwp-mediatypes-perl
  liblwp-protocol-https-perl liblwres80 liblzma5 libmaa3 libmagick++5 libmagickcore5 libmagickcore5-extra libmagickwand5 libmath-bigint-perl
  libmath-round-perl libmatroska5 libmediastreamer1 libmhash2 libminiupnpc5 libmission-control-plugins0 libmjpegutils-2.0-0 libmodule-implementation-perl
  libmodule-runtime-perl libmono-2.0-1 libmono-2.0-dev libmono-accessibility4.0-cil libmono-cairo4.0-cil libmono-codecontracts4.0-cil
  libmono-compilerservices-symbolwriter4.0-cil libmono-corlib4.0-cil libmono-csharp4.0-cil libmono-custommarshalers4.0-cil libmono-data-tds4.0-cil
  libmono-debugger-soft2.0-cil libmono-debugger-soft4.0-cil libmono-http4.0-cil libmono-i18n-cjk4.0-cil libmono-i18n-mideast4.0-cil
  libmono-i18n-other4.0-cil libmono-i18n-rare4.0-cil libmono-i18n-west4.0-cil libmono-i18n4.0-all libmono-i18n4.0-cil libmono-ldap4.0-cil
  libmono-management4.0-cil libmono-messaging-rabbitmq4.0-cil libmono-messaging4.0-cil libmono-microsoft-build-engine4.0-cil
  libmono-microsoft-build-framework4.0-cil libmono-microsoft-build-tasks-v4.0-4.0-cil libmono-microsoft-build-utilities-v4.0-4.0-cil
  libmono-microsoft-csharp4.0-cil libmono-microsoft-visualc10.0-cil libmono-microsoft-web-infrastructure1.0-cil libmono-npgsql4.0-cil
  libmono-opensystem-c4.0-cil libmono-oracle4.0-cil libmono-peapi4.0-cil libmono-posix4.0-cil libmono-rabbitmq4.0-cil libmono-relaxng4.0-cil
  libmono-security4.0-cil libmono-sharpzip4.84-cil libmono-simd4.0-cil libmono-sqlite4.0-cil libmono-system-componentmodel-composition4.0-cil
  libmono-system-componentmodel-dataannotations4.0-cil libmono-system-configuration-install4.0-cil libmono-system-configuration4.0-cil
  libmono-system-core4.0-cil libmono-system-data-datasetextensions4.0-cil libmono-system-data-linq4.0-cil libmono-system-data-services-client4.0-cil
  libmono-system-data-services4.0-cil libmono-system-data4.0-cil libmono-system-design4.0-cil libmono-system-drawing-design4.0-cil
  libmono-system-drawing4.0-cil libmono-system-dynamic4.0-cil libmono-system-enterpriseservices4.0-cil libmono-system-identitymodel-selectors4.0-cil
  libmono-system-identitymodel4.0-cil libmono-system-ldap4.0-cil libmono-system-management4.0-cil libmono-system-messaging4.0-cil
  libmono-system-net4.0-cil libmono-system-numerics4.0-cil libmono-system-runtime-caching4.0-cil libmono-system-runtime-durableinstancing4.0-cil
  libmono-system-runtime-serialization-formatters-soap4.0-cil libmono-system-runtime-serialization4.0-cil libmono-system-runtime4.0-cil
  libmono-system-security4.0-cil libmono-system-servicemodel-discovery4.0-cil libmono-system-servicemodel-routing4.0-cil
  libmono-system-servicemodel-web4.0-cil libmono-system-servicemodel4.0-cil libmono-system-serviceprocess4.0-cil libmono-system-transactions4.0-cil
  libmono-system-web-abstractions4.0-cil libmono-system-web-applicationservices4.0-cil libmono-system-web-dynamicdata4.0-cil
  libmono-system-web-extensions-design4.0-cil libmono-system-web-extensions4.0-cil libmono-system-web-routing4.0-cil libmono-system-web-services4.0-cil
  libmono-system-web4.0-cil libmono-system-windows-forms-datavisualization4.0-cil libmono-system-windows-forms4.0-cil libmono-system-xaml4.0-cil
  libmono-system-xml-linq4.0-cil libmono-system-xml4.0-cil libmono-system4.0-cil libmono-tasklets4.0-cil libmono-web4.0-cil libmono-webbrowser2.0-cil
  libmono-webbrowser4.0-cil libmono-webmatrix-data4.0-cil libmono-windowsbase4.0-cil libmount1 libmozjs10d libmozjs17d libmozjs185-1.0 libmpeg2encpp-2.0-0
  libmplex2-2.0-0 libmtdev1 libmtp-common libmtp-runtime libmtp9 libmupen64plus2 libmusicbrainz-discid-perl libmusicbrainz5-0 libmutter0 libmx-1.0-2
  libmx-bin libmx-common libmysqlclient18 libnatpmp1 libnautilus-extension1a libnet-domain-tld-perl libnet-http-perl libnet-ip-minimal-perl libnetcf1
  libnetfilter-conntrack3 libnettle4 libnewtonsoft-json4.5-cil libnice10 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 libnm-glib4 libnm-gtk-common
  libnm-gtk0 libnm-util2 libnotify4 libnspr4 libnss-winbind libnss3 libnuma1 libnunit2.6-cil liboauth0 libodbc1 liboobs-1-5 libopal3.10.4 libopenal-data
  libopus0 libosip2-7 libp11-2 libp11-kit-dev libp11-kit0 libpackage-stash-xs-perl libpackagekit-glib2-14 libpam-cap libpam-modules-bin libpam-winbind
  libpanel-applet-4-0 libparams-classify-perl libpcre3-dev libpcrecpp0 libpeas-1.0-0 libpeas-common libperl5.14 libpipeline1 libpload4 libpodofo0.9.0
  libpoe-component-resolver-perl libpoppler-glib8 libpoppler19 libportsmf0 libpostproc52 libprocps0 libpst4 libpt2.10.4 libptexenc1 libpython2.7
  libqt4-declarative libqtassistantclient4 libqtdbus4 libqtwebkit4 libquadmath0 libquicktime2 libquorum4 libquvi-scripts libquvi7 libraptor2-0 librasqal3
  libraw5 libregexp-reggrp-perl libreoffice libreoffice-base libreoffice-base-core libreoffice-calc libreoffice-common libreoffice-core libreoffice-draw
  libreoffice-emailmerge libreoffice-evolution libreoffice-filter-binfilter libreoffice-filter-mobiledev libreoffice-gnome libreoffice-gtk
  libreoffice-help-en-us libreoffice-impress libreoffice-java-common libreoffice-math libreoffice-officebean libreoffice-report-builder-bin
  libreoffice-style-galaxy libreoffice-style-tango libreoffice-writer libresid-builder0c2a librest-0.7-0 librest-extras-0.7-0 librhythmbox-core6 librpm3
  librpmbuild3 librpmio3 librpmsign1 libruby1.9.1 libsaamf3 libsackpt3 libsaclm3 libsaevt3 libsalck3 libsam4 libsamsg4 libsane-common
  libsane-extras-common libsatmr3 libsbsms10 libseed-gtk3-0 libsidplay2 libsigsegv2 libsocialweb-client2 libsocialweb-common libsocialweb-service
  libsocialweb0 libsocket-getaddrinfo-perl libsocket-perl libsonic0 libsoundtouch0 libsox2 libspeechd2 libspice-client-glib-2.0-1
  libspice-client-gtk-2.0-1 libspice-server1 libssl-doc libssl1.0.0 libstdc++6-4.7-dev libsvm-tools libswitch-perl libswscale2 libsystemd-daemon0
  libsystemd-login0 libtagc0 libtelepathy-farstream2 libtelepathy-logger2 libtest-warn-perl libtinfo-dev libtinfo5 libtirpc1 libtokyocabinet9 libtotem-pg4
  libtotem0 libtqsllib1 libtracker-sparql-0.14-0 libtree-dagnode-perl libts-dev libucommon5 libumfpack5.4.0 libunique-3.0-0 libupnp6 libusbredirhost1
  libusbredirparser0 libv4lconvert0 libverto-libev1 libverto1 libvisio-0.0-0 libvlccore5 libvo-aacenc0 libvo-amrwbenc0 libvorbisidec1 libvotequorum4
  libvpx1 libvte-2.90-9 libvte-2.90-common libwacom-common libwacom2 libwebkitgtk-1.0-0 libwebkitgtk-1.0-common libwebkitgtk-3.0-0 libwebkitgtk-3.0-common
  libwebp2 libwebrtc-audio-processing-0 libwildmidi-config libwireshark-data libwireshark2 libwiretap2 libwnck-3-0 libwnck-3-common libwpd-0.9-9
  libwpg-0.2-2 libwps-0.2-2 libwsutil2 libwv-1.2-4 libwww-robotrules-perl libx11-doc libx11-protocol-perl libx264-123 libx264-124 libx264-130 libx264-132
  libxalan2-java libxcb-composite0 libxcb-glx0 libxcb-shape0 libxcb-shm0-dev libxcb-util0 libxen-4.1 libxml-commons-external-java
  libxml-commons-resolver1.1-java libxml-sax-base-perl libxmlrpc-c++4 libxmlrpc-core-c3 libxz-java libyajl2 libyaml-0-2 libyaml-perl libyelp0 libzrtpcpp2
  libzvbi-common libzvbi0 lightsoff linphone-nogtk linux-headers-3.2.0-4-amd64 linux-headers-3.2.0-4-common linux-headers-amd64 linux-image-3.2.0-4-amd64
  linux-image-amd64 linux-kbuild-3.2 live-boot-doc live-config-doc live-manual-html mahjongg memtest86+ minissdpd mono-4.0-gac mono-dmcs mscompress
  multiarch-support mupen64plus-audio-all mupen64plus-audio-sdl mupen64plus-data mupen64plus-input-all mupen64plus-input-sdl mupen64plus-rsp-all
  mupen64plus-rsp-hle mupen64plus-rsp-z64 mupen64plus-ui-console mupen64plus-video-all mupen64plus-video-arachnoid mupen64plus-video-glide64
  mupen64plus-video-rice mupen64plus-video-z64 mutter-common mysql-client-5.5 mysql-server-5.5 mysql-server-core-5.5 mythes-en-us openarena-081-maps
  openarena-081-misc openarena-081-players openarena-081-players-mature openarena-081-textures openarena-085-data openarena-088-data packagekit
  packagekit-backend-aptcc packagekit-tools planner-data planner-doc poppler-data printer-driver-all printer-driver-c2050 printer-driver-c2esp
  printer-driver-cjet printer-driver-escpr printer-driver-foo2zjs printer-driver-gutenprint printer-driver-hpcups printer-driver-hpijs
  printer-driver-m2300w printer-driver-min12xxw printer-driver-pnm2ppa printer-driver-postscript-hp printer-driver-ptouch printer-driver-pxljr
  printer-driver-sag-gdi printer-driver-splix psutils python-aptdaemon.gtk3widgets python-aptdaemon.gtkwidgets python-bzrlib python-dbus-dev
  python-debianbts python-defer python-dnspython python-fpconst python-gi python-gi-cairo python-gi-dev python-gobject-2 python-gobject-2-dev
  python-keyring python-launchpadlib python-lazr.restfulclient python-lazr.uri python-liblarch python-liblarch-gtk python-magic python-oauth
  python-packagekit python-pyatspi2 python-pyparsing python-repoze.lru python-routes python-setools python-simplejson python-soappy python-speechd
  python-spice-client-gtk python-wadllib python-webob python-zeitgeist python2.7 python2.7-dev python2.7-minimal qdbus quadrapassel remmina-common
  rhythmbox-data rpcbind rtkit ruby ruby1.9.1 shotwell-common smartdimmer software-properties-common sound-theme-freedesktop speech-dispatcher
  sphinx-common sphinx-doc swell-foop syslinux-themes-debian syslinux-themes-debian-wheezy tdb-tools telepathy-haze telepathy-logger telepathy-rakia
  tex-gyre ttf-marvosym wireless-regdb xbrlapi xorg-sgml-doctools xorriso xserver-xorg-input-mouse xserver-xorg-input-vmmouse xulrunner-17.0 yelp-xsl
  zeitgeist-core zenity-common
The following packages have been kept back:
  acroread-debian-files db4.8-util hibernate ia32-libs ia32-libs-gtk libboost-dev libboost-serialization-dev opensc wine
The following packages will be upgraded:
  abcde abiword abiword-common abiword-plugin-grammar abiword-plugin-mathview acpi acpi-fakekey acpi-support acpi-support-base acpid acroread-data
  acroread-dictionary-en acroread-l10n-en adduser alacarte alsa-base alsa-utils amb-plugins anacron analog ant ant-optional apache2 apache2-doc
  apache2-mpm-prefork apache2-utils apache2.2-bin apache2.2-common app-install-data apt apt-file apt-utils apt-xapian-index aptdaemon aptitude
  aqbanking-tools aspell aspell-en asterisk asterisk-config asterisk-core-sounds-en-gsm asterisk-doc asterisk-voicemail astyle at audacity audacity-data
  augeas-lenses augeas-tools autoconf autoconf-doc automake automake1.9 autopoint autotools-dev avahi-autoipd avahi-daemon avidemux avidemux-common
  avidemux-plugins aview ax25-tools banshee baobab base-files base-passwd bash bash-completion bc bind9-doc bind9-host bind9utils binfmt-support binutils
  bison bluez-cups bogofilter bogofilter-bdb bogofilter-common brasero brasero-common bridge-utils browser-plugin-gnash bsd-mailx bsdmainutils bsdutils
  busybox buzztard buzztard-data bwidget bzip2 bzr bzrtools ca-certificates calibre calibre-bin ccache cd-discid cdebootstrap cdparanoia cdrdao
  checkpolicy cheese cheese-common chromium-browser chromium-browser-inspector cifs-utils cl-asdf cli-common clisp comerr-dev common-lisp-controller
  console-common console-data console-tools consolekit coreutils cowbuilder cowdancer cpio cpp cpp-4.4 cpufrequtils cracklib-runtime crawl-common
  crawl-tiles cron cryptsetup cups cups-bsd cups-client cups-common cups-driver-gutenprint cups-pk-helper cups-ppdc cupsddk curl curlftpfs cvs cw dash
  dasher dasher-data dbus dbus-x11 dc dcraw dctrl-tools debconf debconf-i18n debhelper debian-archive-keyring debian-faq debian-keyring debianutils debirf
  debootstrap desktop-base desktop-file-utils devhelp devhelp-common devscripts dialog dict dictionaries-common diffstat diffutils djtools dkms dmidecode
  dmsetup dnsmasq-base dnsutils doc-debian docbook docbook-dsssl docbook-to-man docbook-utils docbook-xml docbook-xsl docbook-xsl-doc-html docky dosemu
  dosfstools dpatch dpkg dpkg-dev dput dvd+rw-tools dvi2ps dynagen dynamips e2fslibs e2fsprogs ebtables ed eject ekiga emacs23-bin-common emacs23-common
  emacs23-nox emacsen-common emdebian-archive-keyring empathy empathy-common eog epiphany-browser epiphany-browser-data epiphany-extensions esound-common
  espeak espeak-data ethtool evince evince-common evolution evolution-common evolution-data-server evolution-data-server-common evolution-exchange
  evolution-plugins evolution-webcal exif exiftags exim4 exim4-base exim4-config exim4-daemon-light exiv2 f-spot fakechroot fakeroot fancontrol fceu
  fcrackzip fdupes feynmf file file-roller finch findutils firmware-iwlwifi firmware-linux-free firmware-linux-nonfree flac flashrom fldigi flex
  fontconfig fontconfig-config foo2zjs foomatic-db foomatic-db-engine foomatic-db-gutenprint foomatic-filters fping freedesktop-sound-theme freeglut3
  freetds-common ftp fuse-utils g++ g++-4.4 g++-4.4-multilib g++-multilib gawk gcalctool gcc gcc-4.4 gcc-4.4-base gcc-4.4-doc gcc-4.4-multilib
  gcc-doc-base gcc-multilib gcj-jre gcj-jre-headless gconf-defaults-service gconf-editor gconf2 gconf2-common gddrescue gdebi gdebi-core gedit
  gedit-common gedit-plugins genisoimage geoclue geoclue-hostip geoclue-localnet geoclue-manual geoclue-yahoo geoip-database gettext gettext-base
  ghostscript ghostscript-cups gimp gimp-data git git-buildpackage git-core git-svn gitk gksu glade gnash gnash-common gnash-opengl
  gnome-accessibility-themes gnome-applets-data gnome-backgrounds gnome-cards-data gnome-common gnome-control-center gnome-control-center-dev
  gnome-desktop-data gnome-dictionary gnome-disk-utility gnome-do gnome-do-plugins gnome-doc-utils gnome-games gnome-games-data gnome-games-extra-data
  gnome-icon-theme gnome-js-common gnome-keyring gnome-mag gnome-media gnome-menus gnome-nettool gnome-orca gnome-panel-data gnome-pkg-tools
  gnome-power-manager gnome-rdp gnome-screensaver gnome-screenshot gnome-search-tool gnome-session gnome-session-bin gnome-session-canberra
  gnome-session-common gnome-settings-daemon gnome-settings-daemon-dev gnome-system-log gnome-system-monitor gnome-system-tools gnome-terminal
  gnome-terminal-data gnome-user-guide gnomint gnu-fdisk gnucash-docs gnuchess gnumeric gnumeric-common gnupg gnupg-agent gocr google-talkplugin gparted
  gpgv gpredict gpscorrelate grep groff-base grub-common grub-legacy gsfonts-x11 gsmartcontrol gstreamer0.10-alsa gstreamer0.10-buzztard
  gstreamer0.10-buzztard-doc gstreamer0.10-doc gstreamer0.10-ffmpeg gstreamer0.10-ffmpeg-dbg gstreamer0.10-fluendo-mp3 gstreamer0.10-gnonlin
  gstreamer0.10-gnonlin-dbg gstreamer0.10-gnonlin-doc gstreamer0.10-nice gstreamer0.10-plugins-bad gstreamer0.10-plugins-bad-dbg
  gstreamer0.10-plugins-bad-doc gstreamer0.10-plugins-base gstreamer0.10-plugins-base-apps gstreamer0.10-plugins-base-dbg gstreamer0.10-plugins-base-doc
  gstreamer0.10-plugins-good gstreamer0.10-plugins-good-dbg gstreamer0.10-plugins-good-doc gstreamer0.10-plugins-ugly gstreamer0.10-plugins-ugly-dbg
  gstreamer0.10-plugins-ugly-doc gstreamer0.10-pulseaudio gstreamer0.10-tools gstreamer0.10-x gtg gthumb gthumb-data gtk2-engines gtk2-engines-pixbuf
  gucharmap guile-1.6 guile-1.6-libs guile-1.8-libs gvfs gvfs-backends gvfs-bin gzip hal hamster-applet hardinfo hddtemp hdparm hfsprogs hostname hp-ppd
  hpijs hplip hplip-cups hplip-data htmldoc htmldoc-common iamerican ibritish iceweasel ifupdown ijsgutenprint imagemagick imagemagick-doc info
  initramfs-tools initscripts inkscape insserv install-info installation-report intltool iotop iproute ipsec-tools iptables iptraf iputils-ping
  ircd-hybrid irssi isc-dhcp-client isc-dhcp-common isc-dhcp-server iscsitarget-dkms iso-codes ispell jack jadetex java-common jigdo-file keyanalyze
  keyboard-configuration keychain klibc-utils kpartx krb5-admin-server krb5-auth-dialog krb5-config krb5-doc krb5-kdc krb5-kdc-ldap krb5-multidev
  krb5-pkinit krb5-user lacheck lame latex-beamer latex-xcolor less lesstif2 lesstif2-dev lib32asound2 lib32bz2-1.0 lib32gcc1 lib32gomp1 lib32ncurses5
  lib32ncurses5-dev lib32nss-mdns lib32readline5 lib32stdc++6 lib32v4l-0 lib32z1 lib32z1-dev liba52-0.7.4 libaa1 libaa1-dev libacl1 libaften0
  libaiksaurus-1.2-0c2a libaiksaurus-1.2-data libaiksaurusgtk-1.2-0c2a libaio1 libalgorithm-diff-xs-perl libany-moose-perl libanyevent-perl libao-common
  libao4 libapache-dbi-perl libapache2-mod-apreq2 libapache2-mod-dnssd libapache2-mod-perl2 libapache2-mod-php5 libapache2-mod-python
  libapache2-request-perl libappconfig-perl libapr1 libapreq2 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libapt-pkg-perl libaqbanking-data
  libarchive-zip-perl libart-2.0-2 libart-2.0-dev libart2.0-cil libasn1-8-heimdal libasound2 libasound2-dev libasound2-plugins libaspell15 libass4
  libasync-interrupt-perl libasyncns0 libatasmart4 libatk1.0-0 libatk1.0-data libatk1.0-dev libatk1.0-doc libatspi1.0-0 libattr1 libaudio-dev libaudio2
  libaudiofile-dev libaudit0 libaugeas0 libavahi-client-dev libavahi-client3 libavahi-common-data libavahi-common-dev libavahi-common3 libavahi-core7
  libavahi-glib-dev libavahi-glib1 libavahi-gobject0 libavahi-ui0 libavc1394-0 libax25 libb-hooks-endofscope-perl libb-keywords-perl libbind9-60
  libblas3gf libblkid1 libbluetooth3 libbml0 libboo2.0.9-cil libbrlapi0.5 libbs2b0 libbsd0 libburn4 libbusiness-paypal-api-perl
  libbusiness-tax-vat-validation-perl libbuzztard0 libbz2-1.0 libc-ares2 libc-bin libc-dev-bin libc6 libc6-dev libc6-dev-i386 libc6-i386 libcaca-dev
  libcaca0 libcache-fastmmap-perl libcairo-perl libcairo2 libcairo2-dev libcairomm-1.0-1 libcairomm-1.0-dev libcanberra-gtk0 libcanberra0 libcap-ng0
  libcap2 libcap2-bin libcapture-tiny-perl libccid libcdaudio1 libcddb-get-perl libcddb2 libcdparanoia0 libcdt4 libchm-bin libchm1 libck-connector0
  libclass-c3-perl libclass-c3-xs-perl libclass-insideout-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-methodmaker-perl
  libclone-perl libclutter-1.0-0 libcolamd2.7.1 libcolor-calc-perl libcomedi0 libcomerr2 libcommon-sense-perl libcommons-beanutils-java
  libcommons-collections3-java libcommons-compress-java libcommons-digester-java libcommons-logging-java libconfig-inifiles-perl libconfig-json-perl
  libconfig-tiny-perl libconsole libcontextual-return-perl libconvert-asn1-perl libcoro-perl libcorosync4 libcpufreq-dev libcpufreq0 libcrack2 libcroco3
  libcrypt-openssl-bignum-perl libcrypt-openssl-random-perl libcrypt-openssl-rsa-perl libcrypt-passwdmd5-perl libcrypt-ssleay-perl libcss-minifier-xs-perl
  libcss-packer-perl libcups2 libcupscgi1 libcupsdriver1 libcupsimage2 libcupsmime1 libcupsppdc1 libcurl3 libcurl3-gnutls libcurses-perl libcwidget3
  libdata-optlist-perl libdata-structure-util-perl libdata-visitor-perl libdatetime-format-http-perl libdatetime-perl libdatetime-set-perl
  libdatetime-timezone-perl libdatrie1 libdb-dev libdb-je-java libdbd-mysql-perl libdbi-perl libdbus-1-3 libdbus-1-dev libdbus-glib-1-2 libdbus-glib-1-dev
  libdc1394-22 libdca0 libdebian-installer-extra4 libdebian-installer4 libdevel-globaldestruction-perl libdevel-size-perl libdevel-stacktrace-perl
  libdevel-symdump-perl libdevmapper1.02.1 libdigest-hmac-perl libdirac-decoder0 libdirac-encoder0 libdirectfb-1.2-9 libdirectfb-extra libdiscid0
  libdjvulibre-text libdjvulibre21 libdns69 libdpkg-perl libdrm-dev libdrm-intel1 libdrm-nouveau1a libdrm-radeon1 libdrm2 libdv4 libdvdcss2 libdvdnav4
  libdvdread4 libedit2 libelf1 libelfg0 libemail-address-perl libenca0 libenchant1c2a libengine-pkcs11-openssl libepc-common libesd0 libesd0-dev
  libespeak1 libevolution libexception-class-perl libexempi3 libexif12 libexpat1 libexpat1-dev libexpect-perl libfaac0 libfaad2 libfcgi-perl libfcgi0ldbl
  libffi-dev libffi5 libfftw3-3 libfile-homedir-perl libfile-libmagic-perl libfile-mmagic-perl libfile-slurp-perl libfile-which-perl libfilter-perl
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  xfonts-terminus-oblique xfonts-thai xfonts-thai-etl xfonts-thai-manop xfonts-thai-nectec xfonts-thai-poonlap xfonts-thai-vor xfonts-tipa xfonts-unifont
  xfonts-utils xfonts-wqy xindy xindy-rules xinit xkb-data xml-core xorg xorg-docs-core xoscope xsane xsane-common xserver-common xserver-xephyr
  xserver-xorg xserver-xorg-core xserver-xorg-dev xserver-xorg-input-all xserver-xorg-input-evdev xserver-xorg-input-synaptics xserver-xorg-input-wacom
  xserver-xorg-video-apm xserver-xorg-video-ark xserver-xorg-video-ati xserver-xorg-video-chips xserver-xorg-video-cirrus xserver-xorg-video-fbdev
  xserver-xorg-video-i128 xserver-xorg-video-intel xserver-xorg-video-mach64 xserver-xorg-video-mga xserver-xorg-video-neomagic
  xserver-xorg-video-openchrome xserver-xorg-video-r128 xserver-xorg-video-radeon xserver-xorg-video-rendition xserver-xorg-video-s3
  xserver-xorg-video-s3virge xserver-xorg-video-savage xserver-xorg-video-siliconmotion xserver-xorg-video-sis xserver-xorg-video-sisusb
  xserver-xorg-video-tdfx xserver-xorg-video-trident xserver-xorg-video-tseng xserver-xorg-video-vesa xserver-xorg-video-vmware xserver-xorg-video-voodoo
  xsltproc xterm xtightvncviewer xtrans-dev xutils-dev xz-utils yelp yum zenity zip zlib1g zlib1g-dev
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12 August 2013

Joey Hess: good morning

panorama of sunrise Woken at 3 am by fil singing "Join Us Now And Share The Software" (all verses!) I could not get back to sleep and spent 3 hours thinking up a new take on the hopelessly blocked dpkg-source v3 (git) format. A diagram of the new plan, which should meet all ftpmaster requirements, is posted in Hacklab 1. I am looking for reviewers. A rather hard to read photo (DebConf needs mandatory whiteboards!) is available here: Fil has paid me back in full for his drunken carousing by gifting me a Rhombus-Tech system on a chip on a PCMCIA card. I've checked this new computer, which features a modern multicore ARM CPU, into my wallet. And that's 10% of what went on today at DebConf for me, and we've not even gotten to the cheese and wine party tonight.

15 January 2013

Petter Reinholdtsen: Using modalias info to find packages handling my hardware

Yesterday, I wrote about the modalias values provided by the Linux kernel following my hope for better dongle support in Debian. Using this knowledge, I have tested how modalias values attached to package names can be used to map packages to hardware. This allow the system to look up and suggest relevant packages when I plug in some new hardware into my machine, and replace discover and discover-data as the database used to map hardware to packages. I create a modaliases file with entries like the following, containing package name, kernel module name (if relevant, otherwise the package name) and globs matching the relevant hardware modalias.
Package: package-name
Modaliases: module(modaliasglob, modaliasglob, modaliasglob)
It is fairly trivial to write code to find the relevant packages for a given modalias value using this file. An entry like this would suggest the video and picture application cheese for many USB web cameras (interface bus class 0E01):
Package: cheese
Modaliases: cheese(usb:v*p*d*dc*dsc*dp*ic0Eisc01ip*)
An entry like this would suggest the pcmciautils package when a CardBus bridge (bus class 0607) PCI device is present:
Package: pcmciautils
Modaliases: pcmciautils(pci:v*d*sv*sd*bc06sc07i*)
An entry like this would suggest the package colorhug-client when plugging in a ColorHug with USB IDs 04D8:F8DA:
Package: colorhug-client
Modaliases: colorhug-client(usb:v04D8pF8DAd*)
I believe the format is compatible with the format of the Packages file in the Debian archive. Ubuntu already uses their Packages file to store their mappings from packages to hardware. By adding a XB-Modaliases: header in debian/control, any .deb can announce the hardware it support in a way my prototype understand. This allow those publishing packages in an APT source outside the Debian archive as well as those backporting packages to make sure the hardware mapping are included in the package meta information. I've tested such header in the pymissile package, and its modalias mapping is working as it should with my prototype. It even made it to Ubuntu Raring. To test if it was possible to look up supported hardware using only the shell tools available in the Debian installer, I wrote a shell implementation of the lookup code. The idea is to create files for each modalias and let the shell do the matching. Please check out and try the hw-support-lookup shell script. It run without any extra dependencies and fetch the hardware mappings from the Debian archive and the subversion repository where I currently work on my prototype. When I use it on a machine with a yubikey inserted, it suggest to install yubikey-personalization:
% ./hw-support-lookup
yubikey-personalization
%
When I run it on my Thinkpad X40 with a PCMCIA/CardBus slot, it propose to install the pcmciautils package:
% ./hw-support-lookup
pcmciautils
%
If you know of any hardware-package mapping that should be added to my database, please tell me about it. It could be possible to generate several of the mappings between packages and hardware. One source would be to look at packages with kernel modules, ie packages with *.ko files in /lib/modules/, and extract their modalias information. Another would be to look at packages with udev rules, ie packages with files in /lib/udev/rules.d/, and extract their vendor/model information to generate a modalias matching rule. I have not tested any of these to see if it work. If you want to help implementing a system to let us propose what packages to install when new hardware is plugged into a Debian machine, please send me an email or talk to me on #debian-devel.

14 January 2013

Petter Reinholdtsen: Modalias strings - a practical way to map "stuff" to hardware

While looking into how to look up Debian packages based on hardware information, to find the packages that support a given piece of hardware, I refreshed my memory regarding modalias values, and decided to document the details. Here are my findings so far, also available in the Debian Edu subversion repository: Modalias decoded This document try to explain what the different types of modalias values stands for. It is in part based on information from <URL: https://wiki.archlinux.org/index.php/Modalias >, <URL: http://unix.stackexchange.com/questions/26132/how-to-assign-usb-driver-to-device >, <URL: http://code.metager.de/source/history/linux/stable/scripts/mod/file2alias.c > and <URL: http://cvs.savannah.gnu.org/viewvc/dmidecode/dmidecode.c?root=dmidecode&view=markup >. The modalias entries for a given Linux machine can be found using this shell script:
find /sys -name modalias -print0   xargs -0 cat   sort -u
The supported modalias globs for a given kernel module can be found using modinfo:
% /sbin/modinfo psmouse   grep alias:
alias:          serio:ty05pr*id*ex*
alias:          serio:ty01pr*id*ex*
%
PCI subtype A typical PCI entry can look like this. This is an Intel Host Bridge memory controller:
pci:v00008086d00002770sv00001028sd000001ADbc06sc00i00
This represent these values:
 v   00008086  (vendor)
 d   00002770  (device)
 sv  00001028  (subvendor)
 sd  000001AD  (subdevice)
 bc  06        (bus class)
 sc  00        (bus subclass)
 i   00        (interface)
The vendor/device values are the same values outputted from 'lspci -n' as 8086:2770. The bus class/subclass is also shown by lspci as 0600. The 0600 class is a host bridge. Other useful bus values are 0300 (VGA compatible card) and 0200 (Ethernet controller). Not sure how to figure out the interface value, nor what it means. USB subtype Some typical USB entries can look like this. This is an internal USB hub in a laptop:
usb:v1D6Bp0001d0206dc09dsc00dp00ic09isc00ip00
Here is the values included in this alias:
 v    1D6B  (device vendor)
 p    0001  (device product)
 d    0206  (bcddevice)
 dc     09  (device class)
 dsc    00  (device subclass)
 dp     00  (device protocol)
 ic     09  (interface class)
 isc    00  (interface subclass)
 ip     00  (interface protocol)
The 0900 device class/subclass means hub. Some times the relevant class is in the interface class section. For a simple USB web camera, these alias entries show up:
usb:v0AC8p3420d5000dcEFdsc02dp01ic01isc01ip00
usb:v0AC8p3420d5000dcEFdsc02dp01ic01isc02ip00
usb:v0AC8p3420d5000dcEFdsc02dp01ic0Eisc01ip00
usb:v0AC8p3420d5000dcEFdsc02dp01ic0Eisc02ip00
Interface class 0E01 is video control, 0E02 is video streaming (aka camera), 0101 is audio control device and 0102 is audio streaming (aka microphone). Thus this is a camera with microphone included. ACPI subtype The ACPI type is used for several non-PCI/USB stuff. This is an IR receiver in a Thinkpad X40:
acpi:IBM0071:PNP0511:
The values between the colons are IDs. DMI subtype The DMI table contain lots of information about the computer case and model. This is an entry for a IBM Thinkpad X40, fetched from /sys/devices/virtual/dmi/id/modalias:
dmi:bvnIBM:bvr1UETB6WW(1.66):bd06/15/2005:svnIBM:pn2371H4G:pvrThinkPadX40:rvnIBM:rn2371H4G:rvrNotAvailable:cvnIBM:ct10:cvrNotAvailable:
The values present are
 bvn  IBM            (BIOS vendor)
 bvr  1UETB6WW(1.66) (BIOS version)
 bd   06/15/2005     (BIOS date)
 svn  IBM            (system vendor)
 pn   2371H4G        (product name)
 pvr  ThinkPadX40    (product version)
 rvn  IBM            (board vendor)
 rn   2371H4G        (board name)
 rvr  NotAvailable   (board version)
 cvn  IBM            (chassis vendor)
 ct   10             (chassis type)
 cvr  NotAvailable   (chassis version)
The chassis type 10 is Notebook. Other interesting values can be found in the dmidecode source:
  3 Desktop
  4 Low Profile Desktop
  5 Pizza Box
  6 Mini Tower
  7 Tower
  8 Portable
  9 Laptop
 10 Notebook
 11 Hand Held
 12 Docking Station
 13 All In One
 14 Sub Notebook
 15 Space-saving
 16 Lunch Box
 17 Main Server Chassis
 18 Expansion Chassis
 19 Sub Chassis
 20 Bus Expansion Chassis
 21 Peripheral Chassis
 22 RAID Chassis
 23 Rack Mount Chassis
 24 Sealed-case PC
 25 Multi-system
 26 CompactPCI
 27 AdvancedTCA
 28 Blade
 29 Blade Enclosing
The chassis type values are not always accurately set in the DMI table. For example my home server is a tower, but the DMI modalias claim it is a desktop. SerIO subtype This type is used for PS/2 mouse plugs. One example is from my test machine:
serio:ty01pr00id00ex00
The values present are
  ty  01  (type)
  pr  00  (prototype)
  id  00  (id)
  ex  00  (extra)
This type is supported by the psmouse driver. I am not sure what the valid values are. Other subtypes There are heaps of other modalias subtypes according to file2alias.c. There is the rest of the list from that source: amba, ap, bcma, ccw, css, eisa, hid, i2c, ieee1394, input, ipack, isapnp, mdio, of, parisc, pcmcia, platform, scsi, sdio, spi, ssb, vio, virtio, vmbus, x86cpu and zorro. I did not spend time documenting all of these, as they do not seem relevant for my intended use with mapping hardware to packages when new stuff is inserted during run time. Looking up kernel modules using modalias values To check which kernel modules provide support for a given modalias, one can use the following shell script:
  for id in $(find /sys -name modalias -print0   xargs -0 cat   sort -u); do \
    echo "$id" ; \
    /sbin/modprobe --show-depends "$id" sed 's/^/  /' ; \
  done
The output can look like this (only the first few entries as the list is very long on my test machine):
  acpi:ACPI0003:
    insmod /lib/modules/2.6.32-5-686/kernel/drivers/acpi/ac.ko 
  acpi:device:
  FATAL: Module acpi:device: not found.
  acpi:IBM0068:
    insmod /lib/modules/2.6.32-5-686/kernel/drivers/char/nvram.ko 
    insmod /lib/modules/2.6.32-5-686/kernel/drivers/leds/led-class.ko 
    insmod /lib/modules/2.6.32-5-686/kernel/net/rfkill/rfkill.ko 
    insmod /lib/modules/2.6.32-5-686/kernel/drivers/platform/x86/thinkpad_acpi.ko 
  acpi:IBM0071:PNP0511:
    insmod /lib/modules/2.6.32-5-686/kernel/lib/crc-ccitt.ko 
    insmod /lib/modules/2.6.32-5-686/kernel/net/irda/irda.ko 
    insmod /lib/modules/2.6.32-5-686/kernel/drivers/net/irda/nsc-ircc.ko 
  [...]
If you want to help implementing a system to let us propose what packages to install when new hardware is plugged into a Debian machine, please send me an email or talk to me on #debian-devel. Update 2013-01-15: Rewrite "cat $(find ...)" to "find ... -print0 xargs -0 cat" to make sure it handle directories in /sys/ with space in them.

2 September 2012

Dirk Eddelbuettel: Faster creation of binomial matrices

Scott Chamberlain blogged about faster creation of binomial matrices the other day, and even referred to our RcppArmadillo package as a possible solution (though claiming he didn't get it to work, tst tst -- that is what the rcpp-devel list is here to help with). The post also fell short of a good aggregated timing comparison for which we love the rbenchmark package. So in order to rectify this, and to see what we can do here with Rcpp, a quick post revisiting the issue. As preliminaries, we need to load three packages: inline to create compiled code on the fly (which, I should mention, is also used together with Rcpp by the Stan / RStan MCMC sampler which is creating some buzz this week), the compiler package included with R to create byte-compiled code and lastly the aforementioned rbenchmark package to do the timings. We also set row and column dimension, and set them a little higher than the original example to actually have something measurable:
library(inline)
library(compiler)
library(rbenchmark)
n <- 500
k <- 100
The first suggestion was the one by Scott himself. We will wrap this one, and all the following ones, in a function so that all approaches are comparable as being in a function of two dimension arguments:
scott <- function(N, K)  
    mm <- matrix(0, N, K)
    apply(mm, c(1, 2), function(x) sample(c(0, 1), 1))
 
scottComp <- cmpfun(scott)
We also immediatly compute a byte-compiled version (just because we now can) to see if this helps at all with the code. As there are no (explicit !) loops, we do not expect a big pickup. Scott's function works, but sweeps the sample() function across all rows and columns which is probably going to be (relatively) expensive. Next is the first improvement suggested to Scott which came from Ted Hart.
ted <- function(N, K)  
    matrix(rbinom(N * K, 1, 0.5), ncol = K, nrow = N)
 
This is quite a bit smarter as it vectorises the approach, generating N times K elements at once which are then reshaped into a matrix. Another suggestion came from David Smith as well as Rafael Maia. We rewrite it slightly to make it a function with two arguments for the desired dimensions:
david <- function(m, n)  
    matrix(sample(0:1, m * n, replace = TRUE), m, n)
 
This is very clever as it uses sample() over zero and one rather than making (expensive) draws from random number generator. Next we have a version from Luis Apiolaza:
luis <- function(m, n)  
     round(matrix(runif(m * n), m, n))
 
It draws from a random uniform and rounds to zero and one, rather than deploying the binomial. Then we have the version using RcppArmadillo hinted at by Scott, but with actual arguments and a correction for row/column dimensions. Thanks to inline we can write the C++ code as an R character string; inline takes care of everything and we end up with C++-based solution directly callable from R:
arma <- cxxfunction(signature(ns="integer", ks="integer"), plugin = "RcppArmadillo", body='
   int n = Rcpp::as<int>(ns);
   int k = Rcpp::as<int>(ks);
   return wrap(arma::randu(n, k));
')
This works, and is pretty fast. The only problem is that it answers the wrong question as it returns U(0,1) draws and not binomials. We need to truncate or round. So a corrected version is
armaFloor <- cxxfunction(signature(ns="integer", ks="integer"), plugin = "RcppArmadillo", body='
   int n = Rcpp::as<int>(ns);
   int k = Rcpp::as<int>(ks);
   return wrap(arma::floor(arma::randu(n, k) + 0.5));
')
which uses the the old rounding approximation of adding 1/2 before truncating. With Armadillo in the picture, we do wonder how Rcpp sugar would do. Rcpp sugar, described in one of the eight vignettes of the Rcpp package, is using template meta-programming to provide R-like expressiveness (aka "syntactic sugar") at the C++ level. In particular, it gives access to R's RNG functions using the exact same RNGs as R making the results directly substitutable (whereas Armadillo uses its own RNG).
sugar <- cxxfunction(signature(ns="integer", ks="integer"), plugin = "Rcpp", body='
   int n = Rcpp::as<int>(ns);
   int k = Rcpp::as<int>(ks);
   Rcpp::RNGScope tmp;
   Rcpp::NumericVector draws = Rcpp::runif(n*k);
   return Rcpp::NumericMatrix(n, k, draws.begin());
')
Here Rcpp::RNGScope deals with setting/resetting the R RNG state. This draws a vector of N time K uniforms similar to Luis' function -- and just like Luis' R function does so without looping -- and then shapes a matrix of dimension N by K from it. And it does of course have the same problem as the RcppArmadillo approach earlier and we can use the same solution:
sugarFloor <- cxxfunction(signature(ns="integer", ks="integer"), plugin = "Rcpp", body='
   int n = Rcpp::as<int>(ns);
   int k = Rcpp::as<int>(ks);
   Rcpp::RNGScope tmp;
   Rcpp::NumericVector draws = Rcpp::floor(Rcpp::runif(n*k)+0.5);
   return Rcpp::NumericMatrix(n, k, draws.begin());
')
Now that we have all the pieces in place, we can compare:
res <- benchmark(scott(n, k), scottComp(n,k),
                 ted(n, k), david(n, k), luis(n, k),
                 arma(n, k), sugar(n,k),
                 armaFloor(n, k), sugarFloor(n, k),
                 order="relative", replications=100)
print(res[,1:4])
With all the above code example in a small R script we call via littler, we get
edd@max:~/svn/rcpp/pkg$ r /tmp/scott.r 
Loading required package: methods
              test replications elapsed   relative
7      sugar(n, k)          100   0.072   1.000000
9 sugarFloor(n, k)          100   0.088   1.222222
6       arma(n, k)          100   0.126   1.750000
4      david(n, k)          100   0.136   1.888889
8  armaFloor(n, k)          100   0.138   1.916667
3        ted(n, k)          100   0.384   5.333333
5       luis(n, k)          100   0.410   5.694444
1      scott(n, k)          100  33.045 458.958333
2  scottComp(n, k)          100  33.767 468.986111
We can see several takeaways: Thanks to Scott and everybody for suggesting this interesting problem. Trying the rbinom() Rcpp sugar function, or implementing sample() at the C++ level is, as the saying goes, left as an exercise to the reader.

17 August 2012

Dirk Eddelbuettel: Follow-up to Counting CRAN Package Depends, Imports and LinkingTo

A few days ago, I blogged about visualizing CRAN dependency ranks which turned out to be a somewhat popular post. David Smith followed-up at the REvo blog suggesting to exclude packages already shipping with R (which is indicated by their 'Recommended' priority). Good idea! So here is an updated version, where we limit the display to the top twenty packages counted by reverse 'Depends:', and excluding those already shipping with R such as MASS, lattice, survival, Matrix, or nlme. CRAN package chart of Reverse Depends relations excluding Recommended packages The mvtnorm package is still out by a wide margin, but we can note that (cough, cough) our Rcpp package for seamless R and C++ is now tied for second with the coda package for MCMC analysis. Also of note is the fact that CRAN keeps growing relentlessly and moved from 3969 packages to 3981 packages in the space of these few days... Lastly, I have been asked about the code and/or data behind this. It is really pretty simply as the main data.frame can be had from CRAN (where I also found the initial few lines to load it). After that, one only needs a little bit of subsetting as shown below. I look forward to seeing other people riff on this data set.
#!/usr/bin/r
##
## Initial db downloand from http://developer.r-project.org/CRAN/Scripts/depends.R and adapted
require("tools")
## this function is essentially the same as R Core's from the URL
## http://developer.r-project.org/CRAN/Scripts/depends.R
getDB <- function()  
    contrib.url(getOption("repos")["CRAN"], "source") # trigger chooseCRANmirror() if required
    description <- sprintf("%s/web/packages/packages.rds", getOption("repos")["CRAN"])
    con <- if(substring(description, 1L, 7L) == "file://")  
        file(description, "rb")
      else  
        url(description, "rb")
     
    on.exit(close(con))
    db <- readRDS(gzcon(con))
    rownames(db) <- db[,"Package"]
    db
 
db <- getDB()
## count packages
getCounts <- function(db, col)  
    foo <- sapply(db[,col],
                  function(s)   if (is.na(s)) NA else length(strsplit(s, ",")[[1]])   )
 
## build a data.frame with the number of entries for reverse depends, reverse imports,
## reverse linkingto and reverse suggests; also keep Recommended status
ddall <- data.frame(pkg=db[,1],
                    RDepends=getCounts(db, "Reverse depends"),
                    RImports=getCounts(db, "Reverse imports"),
                    RLinkingTo=getCounts(db, "Reverse linking to"),
                    RSuggests=getCounts(db, "Reverse suggests"),
                    Recommended=db[,"Priority"]=="recommended"
                    )
## Subset to non-Recommended packages as in David Smith's follow-up post
dd <- subset(ddall, is.na(ddall[,"Recommended"])   ddall[,"Recommended"] != TRUE)
labeltxt <- paste("Analysis as of", format(Sys.Date(), "%d %b %Y"),
                  "covering", nrow(db), "total CRAN packages")
cutOff <- 20
doPNG <- TRUE
if (doPNG) png("/tmp/CRAN_ReverseDepends.png", width=600, heigh=600)
z <- dd[head(order(dd[,2], decreasing=TRUE), cutOff),c(1,2)]
dotchart(z[,2], labels=z[,1], cex=1, pch=19,
         main="CRAN Packages sorted by Reverse Depends:",
         sub=paste("Limited to top", cutOff, "packages, excluding 'Recommended' ones shipped with R"),
         xlab=labeltxt)
if (doPNG) dev.off()
if (doPNG) png("/tmp/CRAN_ReverseImports.png", width=600, heigh=600)
z <- dd[head(order(dd[,3], decreasing=TRUE), cutOff),c(1,3)]
dotchart(z[,2], labels=z[,1], cex=1, pch=19,
         main="CRAN Packages sorted by Reverse Imports:",
         sub=paste("Limited to top", cutOff, "packages, excluding 'Recommended' ones shipped with R"),
         xlab=labeltxt)
if (doPNG) dev.off()
# no cutOff but rather a na.omit
if (doPNG) png("/tmp/CRAN_ReverseLinkingTo.png", width=600, heigh=600)
z <- na.omit(dd[head(order(dd[,4], decreasing=TRUE), 30),c(1,4)])
dotchart(z[,2], labels=z[,1], pch=19,
         main="CRAN Packages sorted by Reverse LinkingTo:",
         xlab=labeltxt)
if (doPNG) dev.off()

13 May 2012

Gregor Herrmann: RC bugs 2012/19

like in the last two weeks, this week's bug squashing was mostly related to the gcc 4.7 FTBFS bugs:

16 March 2012

Matt Brown: Kindle Reading Stats

I ve written before about my initial investigations into the Kindle, and I ve learnt much more about the software and how it communicates with the Amazon servers since then, but it all requires detailed technical explanation which I can never seem to find the motivation to write down. Extracting reading data out of the system log files is however comparatively simple. I m a big fan of measurement and data so my motivation and goal for the Kindle log files was to see if I could extract some useful information about my Kindle use and reading patterns. In particular, I m interested in tracking my pace of reading, and how much time I spend reading over time. You ll recall from the previous post that the Kindle keeps a fairly detailed syslog containing many events, including power state changes, and changes in the Booklet software system including opening and closing books and position information. You can eyeball any one of those logfiles and understand what is going on fairly quickly, so the analysis scripts are at the core just a set of regexps to extract the relevant lines and a small bit of logic to link them together and calculate time spent in each state/book. You can find the scripts on Github: https://github.com/mattbnz/kindle-utils Of course, they re not quite that simple. The Kindle doesn t seem to have a proper hardware clock (or mine has a broken hardware clock). My Kindle comes back from every reboot thinking it s either at the epoch or somewhere in the middle of 2010, the time doesn t get corrected until it can find a network connection and ping an Amazon server for an update, so if you have the network disabled it might be many days or weeks of reading before the system time is updated to reality. Once it has a network connection it uses the MCC reported by the 3G modem to infer what timezone it should be in, and switches the system clock to local time. Unfortunately the log entries all look like this:
110703:193542 cvm[7908]: I TimezoneService:MCCChanged:mcc=310,old=GB,new=US:
110703:193542 cvm[7908]: I TimezoneService:TimeZoneChange:offset=-25200,zone=America/Los_Angeles,country=US:
110703:193542 cvm[7908]: I LipcService:EventArrived:source=com.lab126.wan,name=localTimeOffsetChanged,arg0=-25200,arg1=1309689302:
110703:193542 cvm[7908]: I TimezoneService:LTOChanged:time=1309689302000,lto=-25200000:
110703:183542 system: I wancontrol:pc:processing "pppstart"
110703:193542 cvm[7908]: I LipcService:EventArrived:source=com.lab126.wan,name=dataStateChanged,arg0=2,arg1=:
110703:183542 cvm[7908]: I ConnectionService:LipcEventArrived:source=com.lab126.cmd,name=intfPropertiesChanged,arg0=
,arg1=wan:
110703:183542 cvm[7908]: W ConnectionService:UnhandledLipcEvent:event=intfPropertiesChanged:
110703:193542 wifid[2486]: I wmgr:event:handleWpasupNotify(<2>CTRL-EVENT-DISCONNECTED), state=Searching:
110703:113542 wifid[2486]: I spectator:conn-assoc-fail:t=374931.469106, bssid=00:00:00:00:00:00:
110703:113542 wifid[2486]: I sysev:dispatch:code=Conn failed:
110703:183542 cvm[7908]: I LipcService:EventArrived:source=com.lab126.wifid,name=cmConnectionFailed,arg0=Failed to connect to WiFi network,arg1=
:
Notice how there is no timezone information associated with the date/time information on each line. Worse still the different daemons are logging in at least 3 different timezones/DST offsets all interspersed within the same logfile. Argh!! So our simple script that just extracts a few regexps and links them together nearly doubles in size to handle the various time and date convolutions that the logs present. Really, the world should just use UTC everywhere. Life would be so much simpler. The end result is a script that spits out information like:

B000FC1PJI: Quicksilver: Read 1 times. Last Finished: Fri Mar 16 18:30:57 2012
- Tue Feb 21 11:06:24 2012 => Fri Mar 16 18:30:57 2012. Reading time 19 hours, 29 mins (p9 => p914)
... Read 51 books in total. 9 days, 2 hours, 29 mins of reading time
I haven t got to the point of actually calculating reading pace yet, but the necessary data is all there and I find the overall reading time stats interesting enough for now. If you have a jailbroken Kindle, I d love for you to have a play and let me know what you think. You ll probably find logs going back at least 2-3 weeks still on your Kindle to start with, and you can use the fetch-logs script to regularly pull them down to more permanent storage if you desire.

16 December 2011

Dominique Dumont: Config::Model new command line: And the winner is

Hello Following the suggestions provided after my post What name for Config::Model s new command line ? cfg or something else ? , I ve considered cmc and cme as a good candidates. But, cmc is used by a C mol compiler software (don t ask me what it is ). cme is also a very good name. So the winner is cme Next version of Config::Model will provide /usr/bin/cme. The old config-edit command will be provided for a few months to preserve backward compatibility. Thanks to all people who took the time to reply :-) All the best

23 August 2011

Vincent Bernat: SSL termination: stunnel, nginx & stud

Here is the short version: to get better performance on your SSL terminator, use stud on 64bit system with patch from meric Brun for SSL session reuse with some AES cipher suite (128 or 256, does not really matter), without DHE, on as many cores as needed, a key size of 1024 bits unless more is needed.

Introduction A quick note: when I say SSL, you should read TLS v1 instead. Look at the article for TLS on Wikipedia for some background on this. One year ago, Adam Langley, from Google, stated SSL was not computationally expensive any more:
In January this year (2010), Gmail switched to using HTTPS for everything by default. Previously it had been introduced as an option, but now all of our users use HTTPS to secure their email between their browsers and Google, all the time. In order to do this we had to deploy no additional machines and no special hardware. On our production frontend machines, SSL/TLS accounts for less than 1% of the CPU load, less than 10KB of memory per connection and less than 2% of network overhead. Many people believe that SSL takes a lot of CPU time and we hope the above numbers (public for the first time) will help to dispel that. If you stop reading now you only need to remember one thing: SSL/TLS is not computationally expensive any more.
This is a very informative post containing tips on how to enhance SSL performance by reducing latency. However, unlike Gmail, you may still be worried by SSL raw performances. Maybe each of your frontends is able to serve 2000 requests per second and CPU overhead for SSL is therefore significative. Maybe you want to terminate SSL in your load balancer (even if you know this is not the best way to scale).

Tuning SSL There are a lot of knobs you can use to get better performances from SSL: choosing the best implementation, using more CPU cores, switching to 64bit system, choosing the right cipher suite and the appropriate key size and enabling a session cache. We will consider three SSL terminators. They all use OpenSSL behind the hood. stunnel is the oldest one and uses a threaded model. stud is a recent attempt to write a simple SSL terminator which is efficient and scalable. It uses the one-process-per-core model. nginx is a web server and it can be used as reverse proxy and therefore act as SSL terminator. It is known to be one of the most efficient web server, hence the choice here. It also features built-in basic load balancing. Since stud and stunnel does not have this feature, we use them with HAProxy, an high performance load-balancer that usually defers the SSL part to stunnel (but stud can act as a drop-in replacement here). Those implementations were already tested by Matt Stancliff. He first concluded nginx sucked at SSL then that nginx did not suck at SSL (in the first case, nginx was the only one to select a DHE cipher suite). The details were very scarce. I hope to bring here more details. This brings the importance of the selected cipher suite. The client and the server must agree on the cipher suite to use for symmetric encryption. The server will select the strongest one it supports from the list proposed by the client. If you enable some expensive cipher suite on your server, it is likely to be selected. The last important knob is SSL session reuse. It matters for both performance and latency. During the first handshake, the server will send a session ID. The client can use this session ID to request an abbreviated handshake. This handshake is shorter (latency improvement by one round-trip) and allows to reuse the previously negociated master secret (performance improvement by skipping the costliest part of the handshake). See the article from Adam Langley for additional information (with helpful drawings). The following table shows what cipher suite is selected by some major web sites. I have also indicated wheter they support session reuse. See this post from Matt Palmer to know how to check this.
Site Cipher Session reuse?
www.google.com RC4-SHA
www.facebook.com RC4-MD5
twitter.com AES256-SHA
windowsupdate.microsoft.com RC4-MD5
www.paypal.com AES256-SHA
www.cmcicpaiement.fr DHE-RSA-AES256-SHA
RFC 5077 defines another mechanism for session resumption that does not require any server-side state. I did not investigate much how this works but it does not rely on the session ID.

Benchmarks All those benchmarks have been run on a HP DL 380 G7, with two Xeon L5630 (running at 2.13GHz for a total of 8 cores), without hyperthreading, using a 2.6.39 kernel (HZ is set to 250) and two Intel 82576 NIC. Linux conntrack subsystem has been disabled and file limits have been raised over 100,000. A Spirent Avalanche 2900 appliance is used to run the benchmarks. We are interested in raw SSL performances in term of handshakes per second. Because we want to observe the effects of session reuse, the scenario runs by most tests lets clients doing four successive requests and reusing the SSL session for three of them. There is no HTTP keepalive. There is no compression. The size of the HTTP answer from the server is 1024 bytes. Those choices are done because our primary target is the number of SSL handshakes per second. It should also be noted that HAProxy alone is able to handle 22,000 TPS on one core. During the tests, it was never the bottleneck.

Implementation We run a first bench to compare nginx, stud and stunnel on one core. This bench runs on a 32bit system, with AES128-SHA1 cipher suite and a 1024bit key size. Here is the result for stud (version 0.1, with meric Brun s patch for SSL session reuse): stud, 1 CPU The most important plot is the top one. The blue line is the attempted number of transactions per second (TPS) while the green one is the successful number of TPS. When the two lines start to diverge, this means we reach some kind of maximum: the number of unsuccessful TPS also starts to raise (the red line). There are several noticeable points: the maximum TPS (788 TPS), the maximum TPS with an average response time less than 100 ms (766 TPS), less than 500 ms (776 TPS) and the maximum TPS with less than 0.01% of packet loss (783 TPS). Let s have a look at nginx (version 1.0.5): nginx, 1 CPU It is able to get the same performance as stud (763 TPS). However, over 512 TPS, you get more than 100 ms of response time. Over 556 TPS, you even get more than 500 ms! I get this behaviour in every bench with nginx (with or without proxy_buffering, with or without tcp_nopush, with or without tcp_nodelay) and I am unable to explain it. Maybe there is something wrong in the configuration. After hitting this limit, nginx starts to process connections by bursts. Therefore, the number of successful TPS is plotted using a dotted line while the moving average over 20 seconds is plotted with a solid line. On the next plot, you can see the compared performance of the three implementations. On this kind of plot, the number of TPS that we keep is the maximum number of TPS where loss is less than 0.1% and average response time is less than 100 ms. stud achieves a performance of 766 TPS while nginx and stunnel are just above 500 TPS. stunnel vs stud vs nginx, 1 CPU

Number of cores With multiple cores, we can affect several of them to do SSL hard work. To get better performance, we pin each processes to a dedicated CPU. Here is the repartition used during the tests:
1 core 2 cores 4 cores 6 cores
CPU 1, Core 1 network network network network + haproxy
CPU 1, Core 2 haproxy haproxy haproxy SSL
CPU 1, Core 3 SSL SSL SSL SSL
CPU 1, Core 4 - SSL SSL SSL
CPU 2, Core 5 - - network SSL
CPU 2, Core 6 - - SSL SSL
CPU 2, Core 7 - - SSL SSL
CPU 2, Core 8 system system system system + haproxy
Remember, we have two CPU, 4 cores on each CPU. Cores on the same CPU share the same L2 cache (on this model). Therefore, the arrangement inside a CPU is not really important. When possible, we try to keep things together on the same CPU. The SSL processes always get exclusive use of a core since they will always be the most busy. The repartition is done with cpuset(7) for userland processes and by setting smp_affinity for network card interrupts. We keep one core for the system. It is quite important to be able to connect and monitor the system correctly even when it is loaded. With so many cores, we can afford to reserve one core for this usage. Beware! There is a trap when pining processes or IRQ to a core. You need to check /proc/cpuinfo to discover the mapping between kernel processors and physical cores. Sometimes, second kernel processor can be the first core of the second physical processor (instead of the second core of the first physical processor). stunnel vs stud vs nginx, 6 CPU As you can see in the plot above, only stud is able to scale properly. stunnel is not able to take advantage of the cores and its performances are worse than with a single core. I think this may be due to its threaded model and the fact that the userland for this 32bit system is a bit old. nginx is able to achieve the same TPS than stud but is disqualified because of the increased latency. We won t use stunnel in the remaining tests.

32bit vs 64bit The easiest way to achieve a performance boost is to switch to a 64bit system. TPS are doubled. On our 64bit system, thanks to the use of a version of OpenSSL with the appropriate support, AES-NI, a CPU extension to improve the speed of AES encryption/decryption, is enabled. Remaining tests are done with a 64bit system. stud vs nginx, 64bit

Ciphers and key sizes In our tests, the influence of ciphers is minimal. There is almost no difference between AES256 and AES128. Using RC4 adds some latency. The use of AES-NI may have helped to avoid this latency for AES. On the other hand, using a 2048bit key size has a huge performance hit. TPS are divided by 5. stud: cipher suites and key sizes

Session cache The last thing to check is the influence of SSL session reuse. Since we are on a local network, we see only one of the positive effects of session reuse: better TPS because of reduced CPU usages. If there was a latency penalty, we should also have seen better TPS thanks to the removed round-trip. stud: session reuse This plot also explains why stud performances fall after the maximum: because of the failed transactions, the session cache is not as efficient. This phenomenon does not exist when session reuse is not enabled.

Conclusion Here is a summary of the maximum TPS reached during the benchmark (with an average response time below 100ms). Our control use case is the following: 64bit, 6 cores, AES128, SHA1, 1024bit key, 4 requests into the same SSL session.
Context nginx 1.0.5 stunnel 4.41 stud 0.1 (patched)
1 core, 32bit 512 TPS 503 TPS 766 TPS
2 cores, 32bit 599 TPS - -
32bit 804 TPS 501 TPS 4251 TPS
- 1799 TPS - 9000 TPS
AES256 - - 8880 TPS
RC4-MD5 - - 7370 TPS
2048bit - - 1643 TPS
no session reuse - - 5844 TPS
80 requests per SSL session - - 10797 TPS
Therefore, stud in our control scenario is able to sustain 1500 TPS per core. It seems to be the best current option for a SSL termination. It is not available in Debian yet, but I intend to package it. Here is how stud is invoked:
# ulimit -n 100000
# stud  -n 2 -f 172.31.200.15,443 -b 127.0.0.1,80 -c ALL \
>   -B 1000 -C 20000 --write-proxy \
>   =(cat server1024.crt server1024.key dhe1024)
You may also want to look at HAProxy configuration, nginx configuration and stunnel configuration.

28 July 2011

Dirk Eddelbuettel: Rcpp 0.9.6

A new maintenance release version 0.9.6 of Rcpp went onto CRAN and into Debian earlier today. This release contains a fix which helps the RppEigen package (mentioned previously on this blog), as well as an addition which permits user-defined finalizers for external pointer objects (following a suggestion on the mailing list). Two new examples where added: a Gibbs sampler illustration (blogged about as well) and a Rcpp-based Fibonacci implementation following a question on StackOverflow. And while that last example is clearly degenerate, the 700+ fold net speedup (as shown in my answer) is still pretty neat. The complete NEWS entry is below; more details are in the ChangeLog file in the package and on the Rcpp Changelog page.
0.9.6   2011-07-26
    o   Added helper traits to facilitate implementation of the RcppEigen
        package: The is_eigen_base traits identifies if a class derives from
        EigenBase using SFINAE; and new dispatch layer was added to wrap() to
        help RcppEigen
    o   XPtr now accepts a second template parameter, which is a function
        taking a pointer to the target class. This allows the developper to
        supply his/her own finalizer. The template parameter has a default
        value which retains the original behaviour (calling delete on the
        pointer)
    o   New example RcppGibbs, extending Sanjog Misra's Rcpp illustration of
        Darren Wilkinson's comparison of MCMC Gibbs Sampler implementations;
        also added short timing on Normal and Gaussian RNG draws between Rcpp
        and GSL as R's rgamma() is seen to significantly slower
    o   New example on recursively computing a Fibonacci number using Rcpp and
        comparing this to R and byte-compiled R for a significant speed gain
Thanks to CRANberries, you can also look at a diff to the previous release 0.9.5. As always, even fuller details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads, the browseable doxygen docs and zip files of doxygen output for the standard formats. A local directory has source and documentation too. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page

15 July 2011

Dirk Eddelbuettel: MCMC and faster Gibbs Sampling using Rcpp

Sanjog Misra, who uses Rcpp for Monte Carlo Markov Chain (MCMC) analyses in quantitative marketing, kindly set me a short example of Rcpp use. The example is based on a blog post by Darren Wilkinson which itself discusses and compares the suitability of R, Python, Java or C for MCMC analysis, using the Gibbs sampler as a concrete example. Darren's post is worth checking out: he stresses the rather pragmatic aspects of how fast and/or easy it is to write the code, rather than just the mere runtime. As such, he is not too concerned with a speed advantage of Python over R which he sees at a factor of around 2.4, leaving him to continue to prototype in R. Similarly, with C 'only' being faster than Java by a factor of two, he prefers Java for the numerically more demanding parts. We do of course advocate the use of Rcpp to combine the best aspects of R and C++, respectively. This Gibbs sampler example provides a nice backdrop. So working with Darren's example, consider the same Gibbs sampler for a bivariate distribution (and apologies for the lack of latex typesetting on my blog)
f(x,y) = k x^2 exp( -x y^2 - y^2 + 2y - 4x)
where the conditional distributions are
f(x y) = (x^2)*exp(-x*(4+y*y))               ## a Gamma density kernel
f(y x) = exp(-0.5*2*(x+1)*(y^2 - 2*y/(x+1))  ## a Gaussian kernel
Sanjog then spotted and corrected a small error in the variance expression in Darren's derivation; this is now acknowledged on Darren's website. Full details are in the R script now committed in SVN. The R code for the Gibbs sample can therefore be written as follows below. Note that this uses thinning to minimize serial correlation in the conditional densities--which renders the computation more demanding as 'N times thin' draws have to be generated:
## Here is the actual Gibbs Sampler
## This is Darren Wilkinsons R code (with the corrected variance)
## But we are returning only his columns 2 and 3 as the 1:N sequence
## is never used below
Rgibbs <- function(N,thin)  
    mat <- matrix(0,ncol=2,nrow=N)
    x <- 0
    y <- 0
    for (i in 1:N)  
        for (j in 1:thin)  
            x <- rgamma(1,3,y*y+4)
            y <- rnorm(1,1/(x+1),1/sqrt(2*(x+1)))
         
        mat[i,] <- c(x,y)
     
    mat
 
A second variant can be computed using the R bytecode compiler which appeared with the recent release of R 2.13.0 (and which we analysed in this blog post from April). This is as easy as
## We can also try the R compiler on this R function
RCgibbs <- cmpfun(Rgibbs)
Thanks to Rcpp and the inline package, we can also write a C++ variant that can be built and launched from R with ease. The C++ code is assigned to an R text variable gibbscode. (And we used to typeset such code on the blog as a character string, ie in a faint red color---but have now switched to highlight it as if it were freestanding C++ code. It really is passed as a single string to R which then uses the cxxfunction() to compile, link and load a C++ function built around the code. See previous posts on the inline package for more.)
## Now for the Rcpp version -- Notice how easy it is to code up!
gibbscode <- '

  using namespace Rcpp;   // inline does that for us already
  // n and thin are SEXPs which the Rcpp::as function maps to C++ vars
  int N   = as<int>(n);
  int thn = as<int>(thin);
  int i,j;
  NumericMatrix mat(N, 2);
  RNGScope scope;         // Initialize Random number generator
  // The rest of the code follows the R version
  double x=0, y=0;
  for (i=0; i<N; i++)  
    for (j=0; j<thn; j++)  
      x = ::Rf_rgamma(3.0,1.0/(y*y+4));
      y = ::Rf_rnorm(1.0/(x+1),1.0/sqrt(2*x+2));
     
    mat(i,0) = x;
    mat(i,1) = y;
   
  return mat;             // Return to R
'
# Compile and Load
RcppGibbs <- cxxfunction(signature(n="int", thin = "int"),
                         gibbscode, plugin="Rcpp")
It is noteworthy how the code logic is essentially identical between the basic R version, and the C++ version. Two nested loops control draws of x from a Gamma distribution, conditional on y, as well as draws of y from a Normal, conditional on x. Add a small amount of parameter passing to obtain the parameters N and thin, allocation of a results matrix and setup of the random number generator state to remain consistent with R, as well as a return of the matrix---and that is all. As Darren's code uses the GNU GSL in its C variant, I also became interested in seeing how a C/C++ hybrid variant using our RcppGSL package would fare. The code is below.
gslgibbsincl <- '
  #include <gsl/gsl_rng.h>
  #include <gsl/gsl_randist.h>
  using namespace Rcpp;  // just to be explicit
'
gslgibbscode <- '
  int N = as<int>(ns);
  int thin = as<int>(thns);
  int i, j;
  gsl_rng *r = gsl_rng_alloc(gsl_rng_mt19937);
  double x=0, y=0;
  NumericMatrix mat(N, 2);
  for (i=0; i<N; i++)  
    for (j=0; j<thin; j++)  
      x = gsl_ran_gamma(r,3.0,1.0/(y*y+4));
      y = 1.0/(x+1)+gsl_ran_gaussian(r,1.0/sqrt(2*x+2));
     
    mat(i,0) = x;
    mat(i,1) = y;
   
  gsl_rng_free(r);
  return mat;           // Return to R
'
## Compile and Load
GSLGibbs <- cxxfunction(signature(ns="int", thns = "int"),
                        body=gslgibbscode, includes=gslgibbsincl,
                        plugin="RcppGSL")
This code is similar to the version using just Rcpp, but we need to allocate space for the GSL random generator object (and later release that memory allocation), and we do of course call the GSL functions. This also necessitates declaring the function using the two header files listed as arguments for the include argument of cxxfunction(). So how is the performance? The script (now committed in Rcpp's SVN repo as examples/RcppGibbs/RcppGibbs.R, and also part of the next release) creates the output below when running in non-interactive mode (whereas interactive mode creates a few charts too):
edd@max:~/svn/rcpp/pkg/Rcpp/inst/examples/RcppGibbs$ r RcppGibbs.R
Replication # 1 complete 
Replication # 2 complete 
Replication # 3 complete 
Replication # 4 complete 
                    N=1000 N=5000 N=10000 N=20000
Elasped Time (R)     0.124  2.650  10.511  41.773
Elasped Time (RC)    0.081  1.916   7.594  30.280
Elapsed Time (Rcpp)  0.003  0.076   0.306   1.221
Elapsed Time (Rgsl)  0.002  0.049   0.196   0.784
SpeedUp Rcomp.       1.530  1.380   1.380   1.380
SpeedUp Rcpp        41.330 34.870  34.350  34.210
SpeedUp GSL         62.000 54.080  53.630  53.280
               test replications elapsed  relative user.self sys.self
4  GSLGibbs(N, thn)           10   7.845  1.000000      7.84        0
3 RcppGibbs(N, thn)           10  12.218  1.557425     12.22        0
2   RCgibbs(N, thn)           10 312.296 39.808286    311.98        0
1    Rgibbs(N, thn)           10 420.953 53.658764    420.59        0
The first block is a hand-computed comparison using four sets of parameters; the second block uses the excellent rbenchmark package to compare ten runs at twenty-thousand draws. We see a nominal increase in performance due to the bytecode compiler, saving roughly 38 percent which seems appropriate given that the R code mostly controls the loops; actual work in undertaken in the already compiled RNG functions. The Rcpp variant is about 34 times faster than the pure R code. Sanjog reported higher increases on his OS X machines (and Darren's post echos a similar order of magnitude). However, on my i7 running Linux I always obtained an improvement in the mid- to high thirties. That is certainly already a rather pleasant result. What surprised and stunned me at first was that the GSL solution scores an improvement of around 53 times (close to the factor of 60 reported by Darren). A closer look at the code (shown above) makes it clear that there are very few compute-intensive operations outside of the RNG draws. I validated this further with a second study timing just one million draws each from a Gaussian and Gamma using R via Rcpp, and using the GSL. It turns out that the R code is about 2.5 times slower for random draws from the Gamma distribution than the GSL. Inspection of the source code---in files src/nmath/rgamma.c for R and randist/gamma.c for the GSL shows why. R uses a much more complex (and presumably more precise) algorithm. I may follow up with Martin Maechler to see if we can illustrative the numerical benefits of this more expensive approach---this blog entry is getting long enough already. So to sum up: Gibbs sampling is a somewhat resource-heavy Monte Carlo Markov Chain method for investigating multivariate distributions. R excels at quick and simple explorations, albeit at somewhat slower execution speed. The Rcpp package can help by providing easy means to accelerate simulations by a significant factor. The example discussed here is now in SVN repository for Rcpp and will be part of the next release.

Updated 2011-07-16: Darren has just updated his comparison; fixed two typos here too.

7 January 2011

Paul Wise: Another year, another log entry

It has been almost a full year since my last log entry. It has been a busy work year, I attended some nice conferences and did minimal FLOSS stuff. On the work side of things I was a third of an Australian VoIP startup that came and went. I setup Debian servers, installed OpenSIPS and associated software, wrote OpenSIPS scripts, wrote peripheral software and did customer support. We had a good thing going there for a while, some fans on the Whirlpool forums but in the end there wasn't enough money for the requisite marketing and local market circumstances were squeezing Australian VoIP providers anyway. On the conference side of things I went to LCA 2010, the Thai Mini-DebCamp 2010, DebConf10 and FOSSASIA 2010. Had a great time at all of them. At LCA 2010 in windy Wellington, New Zealand the distributions summit organised by Martin Krafft was one of the highlights. It was dominated by Debian/Ubuntu talks but there were some other interesting ones, especially the one on GoboLinux's integration of domain-specific package managers. Also excellent were the keynotes given by Gabriella Coleman (Best & worst of times), Mako Hill (Antifeatures) and others, which I felt gave LCA an improved and very welcome focus on software freedom. There were quite a few Debian folks at LCA, it was great to hang out with them during the week and afterwards. Monopedal sumo with mako and others was hilarious fun. At the Thailand Mini-DebCamp 2010 in Khon Kaen, I was glad to see Andrew Lee (Taiwan) and Christian Perrier (France) again and meet Yukiharu YABUKI (Japan) and Daiki Ueno (Japan). In addition to the five international folks, there were quite a few locals, including Thailand's currently sole Debian member, Theppitak Karoonboonyanan. The event was hosted at Khon Kaen University and opened with my talk about the Debian Social Contract and the Debian Free Software Guidelines. This was followed by a number of talks about Debian package building, a 3-day BSP where we touched 57 bugs, a great day of sightseeing and talks about i18n, derivative distros, keysigning, mirrors, contribution and a discussion about DebConf. During the week there was also the usual beersigning, combined with eating of unfamiliar and "interesting" Thai snacks. After the conference Andrew and I roamed some markets in Bangkok and got Thai massages. Beforehand I also visited a friend from my travels on the RV Heraclitus in Chiang Mai, once again experiencing the awesomeness of trains in Asia, unfortunately during the dry season this time. I took a lot of photos during my time in Thailand and ate a lot of great and spicy food. As a vegetarian I especially appreciated the organiser's efforts to accommodate this during the conference. At DebConf10 in New York City, by far the highlight was Eben Moglen's vision of the FreedomBox. Negotiating the hot rickety subways was fun, the party at the NYC Resistor space was most excellent, Coney Island was hot and the water a bit yuck, zack threw a ball, the food and campus was really nice. Really enjoyed the lintian BoF, ARM discussions, shy folks, GPLv3 question time, paulproteus' comments & insights, wiki BoF, puppet BoF, derivatives BoF, Sita, astronomy rooftop, cheese, virt BoF, Libravatar, DebConf11, Brave new Multimedia World, bagels for breakfast, CUT, OpenStreetMap & lightning talks. Having my power supply die was not fun at all. Afterwards I hung out with a couple of the exhausted organisers, ate awesome vegan food and fell asleep watching a movie about dreams. One weird thing about DebConf10 was that relatively few folks used the DebConf gallery to host their photos, months later only myself and Aigars Mahinovs posted any photos there. At FOSSASIA 2010 in H Ch Minh City (HCMC) was a mini-DebConf. I arrived at the HCMC airport and was greeted by Huyen (thanks!!), one of FOSSASIA's numerous volunteers, who bundled me into a taxi bound for the speakers accommodation and pre-event meetup at The Spotted Cow Bar. The next day the conference opened at the Raffles International College and after looking at the schedule I noticed that I was to give a talk about Debian that day. Since I didn't volunteer for such a talk and had nothing prepared, the schedule took me by surprise. So shortly after an awesome lunch of Vietnamese pancakes we gathered some Debian folks and a random Fedora dude and prepared a short intro to Debian. The rest of the day the highlights were the intro, video greetings and the fonts, YaCy and HTML5 talks. The next day the Debian MiniConf began with Arne Goetje and everyone trying to get Debian Live LXDE USB keys booted on as many machines in the classroom as possible (many didn't boot). Once people started showing up we kicked off with Thomas Goirand's introduction to the breadth of Debian. Others talked about Debian pure blends, Gnuk and building community and packages. The second last session was about showing the Vietnamese folks in the room how to do l10n and translation since Debian had only one Vietnamese translator (Clytie Siddall). After manually switching keyboard layouts (seems LXDE doesn't have a GUI for that) on the English LXDE installs, the two Cambodian folks were able to do some Khmer translation too. This was a great session and it resulted in two extra Vietnamese translators joining Debian. It went over time so I didn't end up doing my presentation about package reviewing. We rushed off to a university where the random Fedora ch^Wambassador was hosting a Fedora 14 release party in a huge packed classroom. There were a lot of excited faces, interesting and advanced questions and it was in general a success. Afterwards we had some food, joined up with some other speakers and ended up in a bar in the gross tourist zone. On the final day we hung around in the Debian room, went downstairs for the group photo and final goodbyes. Later we found a place with baked goods, coffee and juices and navigated the crazy traffic to a nice local restaurant. The next morning Arne & I went to the airport, others went on a Mekong Delta tour and Jonas hung out with the organisers. I took less photos than at other events but got a few interesting ones. I avoided doing a lot of FLOSS stuff over the last year, I hope to work on some things in the coming months; I'm also planning some interesting travel and acquiring some new technological goods, more on those in some later posts.

11 December 2010

David Bremner: Converting META.yml to META.json

Before I discovered you could just point your browser at http://search.cpan.org/meta/Dist-Name-0.007/META.json to automagically convert META.yml and META.json, I wrote a script to do it.
Anyway, it goes with my "I hate the cloud" prejudices :).
use CPAN::Meta;
use CPAN::Meta::Converter;
use Data::Dumper;
my $meta = CPAN::Meta->load_file("META.yml");
my $cmc = CPAN::Meta::Converter->new($meta);
my $new=CPAN::Meta->new($cmc->convert(version=>"2"));
$new->save("META.json");

8 September 2010

Dirk Eddelbuettel: Straight, curly, or compiled?

Christian Robert, whose blog I commented-on here once before, had followed up on a recent set of posts by Radford Neal which had appeared both on Radford's blog and on the r-devel mailing list. Now, let me prefix this by saying that I really enjoyed Radford's posts. He obviously put a lot of time into finding a number of (all somewhat small in isolation) inefficiencies in R which, when taken together, can make a difference in performance. I already spotted one commit by Duncan in the SVN logs for R so this is being looked at. Yet Christian, on the other hand, goes a little overboard in bemoaning performance differences somewhere between ten and fifteen percent -- the difference between curly and straight braces (as noticed in Radford's first post). Maybe he spent too much time waiting for his MCMC runs to finish to realize the obvious: compiled code is evidently much faster. And before everybody goes and moans and groans that that is hard, allow me to just interject and note that it is not. It really doesn't have to be. Here is a quick cleaned up version of Christian's example code, with proper assigment operators and a second variable x. We then get to the meat and potatoes and load our Rcpp package as well as inline to define the same little test function in C++. Throw in rbenchmark which I am becoming increasingly fond of for these little timing tests, et voila, we have ourselves a horserace:
# Xian's code, using <- for assignments and passing x down
f <- function(n, x=1) for (i in 1:n) x=1/(1+x)
g <- function(n, x=1) for (i in 1:n) x=(1/(1+x))
h <- function(n, x=1) for (i in 1:n) x=(1+x)^(-1)
j <- function(n, x=1) for (i in 1:n) x= 1/ 1+x 
k <- function(n, x=1) for (i in 1:n) x=1/ 1+x 
# now load some tools
library(Rcpp)
library(inline)
# and define our version in C++
l <- cxxfunction(signature(ns="integer", xs="numeric"),
                 'int n = as<int>(ns); double x=as<double>(xs);
                  for (int i=0; i<n; i++) x=1/(1+x);
                  return wrap(x); ',
                 plugin="Rcpp")
# more tools
library(rbenchmark)
# now run the benchmark
N <- 1e6
benchmark(f(N, 1), g(N, 1), h(N, 1), j(N, 1), k(N, 1), l(N, 1),
          columns=c("test", "replications", "elapsed", "relative"),
          order="relative", replications=10)
And how does it do? Well, glad you asked. On my i7, which the other three cores standing around and watching, we get an eighty-fold increase relative to the best interpreted version:
/tmp$ Rscript xian.R
Loading required package: methods
     test replications elapsed relative
6 l(N, 1)           10   0.122    1.000
5 k(N, 1)           10   9.880   80.984
1 f(N, 1)           10   9.978   81.787
4 j(N, 1)           10  11.293   92.566
2 g(N, 1)           10  12.027   98.582
3 h(N, 1)           10  15.372  126.000
/tmp$ 
So do we really want to spend time arguing about the ten and fifteen percent differences? Moore's law gets you those gains in a couple of weeks anyway. I'd much rather have a conversation about how we can get people speed increases that are orders of magnitude, not fractions. Rcpp is one such tool. Let's get more of them.

8 June 2010

Russell Coker: Is the PC Dying?

I just read an interesting article about the dispute between Microsoft and Apple about types of PC [1]. Steve Jobs predicted a switch from desktop PCs to portable devices, while Steve Ballmer of Microsoft claimed that the iPad is just a new PC. Defining a PC I think that the defining characteristic of the IBM Compatible PC was it s open architecture. Right from the start the PC could have it s hardware expanded by adding new circuit boards into slots on the motherboard (similar to other PC systems of that era such as the Apple 2 and the S-100 bus). The deal with IBM included Intel sharing all it s CPU designs with other manufacturers such as NEC and AMD from the 8086 until the mid-90 s. AMD specialised in chips that were close copies of Intel chips at low prices and higher clock rates while NEC added new instructions. Compaq started the PC clone market as well as the laptop market, and system software for the IBM compatible PCs was primarily available from IBM and Microsoft in the early days, along with less popular variants such as CP/M86, Novell Netware and others. In the late 80 s there was OS/2 as an alternate OS and Windows as one of several optional GUI environments to run on top of MS-DOS or PC-DOS. In the mid 90 s PCs were used for running protected mode OSs such as Linux and Windows/NT. Now if we look at a system such as a Netbook then it clearly misses some of the defining characteristics of the desktop PC. I can t upgrade a Netbook in any meaningful way changing a storage device or adding more RAM does not compare to adding an ISA/MCA/EISA/VL-Bus/PCI/PCIe expansion card. With my EeePC 701 I don t even have an option of replacing the storage as it is soldered to the motherboard! A laptop allows me to add a PCMCIA or PC-Card device to expand it, but with a maximum of two cards and a high price this isn t a great option. What is Best for Home Users? For a while now my parents have been using 3G net access for their home Internet use [2]. So it seems that a laptop provides greater benefits for their use now than it previously did when they used Cable and ADSL net access. My parents have been considering getting a new monitor (1920*1080 resolution monitors are getting insanely cheap nowadays) and driving such a monitor effectively might require a more capable PC. I recently bought myself a nice refurbished Thinkpad for $796 [3], it seems likely that I could find a refurbished Thinkpad at auction which is a little older and slower for a lower price, even buying an old T41p would be a reasonable option. This would give my parents not only the option of using the Internet when on holidays, but also in a different part of their house when they are at home. The Apple iPad would probably be quite a reasonable Internet platform for my parents if it wasn t for the fact that it uses DRM. While it s not a great platform for writing, my parents probably don t do enough that it would be a huge problem for them. So I might look for a less restrictive tablet platform for my parents. At the moment the best resolution for a tablet seems to be 1024*768, but I expect that some tablets (maybe with a hybrid tablet/laptop design like the Always Innovating Smartbook [4]) with a higher resolution will be released soon. I hope that the iPad and other closed devices don t get any serious market share, but it seems likely that OSs such as Android which are only slightly more open will have a significant market share. Ultra-Mobile Design vs PCs Design One significant problem with ultra-mobile devices is that they make significant engineering trade-offs to get the small size. For a desktop system there are lots of ways of doing things inefficiently, running the AMD64 or i386 architecture which is wasteful of energy and having lots of unused space inside the box in case you decide to upgrade it. But for a laptop there are few opportunities for being inefficient, and for a tablet or smart phone everything has to be optimised. When the optimisation of a device starts by choosing a CPU that s unlike most other systems (note that there is a significant range of ARM CPUs that are not fully compatible with each other) it makes it very difficult to produce free software to run it. I can salvage a desktop PC from a rubbish bin and run Linux on it (and I ve done that many times), but I wouldn t even bother trying to run Linux on an old mobile phone. It seems that in the near future my parents (and many other people with similar needs) will be best suited by having a limited device such as a tablet that stores all data on the Internet and not having anything that greatly resembles a PC. In many ways it would be easier for me to support my parents by storing their data in the cloud and then automatically backing it up to removable SATA disks than with my current situation of supporting a fully capable PC and backing it up to a USB device whenever I visit them. I m also considering what to do for some relatives who are about to go on a holiday in Europe, they want to be able to send email etc. It might not be possible just yet, but it seems like an ideal way of doing this would be to provide them with something like an iPad that they can use with a local 3G SIM for the country that they stay in and they could then upload all their best photos to some server that I can backup and send email to everyone they know. An iPad isn t good for this now as you don t want to go on holidays in another country while carrying something that is really desirable to thieves. Ultra Mobile Devices are Killing PCs It seems to me that Google Android and the Apple iPad/iPhone OS are taking over significant parts of the PC market. The people who are doing traditional PC things are increasingly using Laptops and Netbooks, and the number of people who get the freedom that a PC user did in the 80 s and 90 s is decreasing rapidly. I predict that by 2012 the majority of Linux systems will be running Google Android on hardware that doesn t easily allow upgrading to more open software. At the moment probably the majority of Linux systems are wireless routers and other embedded devices that people don t generally think about. But when iPad type devices running a locked-down Linux installation start replacing Ubuntu and Fedora desktop systems people will take notice. I don t think that the death of the PC platform as we know it will kill Linux, but it certainly won t do us any good. If there were smarter people at Microsoft then they would be trying to work with the Linux community on developing innovative new ways of using desktop PCs. Of all the attempts that Microsoft has made to leave the PC platform the only success has been the X-Box which is apparently doing well. Tablet devices such as the iPad could work really well in a corporate environment (where MS makes most of it s money). On many occasions I ve been in a meeting and we had to adjourn due to someone needing to go to their desk to look something up. If everyone had an iPad type device at their desk that used a wired network when it was available and encrypted wireless otherwise then for a meeting everyone could take their tablet without it s keyboard and be able to consult all the usual sources of data without any interruption. Could a high-resolution version of the iPad kill MS-Windows in the corporate environment?

15 March 2010

Russell Coker: Types of Security Tokens

The Security Token Wikipedia page doesn t seem to clearly describe the types of token. Categories of Security Token It seems to me that the following categories encompass all security tokens:
  1. Biometric tokens which seems rather pointless to me. Having a device I control verify my biometric data doesn t seem to provide a benefit. The only possible benefit seems to be if the biometric token verifies the identity of the person holding it before acting as one of the other types of token.
  2. Challenge-response devices. The server will send a challenge (usually a random number) and will expect a response (usually some sort of cryptographically secure hash of the number and a shared secret). A challenge-response device may take a password from the user and combine it with the challenge from the server and the shared secret when calculating the response.
  3. Time-based tokens (one-time passwords). They will provide a new pseudo-random number that changes periodically, often a 30 second time interval is used and the number is presumably a cryptographically secure hash of the time and a shared secret. This requires a battery in the token and the token will become useless when the battery runs out. It also requires that the server have an accurate clock.
  4. Use-based tokens. They will give a new pseudo-random number every time a button is pressed (or some other event happens to indicate that a number has been used). These do not work well if you have multiple independent servers and an untrusted network.
Here is my analysis of the theory of token use, note that I am not sure how the implementations of the various token systems deal with these issues.
  1. Biometric security seems like a bad idea for most non-government use. I have seen a retina scanner in use at a government office that made some sense as the people being scanned were in a secure area (they had passed some prior checks) and they were observed (to prevent coercion and the use of fake eyes). Biometric authentication for logging in over the net just seems like a bad idea as you will never know if you can trust the scanner.
  2. It seems to me that challenge-response devices are by far the most secure option. CR is resistant to replay attacks provided that it is not possible to have re-used challenges. If the calculation of the response includes a password (which is performed on some tokens that resemble pocket calculators) then a CR token will meet the something you have and something you know criteria.
    One potential problem with CR systems is that of not including the server or account ID in the calculation. So if I was to use a terminal in an insecure location to login to a server or account with data that is not particularly important then it would be possible for an attacker who had compromised the terminal to perform a Man In The Middle (MITM) attack against other servers. Of course you are supposed to use a different password for each account, if you do this then a CR token that includes a password will be resistant to this attack but I expect that people who use tokens are more likely to use one password for multiple accounts.
  3. Time-based tokens have a weakness in that an attacker who can immediately discover the number used for one connection could then immediately login to other servers. One example of a potential attack using this avenue would be to compromise a terminal in an Internet cafe, steal a hash used for logging in to server A and then immediately login to server B. This means that it may not be safe to use the same token for logging in to servers (or accounts) that have different sensitivity levels unless a strong password was used as well I expect that people who have hardware tokens tend to use weaker passwords.
    Also one factor that will make some MITM attacks a lot easier is the fact that the combination of the hash from the token and the password are valid for a period of time so an attacker could establish a second connection within the 30 second interval. It seems that only allowing one login with a particular time-coded password is the correct thing to do, but this may be impossible if multiple independent servers use the same token.
    Time based tokens expire when the battery runs out. The measures taken to make them tamper-proof may make it difficult or impossible to replace the battery so a new token must be purchased every few years.
  4. Use-based tokens are very similar to time-based tokens, it s just a different number that is used for generating the hash. The difference in the token is that a time-based token needs a battery so that it can track the time while a use-based token needs a small amount of flash memory to store the usage count. The difference at the server end is that for a use-based token the server needs a database of the use count of each token, which is usually not overly difficult for a single server.
    One problem is the case of a restore from backup of the server which maintains the use count database. The only secure way of managing this is to either inspect every token (to discover it s use count) or to issue a new password (for using password plus token authentication). Either option would be really painful if you have many users at remote sites. Also it would be required to get the database transaction committed to disk before an authentication attempt is acknowledged so that a server crash could not lose the count this should be obvious but many people get these things wrong.
    An additional complication for use-based tokens comes with the case of a token that is used for multiple servers. One server needs to maintain the database of the usage counts and the other servers need to query it by secure links. If a login attempt with use count 100 has been made to server A then server B must not accept a login with a hash that has a use count less than or equal to 100. This is firstly to cover the case where a MITM attack is used to login to server B with credentials that were previously used for server A. The second aim of this is to cover the case where a token that is temporarily unguarded is used to generate dozens of hashes while the hashes could be immediately used it is desirable to have them expire as soon as possible, and having the next login update the use count and invalidate such hashes is a good thing.
    The requirement that all servers know the current use count requires that they all trust a single server. In some situations this may not be possible, so it seems that this only works for servers within a single authentication domain or for access to less important data.
Methods of Accessing Tokens It seems that the following are the main ways of accessing tokens. To avoid driver issues and allow the use on random machines it seems that the USB keyboard and manual entry types of token are best. While for corporate Intranet use it seems that a SmartCard is best as it can be used for opening doors as well, you could use a USB keyboard token (such as a Yubikey) to open doors but it would be slower and there is no off the shelf hardware. For low cost and ease of implementation it seems that use-based tokens that connect via the USB keyboard interface are best. For best security it seems that a smart-card or USB interface to a device with a keypad for entering a password is ideal.

21 October 2009

Ingo Juergensmann: Webcam driver gspca with newer kernels?

Apparently in newer kernels my webcam, a Logitech QuickCam Communicate STX, does not work anymore. At least not the way it worked still in 2.6.26.2. There are some results in Google search showing that I'm not alone with that problem. Like this one.

But for the records: when I start, for example, camstream, I get the following output:

QUOTE:

[...]
D: CCamPanel::SetVisibleSize(640x480)
>> void CWebCamViewer::RecalcTotalViewSize()
<< void CWebCamViewer::RecalcTotalViewSize()
<< CWebCamViewer::CWebCamViewer(CVideoDevice*, QWidget*, const char*)
D: >> CVideoDevice::IncrementPalette(0)
D: >> CVideoDeviceLinux::StartCapture()
D: CVideoDeviceLinux::SetPalette picked palette 0 []
W: Unknown palette
D: >> CVideoDeviceLinux::CreateImagesRGB()
D: << CVideoDeviceLinux::CreateImagesRGB()
D: << CVideoDeviceLinux::StartCapture()
D: << CVideoDevice::IncrementPalette()
D: >> CVideoDeviceLinux::run()...
W: Unsupported palette 0
W: run(): VIDIOCSYNC(1) failed (Invalid argument)
W: VDLinux::run() VIDIOCMCAPTURE failed (Invalid argument)
W: run(): VIDIOCSYNC(1) failed (Invalid argument)
W: VDLinux::run() VIDIOCMCAPTURE failed (Invalid argument)
W: run(): VIDIOCSYNC(1) failed (Invalid argument)
W: VDLinux::run() VIDIOCMCAPTURE failed (Invalid argument)
W: run(): VIDIOCSYNC(1) failed (Invalid argument)
W: VDLinux::run() VIDIOCMCAPTURE failed (Invalid argument)
.
.
.


When I run camstream with the LD_PRELOAD trick from that Ubuntu launchpad entry above, I get this:

QUOTE:

[...]
D: CCamPanel::SetVisibleSize(640x480)
>> void CWebCamViewer::RecalcTotalViewSize()
<< void CWebCamViewer::RecalcTotalViewSize()
<< CWebCamViewer::CWebCamViewer(CVideoDevice*, QWidget*, const char*)
D: >> CVideoDevice::IncrementPalette(0)
D: >> CVideoDeviceLinux::StartCapture()
D: CVideoDeviceLinux::SetPalette picked palette 4 [rgb24]
D: >> CVideoDeviceLinux::CreateImagesRGB()
D: << CVideoDeviceLinux::CreateImagesRGB()
D: << CVideoDeviceLinux::StartCapture()
D: << CVideoDevice::IncrementPalette()
D: >> CVideoDeviceLinux::run()...
libv4lconvert: Error decompressing JPEG: unknown huffman code: 0000ffd9


This gives me a working video image from my webcam, but sadly, the colors are bad/wrong. So, it's not usuable as well:

Snapshot with gspca webcam


As you can see, the colors are bad. Red is for example blueish/purple. The two folder on the right in thet shelf are coloured yellow and red in reality, but in the snapshot they appear to be light teal and purple.

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