On how useful are R packages in Debian

Debian distributes the R language for statistical analysis, data mining or bioinformatics (among others). Satellite to R are hundreds of packages (kind of function libraries), mostly distributed by CRAN and Bioconductor, which contribute a lot to the richness and versatility of the R ecosystem. Debian redistributes some of these packages in the Debian format. Like in all similar cases of "redistribution of a distribution", there is a tension between Debian's goals for its stable version, and the expectations of novelty for the users (in part because the development cycle of R is 6 months), and one sometimes wonder if there is a point for using the packages through Debian and not through the upstream repositories.

Today, after installing a minimal system in a "schroot" container, I installed a R package and all its dependencies natively, that is by downloading their sources through the R command line, which made me wait for 90 minutes until everything compiles, while the R packages redistributed in Debian are already compiled. 90 minutes of compilation for 10 minutes of work; 90 minutes of waiting that I could have avoided with a couple of well-chosen "apt install" commands. Thus, many thanks to all who maintain R packages in Debian!

I moved to Okinawa!

I moved with my family to Okinawa in August, in the Akano neighborhood in the Uruma city. We arrived on time to see a bunch of eisaa, traditional dances using lots for drums, that often take place at the end of August. Each neighborhood has its own band and we hope we can join next year.

We live in a concrete building with a shared optic fiber connection. It has a good ping to the mainland, but the speed for big downloads is catastrophic in the evenings, when all families are using the fiber at the same time. Impossible to manage a simple sbuild-update -dragu unstable, and I could not contribute anything to Debian since them. It is frustrating; however there might be solutions through our GitLab forge.

On the work side, I joined the Okinawa Institute of Science and Technology Graduate University (OIST). It is a formidable place, open to the public even on week-end (note the opening hours of the café). If you come visit, please let me know!

Print with Brother from Debian

I ran into circles for more than one hour, before eventually understanding that one needs to install the lib32stdc++6 package in order to use the Brother drivers (HL-L2365DW printer) on an amd64 system, since they are provided as i386 packages. Only after, I realised that there was more than a hint in the online instructions. The hardest part was that without lib32stdc++6, everything seemed to work fine, except that nothing was coming out from the printer.

Still not going to Debconf....

I was looking forward to this year's Debconf in Taiwan, the first in Asia, and the perspective of attending it with no jet lag, but I happen to be moving to Okinawa and changing jobs on August 1st, right at the middle of it...

Moving is a mixed feeling of happiness and excitation for what I am about to find, and melancholy about what and whom I am about to leave. But flights to Tôkyô and Yokohama are very affordable.

Special thanks to the Tôkyô Debian study group, where I got my GPG key signed by Debian developers a long time ago :)

[solved] Beware of libinput 1.6.0-1

Since I updated this evening, touch to click with my touchpad is almost totally broken. Fortunately, a correction is pending.

update: To reinstall packages version 1.5.5-4 solves the problem in the meantime.

update: The packages version [1.6.1-1] in Sid work perfectly. Thanks!

apt purge ifupdown

...oh wow, it still works... I never had realised that network-manager did not need ifupdown.

I just finished to read the Imperial Radch trilogy.

I liked it a lot. There are already many comments on Internet (thanks Russ for making me discover these novels), so I will not go into details. And it is hard to summarise without spoiling. In brief:

The first tome, Ancillary Justice, makes us visit various worlds and cultures, and give us an impression of what it feels to be a demigod. The main culture does not make a difference between the two sexes, and the grammar of its language does not have genders. This gives an original taste to the story, for instance when the hero speaks a foreign language, he has difficulties to correctly address people without risking to frown them. Unfortunately the English language itself does not use gender very much, so the literary effect is a bit weakened. Perhaps the French translation (which I have not read) could be more interesting in that respect?

The second tome, Ancillary Sword, shows us how one can communicate things in a surveillance society without privacy, by subtle variations on how to serve tea. Gallons of tea are drunk in this tome, of which the main interest is the relation between the characters and heir conversations.

In the third tome, Ancillary Mercy, asks the question of what makes us human. Among the most interesting characters, there is a kind of synthetic human, who acts as ambassador for an alien race. At first, he indeed behaves completely alien, but in the end, he is not very different from a newborn who would happen by miracle to know how to speak: in the beginning the World makes no sense, but step by step and by experimenting, he deduces how it works. This is how this character ends up understanding that what is called "war" is a complex phenomenon where one of the consequences is a shortage of fish sauce.

I was a bit surprised that no book lead us at the heart of the Radch empire, but I just see on Wikipedia that one more novel is in preparation... One can speculate that central Radch resembles to a future dystopian West, in which surveillance of everybody is total and constant, but where people think they are happy, and peace and well-being inside are kept possible thanks to military operations outside, mostly performed by killer robots controlled by artificial intelligences. A not so distant future ?

It is a matter of course that there does not seem to by any Free software in the Radch empire. That reminds me that I did not contribute much to Debian while I was reading...

Who finished DEP 5?

Many people worked on finishing DEP 5. I think that the blog of Lars does not show enough how collective the effort was.

Looking in the specification's text, one finds:

The following alphabetical list is incomplete; please suggest missing people:
Russ Allbery, Ben Finney, Sam Hocevar, Steve Langasek, Charles Plessy, Noah
Slater, Jonas Smedegaard, Lars Wirzenius.

The Policy's changelog mentions:

  * Include the new (optional) copyright format that was drafted as
    DEP-5.  This is not yet a final version; that's expected to come in
    the release.  Thanks to all the DEP-5 contributors and to
    Lars Wirzenius and Charles Plessy for the integration into the
    Policy package.  (Closes: #609160)

 -- Russ Allbery <rra@debian.org>  Wed, 06 Apr 2011 22:48:55 -0700


debian-policy ( unstable; urgency=low

  [ Russ Allbery ]
  * Update the copyright format document to the version of DEP-5 from the
    DEP web site and apply additional changes from subsequent discussion
    in debian-devel and debian-project.  Revise for clarity, to add more
    examples, and to update the GFDL license versions.  Thanks, Steve
    Langasek, Charles Plessy, Justin B Rye, and Jonathan Nieder.
    (Closes: #658209, #648387)

On my side, I am very grateful to Bill Alombert for having committed the document in the Git repository, which ended the debates.

Amazon cloud: refreshing my skills.

For a few years I did not attempt any serious task on the Amazon cloud. It took me a bit of time to get back my automatisms and adapt myself to the changes. In particular, the cheapest instances, t2.nano, are only accessible via virtual private clouds (VPC), and it was a bit difficult for me to find how to create a simple one. Perhaps this is because all AWS accounts created after March 18, 2013, automatically have a default VPC, and everybody else who needed their own simple VPC have created it a long time ago already. In the end, this was not complicated at all. This is probably why I could not find a tutorial.

In brief, one needs first to create a VPC. If it is just for spawning an instance from time to time, the IP range does not matter much. Default VPCs are using, so let's do the same.

aws ec2 create-vpc --cidr-block $CIDR_BLOCK

In the command's output, there is the VPC's identifier, that I paste by hand in a variable called VPC. The same pattern will be repeated for each command creating something. One can also find the VPC's identifier with the command aws ec2 describe-vpcs.


Then, create a subnet. Again, no need for complications, in our simple case one can give the full IP range. I cut and paste the returned identifier in the variable SUBNET. In order that the instances receive a public IP address like in default VPCs and like in the usual behaviour of the VPC-less Cloud, one needs to set the attribute MapPublicIpOnLaunch.

aws ec2 create-subnet --vpc-id $VPC --cidr-block $CIDR_BLOCK
aws ec2 modify-subnet-attribute --subnet-id $SUBNET --map-public-ip-on-launch 

Then, create a gateway (paste the identifier in GATEWAY) and attach it to the VPC.

aws ec2 create-internet-gateway
aws ec2 attach-internet-gateway --internet-gateway-id $GATEWAY --vpc-id $VPC

A routing table was created automatically, and one can find its identifier via the command describe-route-tables. Then, create a default route to the gateway.

aws ec2 describe-route-tables
aws ec2 create-route --route-table-id $ROUTETABLE --destination-cidr-block --gateway-id $GATEWAY

Of course, if one does not open the traffic, no instance can be contacted from outside... Here I open port 22 for SSH.

aws ec2 describe-security-groups
aws ec2 authorize-security-group-ingress --group-id $SECURITY_GROUP --protocol tcp --port 22 --cidr

Other novelty, now Amazon distributes some Free tools for the command line, that are more comprehensive than euca2ools.

Next, I will try again the Debian Installer in the Cloud.