Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Do not use Hermes Paketversand for packages delivery in Germany

    2nd September 2014

    Note: this is a rant. Unless you are specifically interested in the subject (keywords: delivery, hermes, failure, amazon), you should not read this.

    I buy a lot on amazon.de – this is easy and convenient. Most of the time it also works good, with items arriving as promised or (mostly) earlier. Sometimes there are minor problems, but nothing worth remembering or mentioning. However, my latest order, “delivered” by Hermes Paketversand, was such a spectacular failure, that it deserves a blog post.

    My item was expected to arrive on Tuesday, the 5th of August. In the evening of that day we found an important message from Hermes in our mailbox, saying that We were unable to deliver your package, we come again tomorrow, on the 6th of August. Hmmm. That is strange. My wife was at home in the 1st half of the day, when Hermes, supposedly, was delivering my package (I learned about their delivery time later from delivery tracking page). This is what I would call a minor problem, not really an issue. Maybe, for some reason, the door bell wasn’t heard, and our delivery did not reach us. But it comes next day, right? Right?…

    There was absolutely nothing – not even a note – delivered in the following 4 days. On Saturday I started worrying. I checked Amazon package delivery status (detailed), which said that we have missed 3 (!) delivery attempts between 9:00 and 13:00 on August 5-7. I could have believed one miss, but three in a row, with my wife at home… that is extremely strange, to say the least. Anyway, I was ready to forgive this, as long as I get the package.
    Read the rest of this entry »

    Posted in Misc, Rant | No Comments »

    How to update a multisite Drupal 6/7 installation using Drush

    25th August 2014

    There are quite a lot of posts on how to do this, but my differs a tiny little bit, so I’m saving it for my own future reference, and also for the benefits of the wider audience.

    I am updating a multisite Drupal 6 installation. To the best of my knowledge, the only difference for Drupal 7 is that instead of the site_offline D6 variable the maintenance_mode variable is used in D7.

    On Debian stable and later, you can sudo aptitude install drush and then just use it immediately after that.

    Note: I recommend su webuser (or sudo -s followed by sudo -s -u webuser) before you run any non-testing drush commands, where webuser is the user which owns your web-exposed files (e.g. Debian’s default is, I think, www-data). I’ve seen a lot of recommendations to run drush as a super-user, but that does not make sense, and may actually cause problems with file ownership.

    One last thing before we start: if your drush seems to work fine but hangs when untarring modules – check this solution.

    Read the rest of this entry »

    Posted in *nix, Drupal, how-to, Notepad, PHP, Programming, Software, Web | 1 Comment »

    drush pm-update fails: tar hangs when extracting *.tar.gz module archives from drupal.org

    25th August 2014

    Drush is awesome, especially for updating multisite Drupal installations.
    I had only started using it a few days ago, and I’ve immediately hit a problem, to which I did find a workaround.

    Symptoms

    • running drush @sites pm-update results in normal execution up to after answering ‘y[es]‘; then drush seems to hang indefinitely (haven’t waited beyond about 10 minutes, maybe it does produce an error after a long while);
    • running the same command with --debug shows that drush hangs when trying to untar the downloaded module.tar.gz archive; there are no errors/warnings, it just hangs with no CPU usage;
    • trying to untar any of the modules downloaded from drupal.org manually is also unsuccessful: tar -xzvf module.tar.gz seems to do nothing, it also hangs with zero CPU usage/time and no warnings/errors;
    • interestingly, if I create some test.tar.gz locally, tar does happily extract that;
    • finally, running strace tar -xzvf module.tar.gz shows a number of unexpected lines, such as references to NSS and libnss files (I am only showing some of the lines of strace output, including the last line):

      open(“/etc/nsswitch.conf”, O_RDONLY) = 4
      read(4, “# /etc/nsswitch.conf\n#\n# Example”…, 4096) = 683
      open(“/lib/x86_64-linux-gnu/libnss_nis.so.2″, O_RDONLY) = 4
      open(“/lib/x86_64-linux-gnu/libnss_files.so.2″, O_RDONLY) = 4
      open(“/etc/passwd”, O_RDONLY|O_CLOEXEC) = 4
      open(“/usr/lib/x86_64-linux-gnu/libnss_mysql.so.2″, O_RDONLY) = 4
      open(“/etc/group”, O_RDONLY|O_CLOEXEC) = 4
      open(“/etc/libnss-mysql.cfg”, O_RDONLY) = -1 EACCES (Permission denied)
      open(“/etc/libnss-mysql-root.cfg”, O_RDONLY) = -1 EACCES (Permission denied)
      futex(0x7fd0816e8c48, FUTEX_WAIT_PRIVATE, 2, NULL

    Read the rest of this entry »

    Posted in *nix, Drupal, Notepad, Software | No Comments »

    Good hands-on explanation of differences between Spearman’s and Pearson’s correlation

    22nd April 2014

    Linear correlation vs. Rank order correlation: drag 11 data points around the plot and observe how both Spearman’s and Pearson’s correlation measures change. But first follow the Next button at the bottom-right for a guided tour of data manipulations.

    Posted in Links, Science | No Comments »

    Stopfake.org: journalists fight against pro-war, anti-Ukrainian propaganda in Russian state mass-media

    27th March 2014

    Since December 2013 Russian state mass-media were supporting the former president of Ukraine V. Yanukovych and his criminal, authoritarian kleptocracy.

    Manipulating and distorting facts, and even making up fictitious “events”, Russian state mass-media (and personally Dmitri Kiselyov) tried very hard to depict protesters in the least favorable light possible – as violent gangsters, thugs, fascists, attackers of innocent policemen. (Dmitri Kiselyov, apparently for his fervent propaganda services, was promoted by Putin to become the head of the newly-created Russian state news agency.)

    Russian state mass-media never reported about kidnapped and tortured and murdered protesters, protesters who lost eyes after being shot to the head with rubber bullets, heavily beaten protesters with broken ribs and internal organs rupture.

    They also somehow failed to notice that after the night of November, 30, 2013, the protests were no longer about the EU association treaty, but about the responsibility of those guilty of badly exceeding authority during the night beatings of protesters in Kyiv.

    Further escalation of the crisis and street protests was always the (delayed) consequence of authorities using illegally excessive force against the protesters. After the “Party of regions” tried to basically forbid the entire protest movement with a set of laws in mid-January (while the president-controlled police and prosecutors office were opening hundreds of criminal prosecution cases against the protesters), Euromaidan, out of well-understandable desperation, escalated into open fighting with the now-disbanded “Berkut” special police forces. The Russian propaganda machine was omitting causal events, while depicting the protesters’ response to (unrevealed) oppression, and this was probably the least disgusting technique used.

    Further Yanukovych actions made crystal-clear the primary reason for strong Russian media support: Yanukovych response to the protests was fully coordinated with (and, highly likely, suggested or even ordered by) Moscow. Multiple pieces of evidence support this claim, I’ll only mention two:

    • according to, if I remember correctly, Inna Bohoslovska (member of parliament, the former president’s “Party of regions” faction), every time after tension-decreasing agreements were negotiated and nearly finalized between the former president and opposition leaders (who were representing protesters), the phone call to Moscow followed, after which negotiations were aborted without finalizing any agreements;
    • when the EU officials had a night-long negotiation with Yanukovych, discussing ways out of the crisis, Yanukovych interrupted negotiations to call Putin.

    Clearly, Yanukovych was good for Putin because he was, in fact, a nearly-puppet “president”. Had Yanukovych survived the crisis, the 2015 presidential elections in Ukraine would be as clear and honest as the Crimean referendum, most likely extending Yanukovych presidency for the 2nd term. He could have then followed in the steps of the presidents of Belarus or Kazakhstan (who keep being presidents for many years and even decades). A controllable president of Ukraine was a clear win for Putin, and he didn’t care (and still doesn’t care, of course) about the citizens of Ukraine.

    But I digress, as there is indeed a lot to write on the subject. When the Russian military invasion into Ukraine started at the end of February, Russian mass-media kept generating propaganda; now it had the goal to help Putin gain support inside Russia, to brainwash the citizens of Russian Federation (and, to a certain extent, the Russian-speaking Ukrainian citizens who haven’t yet realized that Russian mass-media are poisonous) into believing in (totally ungrounded) scary tales about the hardships and life-threatening conditions of Russian-speaking people in Ukraine.

    To counter Russian propaganda, a group of journalists and volunteers created an anti-propaganda, anti-lies website StopFake.org, which collects lies from Russian mass-media and finds materials proving those are indeed lies.

    Rule of thumb: don’t trust Russian media.
    Especially when they are talking about Ukraine.

    Posted in Society, Ukraine | No Comments »

    How to cite PHYLIP

    10th January 2014

    Official PHYLIP FAQ does suggest a few ways to cite the software, but I believe that the best citation is mentioned in the wikipedia PHYLIP article: pubmed reference for PMID 7288891. This PubMed citations seems the best, because

    • it does mention the software tool implementing the maximum likelihood approach,
    • it is likely the earliest mention of the PHYLIP software (which was distributed since around 1980),
    • it refers to a journal indexed by pubmed, and
    • according to Google Scholar, it was already cited over 6660 times :)

    Posted in Links, Science, Software | No Comments »

    Debian command of the day: popcon-largest-unused

    2nd January 2014

    From the Debian squeeze to wheezy upgrade guide:

    Remove packages that take up too much space and are not currently needed (you can always reinstall them after the upgrade). If you have popularity-contest installed, you can use sudo popcon-largest-unused to list the packages you do not use that occupy the most space. You can find the packages that just take up the most disk space with dpigs (available in the debian-goodies package) or with wajig (running wajig size). They can also be found with aptitude. Start aptitude in “visual mode”, select Views → New Flat Package List, press l and enter ~i, then press S and enter ~installsize. This will give you a handy list to work with.

    Posted in *nix | No Comments »