Search Results: "nate"

26 April 2017

Dirk Eddelbuettel: RcppTOML 0.1.3

A bug fix release of RcppTOML arrived on CRAN today. Table arrays were (wrongly) not allowing for nesting; a simply recursion fix addresses this. RcppTOML brings TOML to R. TOML is a file format that is most suitable for configurations, as it is meant to be edited by humans but read by computers. It emphasizes strong readability for humans while at the same time supporting strong typing as well as immediate and clear error reports. On small typos you get parse errors, rather than silently corrupted garbage. Much preferable to any and all of XML, JSON or YAML -- though sadly these may be too ubiquitous now. TOML is making good inroads with newer and more flexible projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka "packages") for the Rust language.

Changes in version 0.1.3 (2017-04-25)
  • Nested TableArray types are now correctly handled (#16)

Courtesy of CRANberries, there is a diffstat report for this release. More information is on the RcppTOML page page. Issues and bugreports should go to the GitHub issue tracker.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

23 April 2017

Mark Brown: Bronica Motor Drive SQ-i

I recently got a Bronica SQ-Ai medium format film camera which came with the Motor Drive SQ-i. Since I couldn t find any documentation at all about it on the internet and had to figure it out for myself I figured I d put what I figured out here. Hopefully this will help the next person trying to figure one out, or at least by virtue of being wrong on the internet I ll be able to get someone who knows what they re doing to tell me how the thing really works. Bottom plate The motor drive attaches to the camera using the tripod socket, a replacement tripod socket is provided on the base of plate. There s also a metal plate with the bottom of the hand grip attached to it held on to the base plate with a thumb screw. When this is released it gives access to the screw holding in the battery compartment which (very conveniently) takes 6 AA batteries. This also provides power to the camera body when attached. Bottom plate with battery compartment visible On the back of the base of the camera there s a button with a red LED next to it which illuminates slightly when the button is pressed (it s visible in low light only). I m not 100% sure what this is for, I d have guessed a battery check if the light were easier to see. Top of drive On the top of the camera there is a hot shoe (with a plastic blanking plate, a nice touch), a mode selector and two buttons. The larger button on the front replicates the shutter release button on the body (which continues to function as well) while the smaller button to the rear of the camera controls the motor depending on the current state of the camera it cocks the shutter, winds the film and resets the mirror when it is locked up. The mode dial offers three modes: off, S and C. S and C appear to correspond to the S and C modes of the main camera, single and continuous mirror lockup shots. Overall with this grip fitted and a prism attached the camera operates very similarly to a 35mm SLR in terms of film winding and so on. It is of course heavier (the whole setup weighs in at 2.5kg) but balanced very well and the grip is very comfortable to use.

22 April 2017

Manuel A. Fernandez Montecelo: Debian GNU/Linux port for RISC-V 64-bit (riscv64)

This is a post describing my involvement with the Debian GNU/Linux port for RISC-V (unofficial and not endorsed by Debian at the moment) and announcing the availability of the repository (still very much WIP) with packages built for this architecture. If not interested in the story but you want to check the repository, just jump to the bottom. Roots A while ago, mostly during 2014, I was involved in the Debian port for OpenRISC (or1k) about which I posted (by coincidence) exactly 2 years ago. The two of us working on the port stopped in August or September of that year, after knowing that the copyright of the code to add support for this architecture in GCC would not be assigned to the FSF, so it would never be added to GCC upstream unless the original authors changed their mind (which they didn't) or there was a clean-room reimplementation (which didn't happen so far). But a few other key things contributed to the decision to stop working on that port, which bear direct relationship to this story. One thing that particularly influenced me to stop working on it was a sense of lack of purpose, all things considered, for the OpenRISC port that we were working on. For example, these chips are sometimes used as part of bigger devices by Samsung to control or wake up other chips; but it was not clear whether there would ever be devices with OpenRISC as the main chip, specially in devices powerful enough to run Linux or similar kernels, and Debian on top. One can use FPGAs to synthesise OpenRISC or1k, but these are slow, and expensive when using lots of memory. Without prospects of having hardware easily available to users, there's not much point in having a whole Debian port ready to run on hardware that never comes to be. Yeah, sure, it's fun to create such a port, but it's tons of work to maintain and keep it up to-date forever, and with close to zero users it's very unrewarding. Another thing that contributed to decide to stop is that, at least in my opinion, 32-bit was not future-proof enough for general purpose computing, specially for new devices and ports starting to take off on that time and age. There was some incipient work to create another OpenRISC design for 64-bits, but it was still in an early phase. My secret hope and ultimate goal was to be able to run as much a free-ish computer as possible as my main system. Still today many people are buying and using 32-bit devices, like small boards; but very few use it as their main computer or servers for demanding workloads or complex services. So for me, even if feasible if one is very austere and dedicated, OpenRISC or1k failed that test. And lastly, another thing happened at the time... Enter RISC-V In August 2014, at the point when we were fully acknowledging the problem of upstreaming (or rather, lack thereof) the support for OpenRISC in GCC, RISC-V was announced to the world, bringing along papers with suggestive titles such as Instruction Sets Should Be Free: The Case For RISC-V (pdf) and articles like RISC-V: An Open Standard for SoCs - The case for an open ISA in EE Times. RISC-V (as the previous RISC-n marks) had been designed (or rather, was being designed, because it was and is an as yet unfinished standard) by people from UC Berkeley, including David Patterson, the pioneer of RISC computer designs and co-author of the seminal book Computer Architecture: A Quantitative Approach . Other very capable people are also also leading the project, doing the design and legwork to make it happen see the list of contributors. But, apart from throwing names, the project has many other merits. Similarly to OpenRISC, RISC-V is an open instruction set architecture (ISA), but with the advantage of being designed in more recent times (thus avoiding some mistakes and optimising for problems discovered more recently, as technology evolves); with more resources; with support for instruction widths of 32, 64 and even 128 bits; with a clean set of standard but optional extensions (atomics, float, double, quad, vector, ...); and with reserved space to add new extensions in ordered and compatible ways. In the view of some people in the OpenRISC community, this unexpected development in a way made irrelevant the ongoing update of OpenRISC for 64-bits, and from what I know and for better or worse, all efforts on that front stopped. Also interestingly (if nothing else, for my purposes of running as much a free system as possible), was that the people behind RISC-V had strong intentions to make it useful to create modern hardware, and were pushing heavily towards it from the beginning. And together with this announcement or soonly after, it came the promise of free-ish hardware in the form of the lowRISC project. Although still today it seems to be a long way from actually shipping hardware, at least there was some prospect of getting it some day. On top of all that, about the freedom aspect, both the Berkeley and lowRISC teams engaged since very early on with the free hardware community, including attending and presenting at OpenRISC events; and lowRISC intended to have as much free hardware as possible in their planned SoC. Starting to work on the Debian port, this time for RISC-V So in late 2014 I slowly started to prepare the Debian port, switching on and off. The Userland spec was frozen in 2014 just before the announcement, the Privilege one is still not frozen today, so there was no need to rush. There were plans to upstream the support in the toolchain for RISC-V (GNU binutils, glibc and GCC; Linux and other useful software like Qemu) in 2015, but sadly these did not materialise until late 2016 and 2017. One of the main reasons for the delay was due to the slowness to sort out the copyright assignment of the code to the FSF (again). Still today, only binutils and GCC are upstreamed, and Linux and glibc depend on the Privilege spec being finished, so it will take a while. After the experience with OpenRISC and the support in GCC, I didn't want to invest too much time, lest it all became another dead-end due to lack of upstreaming so I was just cross-compiling here and there, testing Qemu (which still today is very limited for this architecture, e.g. no network support and very limited character and block devices) and trying to find and report bugs in the implementations, and send patches (although I did not contribute much in the end). Incompatible changes in the toolchain In terms of compiling packages and building-up a repository, things were complicate, and less mature and stable than the OpenRISC ones were even back in 2014. In theory, with the Userland spec being frozen, regular programs (below the Operating System level) compiled at any time could have run today; but in practice what happened is that there were several rounds of profound or, at least, disrupting changes in the toolchain before and while being upstreamed, which made the binary packages that I had built to not work at all (changes in dynamic loader, registers where arguments are stored when jumping functions, etc.). These major breakages happened several times already, and kind of unexpectedly at least for the people not heavily involved in the implementation. When the different pieces are upstreamed it is expected that these breakages won't happen; but still there's at least the fundamental bit of glibc, which will probably change things once again in incompatible ways before or while being upstreamed. Outside Debian but within the FOSS / Linux world, the main project that I know of is that some people from Fedora also started a port in mid 2016 and did great advances, but from what I know they put the project in the freezer in late 2016 until all such problems are resolved they don't want to spend time rebootstrapping again and again. What happened recently on the Debian front In early 2016 I created the page for RISC-V in the Debian wiki, expecting that things were at last fully stable and the important bits of the toolchain upstreamed during that year I was too optimistic. Some other people (including Debian folks) have been contributing for a while, in the wiki, mailing lists and IRC channels, and in the RISC-V project mailing lists you will see their names everywhere. However, due to the combination of lack of hardware, software not upstreamed and shortcomings of emulators (chiefly Qemu) make contributions hard and very tedious, nothing much happened recently visible to the outside world in terms of software. The private repository-in-the-making In late 2015 and beginning of 2016, having some free time in my hands and expecting that all things would coalesce quickly, I started to build a repository of binary packages in a more systematic way, with most of the basic software that one can expect in a basic Debian system (including things common to all Linux systems, and also specific Debian software like dpkg or apt, and even aptitude!). After that I also built many others outside the basic system (more than 1000 source packages and 2000 or 3000 arch-dependent binary packages in total), specially popular libraries (e.g. boost, gtk+ version 2 and 3), interpreters (several versions of lua, perl and python, also version 2 and 3) and in general packages that are needed to build many other packages (like doxygen). Unfortunately, some of these most interesting packages do not compile cleanly (more because of obscure or silly errors than proper porting), so they are not included at the moment. I intentionally avoided trying to compile thousands of packages in the archive which would be of nobody's use at this point; but many more could be compiled without much effort. About the how, initially I started cross-compiling and using rebootstrap, which was of great help in the beginning. Some of the packages that I cross-compiled had bugs that I did not know how to debug without a live and native (within emulators) system, so I tried to switch to natively built packages very early on. For that I needed many packages built natively (like doxygen or cmake) which would be unnecessary if I remained cross-compiling the host tools would be used in that case. But this also forced me to eat my own dog food, which even if much slower and tedious, it was on the whole a more instructive experience; and above all, it helped to test and make sure that the the tools and the whole stack was working well enough to build hundreds of packages. Why the repository-in-the-making was private Until now I did not attempt to make the repository available on-line, for several reasons. First because it would be kind of useless to publish files that were not working or would soon not work, due to the incompatible changes in the toolchain, rendering many or most of the packages built useless. And because, for many months now, I expected that things would stabilise and to have something stable really soon now but this didn't happen yet. Second because of lack of resources and time since mid 2016, and because I got some packages only compiled thanks to (mostly small and unimportant, but undocumented and unsaved) hacks, often working around temporary bugs and thus not worth sending upstream; but I couldn't share the binaries without sharing the full source and fulfill licenses like the GNU GPL. I did a new round of clean rebuilds in the last few weeks, just finished, the result is close to 1000 arch-dependent packages. And third, because of lack of demand. This changed in the last few weeks, when other people started to ask me to share the results even if incomplete or not working properly (I had one request in the past, but couldn't oblige in time at the time). Finally, the work so far: repository now on-line So finally, with the great help from Kurt Keville from MIT, and Bytemark sponsoring a machine where most of the packages were built, here we have the repository: The lines for /etc/apt/sources.list are:
 deb [ arch=riscv64 signed-by=/usr/share/keyrings/debian-keyring.gpg ] http://riscv.mit.edu/debian unstable main
 deb-src [ signed-by=/usr/share/keyrings/debian-keyring.gpg ] http://riscv.mit.edu/debian unstable main
The repository is signed with my key as Debian Developer, contained in the file /usr/share/keyrings/debian-keyring.gpg, which is part of the package debian-keyring (available from Debian and derivatives). WARNING!! This repository, though, is very much WIP, incomplete (some package dependencies cannot be fulfilled, and it's only a small percentage of the Debian archive, not trying to be comprehensive at the moment) and probably does not work at all in your system at this point, for the following reasons: The combination of all these shortcomings is specially unfortunate, because without glibc provided it will be difficult that you can get the binaries to run at all; but there are some packages that are arch-dependent but not too tied to libc or the dynamic loader will not be affected. At least you can try one the few static packages present in Debian, like the one in the package bash-static. When one removes moving parts like the dynamic loader and libc, since the basic machine instructions are stable for several years now, it should work, but I wouldn't discard some dark magic that prevents even static binaries from working. Still, I hope that the respository in its current state is useful to some people, at least for those who requested it. If one has the environment set-up, it's easy to unpack the contents of the .deb files and try out the software (which often is not trivial or very slow to compile, or needs lots of dependencies to be built first first). ... and finally, even if not useful at all for most people at the moment, by doing this I also hope that efforts like this spark your interest to contribute to free software, free hardware, or both! :-)

21 April 2017

Rhonda D'Vine: Home

A fair amount of things happened since I last blogged something else than music. First of all we did actually hold a Debian Diversity meeting. It was quite nice, less people around than hoped for, and I account that to some extend to the trolls and haters that defaced the titanpad page for the agenda and destroyed the doodle entry for settling on a date for the meeting. They even tried to troll my blog with comments, and while I did approve controversial responses in the past, those went over the line of being acceptable and didn't carry any relevant content. One response that I didn't approve but kept in my mailbox is even giving me strength to carry on. There is one sentence in it that speaks to me: Think you can stop us? You can't you stupid b*tch. You have ruined the Debian community for us. The rest of the message is of no further relevance, but even though I can't take credit for being responsible for that, I'm glad to be a perceived part of ruining the Debian community for intolerant and hateful people. A lot of other things happened since too. Mostly locally here in Vienna, several queer empowering groups were founding around me, some of them existed already, some formed with the help of myself. We now have several great regular meetings for non-binary people, for queer polyamory people about which we gave an interview, a queer playfight (I might explain that concept another time), a polyamory discussion group, two bi-/pansexual groups, a queer-feminist choir, and there will be an European Lesbian* Conference in October where I help with the organization and on June 21st I'll finally receive the keys to my flat in Que[e]rbau Seestadt. I'm sooo looking forward to it. It will be part of the Let me come Home experience that I'm currently in. Another part of that experience is that I started changing my name (and gender marker) officially. I had my first appointment in the corresponding bureau, and I hope that it won't last too long because I have to get my papers in time for booking my flight to Montreal, and somewhen along the process my current passport won't contain correct data anymore. So for the people who have it in their signing policy to see government IDs this might be your chance to finally sign my key then. I plan to do a diversity BoF at debconf where we can speak more directly on where we want to head with the project. I hope I'll find the time to do an IRC meeting beforehand. I'm just uncertain how to coordinate that one to make it accessible for interested parties while keeping the destructive trolls out. I'm open for ideas here.

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Dirk Eddelbuettel: Rblpapi 0.3.6

Time for a new release of Rblpapi -- version 0.3.6 is now on CRAN. Rblpapi provides a direct interface between R and the Bloomberg Terminal via the C++ API provided by Bloomberg Labs (but note that a valid Bloomberg license and installation is required). This is the seventh release since the package first appeared on CRAN last year. This release brings a very nice new function lookupSecurity() contributed by Kevin Jin as well as a number of small fixes and enhancements. Details below:

Changes in Rblpapi version 0.3.6 (2017-04-20)
  • bdh can now store in double preventing overflow (Whit and John in #205 closing #163)
  • bdp documentation has another ovveride example
  • A new function lookupSecurity can search for securities, optionally filtered by yellow key (Kevin Jin and Dirk in #216 and #217 closing #215)
  • Added file init.c with calls to R_registerRoutines() and R_useDynamicSymbols(); also use .registration=TRUE in useDynLib in NAMESPACE (Dirk in #220)
  • getBars and getTicks can now return data.table objects (Dirk in #221)
  • bds has improved internal protect logic via Rcpp::Shield (Dirk in #222)

Courtesy of CRANberries, there is also a diffstat report for the this release. As always, more detailed information is on the Rblpapi page. Questions, comments etc should go to the issue tickets system at the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

20 April 2017

Dirk Eddelbuettel: RcppQuantuccia 0.0.1

New package! And, as it happens, a effectively a subset or variant of one my oldest packages, RQuantLib. Fairly recently, Peter Caspers started to put together a header-only subset of QuantLib. He called this Quantuccia, and, upon me asking, said that it stands for "little sister" of QuantLib. Very nice. One design goal is to keep Quantuccia header-only. This makes distribution and deployment much easier. In the fifteen years that we have worked with QuantLib by providing the R bindings via RQuantLib, it has always been a concern to provide current QuantLib libraries on all required operating systems. Many people helped over the years but it is still an issue, and e.g. right now we have no Windows package as there is no library build it against. Enter RcppQuantuccia. It only depends on R, Rcpp (for seamless R and C++ integrations) and BH bringing Boost headers. This will make it much easier to have Windows and macOS binaries. So what can it do right now? We started with calendaring, and you can compute date pertaining to different (ISDA and other) business day conventions, and compute holiday schedules. Here is one example computing inter alia under the NYSE holiday schedule common for US equity and futures markets:
R> library(RcppQuantuccia)
R> fromD <- as.Date("2017-01-01")
R> toD <- as.Date("2017-12-31")
R> getHolidays(fromD, toD)        # default calender ie TARGET
[1] "2017-04-14" "2017-04-17" "2017-05-01" "2017-12-25" "2017-12-26"
R> setCalendar("UnitedStates")
R> getHolidays(fromD, toD)        # US aka US::Settlement
[1] "2017-01-02" "2017-01-16" "2017-02-20" "2017-05-29" "2017-07-04" "2017-09-04"
[7] "2017-10-09" "2017-11-10" "2017-11-23" "2017-12-25"
R> setCalendar("UnitedStates::NYSE")
R> getHolidays(fromD, toD)        # US New York Stock Exchange
[1] "2017-01-02" "2017-01-16" "2017-02-20" "2017-04-14" "2017-05-29" "2017-07-04"
[7] "2017-09-04" "2017-11-23" "2017-12-25"
R>
The GitHub repo already has a few more calendars, and more are expected. Help is of course welcome for both this, and for porting over actual quantitative finance calculations. More information is on the RcppQuantuccia page. Issues and bugreports should go to the GitHub issue tracker.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

17 April 2017

Ross Gammon: My March 2017 Activities

March was a busy month, so this monthly report is a little late. I worked two weekends, and I was planning my Easter holiday, so there wasn t a lot of spare time. Debian
  • Updated Dominate to the latest version and uploaded to experimental (due to the Debian Stretch release freeze).
  • Uploaded the latest version of abcmidi (also to experimental).
  • Pinged the bugs for reverse dependencies of pygoocanvas and goocanvas with a view to getting them removed from the archive during the Buster cycle.
  • Asked for help on the Ubuntu Studio developers and users mailing lists to test the coming Ubuntu Studio 17.04 release ISO, because I would be away on holiday for most of it.
Ubuntu
  • Worked on ubuntustudio-controls, reverting it back to an earlier revision that Len said was working fine. Unfortunately, when I built and installed it from my ppa, it crashed. Eventually found my mistake with the bzr reversion, fixed it and prepared an upload ready for sponsorship. Submitted a Freeze Exception bug in the hope that the Release Team would accept it even though we had missed the Final Beta.
  • Put a new power supply in an old computer that was kaput, and got it working again. Set up Ubuntu Server 16.04 on it so that I could get a bit more experience with running a server. It won t last very long, because it is a 32 bit machine, and Ubuntu will probably drop support for that architecture eventually. I used two small spare drives to set up RAID 1 & LVM (so that I can add more space to it later). I set up some Samba shares, so that my wife will be able to get at them from her Windows machine. For music streaming, I set up Emby Server. I wold be great to see this packaged for Debian. I uploaded all of my photos and music for Emby to serve around the home (and remotely as well). Set up Obnam to back up the server to an external USB stick (temporarily until I set up something remote). Set LetsEncrypt with the wonderful Certbot program.
  • Did the Release Notes for Ubuntu Studio 17.04 Final Beta. As I was in Brussels for two days, I was not able to do any ISO testing myself.
Other
  • Measured up the new model railway layout and documented it in xtrkcad.
  • Started learning Ansible some more by setting up ssh on all my machines so that I could access them with Ansible and manipulate them using a playbook.
  • Went to the Open Source Days conference just down the road in Copenhagen. Saw some good presentations. Of interest for my previous work in the Debian GIS Team, was a presentation from the Danish Municipalities on how they run projects using Open Source. I noted how their use of Proj 4 and OSGeo. I was also pleased to see a presentation from Ximin Luo on Reproducible Builds, and introduced myself briefly after his talk (during the break).
  • Started looking at creating a Django website to store and publish my One Name Study sources (indexes). Started by creating a library to list some of my recently read Journals. I will eventually need to import all the others I have listed in a cvs spreadsheet that was originally exported from the commercial (Windows only) Custodian software.
Plan status from last month & update for next month Debian For the Debian Stretch release:
  • Keep an eye on the Release Critical bugs list, and see if I can help fix any. In Progress
Generally:
  • Package all the latest upstream versions of my Debian packages, and upload them to Experimental to keep them out of the way of the Stretch release. In Progress
  • Begin working again on all the new stuff I want packaged in Debian.
Ubuntu
  • Start working on an Ubuntu Studio package tracker website so that we can keep an eye on the status of the packages we are interested in. Started
  • Start testing & bug triaging Ubuntu Studio packages. In progress
  • Test Len s work on ubuntustudio-controls Done
  • Do the Ubuntu Studio Zesty 17.04 Final Beta release. Done
  • Sort out the Blueprints for the coming Ubuntu Studio 17.10 release cycle.
Other
  • Give JMRI a good try out and look at what it would take to package it. In progress
  • Also look at OpenPLC for simulating the relay logic of real railway interlockings (i.e. a little bit of the day job at home involving free software fun!). In progress

15 April 2017

Dirk Eddelbuettel: Rcpp now used by 1000 CRAN packages

800 Rcpp packages Moments ago Rcpp passed a big milestone as there are now 1000 packages on CRAN depending on it (as measured by Depends, Imports and LinkingTo, but excluding Suggests). The graph is on the left depicts the growth of Rcpp usage over time. One easy way to compute such reverse dependency counts is the tools::dependsOnPkgs() function that was just mentioned in yesterday's R^4 blog post. Another way is to use the reverse_dependencies_with_maintainers() function from this helper scripts file on CRAN. Lastly, devtools has a function revdep() but it has the wrong default parameters as it includes Suggests: which you'd have to override to get the count I use here (it currently gets 1012 in this wider measure). Rcpp cleared 300 packages in November 2014. It passed 400 packages in June 2015 (when I only tweeted about it), 500 packages in late October 2015, 600 packages last March, 700 packages last July, 800 packages last October and 900 packages early January. The chart extends to the very beginning via manually compiled data from CRANberries and checked with crandb. The next part uses manually saved entries. The core (and by far largest) part of the data set was generated semi-automatically via a short script appending updates to a small file-based backend. A list of packages using Rcpp is kept on this page. Also displayed in the graph is the relative proportion of CRAN packages using Rcpp. The four per-cent hurdle was cleared just before useR! 2014 where I showed a similar graph (as two distinct graphs) in my invited talk. We passed five percent in December of 2014, six percent July of 2015, seven percent just before Christmas 2015, eight percent last summer, and nine percent mid-December 2016. Ten percent is next; we may get there during the summer. 1000 user packages is a really large number. This puts a whole lot of responsibility on us in the Rcpp team as we continue to keep Rcpp as performant and reliable as it has been. And with that a very big Thank You! to all users and contributors of Rcpp for help, suggestions, bug reports, documentation or, of course, code.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

Dirk Eddelbuettel: #5: Easy package information

Welcome to the fifth post in the recklessly rambling R rants series, or R4 for short. The third post showed an easy way to follow R development by monitoring (curated) changes on the NEWS file for the development version r-devel. As a concrete example, I mentioned that it has shown a nice new function (tools::CRAN_package_db()) coming up in R 3.4.0. Today we will build on that. Consider the following short snippet:
library(data.table)
getPkgInfo <- function()  
    if (exists("tools::CRAN_package_db"))  
        dat <- tools::CRAN_package_db()
      else  
        tf <- tempfile()
        download.file("https://cloud.r-project.org/src/contrib/PACKAGES.rds", tf, quiet=TRUE)
        dat <- readRDS(tf)              # r-devel can now readRDS off a URL too
     
    dat <- as.data.frame(dat)
    setDT(dat)
    dat
 
It defines a simple function getPkgInfo() as a wrapper around said new function from R 3.4.0, ie tools::CRAN_package_db(), and a fallback alternative using a tempfile (in the automagically cleaned R temp directory) and an explicit download and read of the underlying RDS file. As an aside, just this week the r-devel NEWS told us that such readRDS() operations can now read directly from URL connection. Very nice---as RDS is a fantastic file format when you are working in R. Anyway, back to the RDS file! The snippet above returns a data.table object with as many rows as there are packages on CRAN, and basically all their (parsed !!) DESCRIPTION info and then some. A gold mine! Consider this to see how many package have a dependency (in the sense of Depends, Imports or LinkingTo, but not Suggests because Suggests != Depends) on Rcpp:
R> dat <- getPkgInfo()
R> rcppRevDepInd <- as.integer(tools::dependsOnPkgs("Rcpp", recursive=FALSE, installed=dat))
R> length(rcppRevDepInd)
[1] 998
R>
So exciting---we will hit 1000 within days! But let's do some more analysis:
R> dat[ rcppRevDepInd, RcppRevDep := TRUE]  # set to TRUE for given set
R> dat[ RcppRevDep==TRUE, 1:2]
           Package Version
  1:      ABCoptim  0.14.0
  2: AbsFilterGSEA     1.5
  3:           acc   1.3.3
  4: accelerometry   2.2.5
  5:      acebayes   1.3.4
 ---                      
994:        yakmoR   0.1.1
995:  yCrypticRNAs  0.99.2
996:         yuima   1.5.9
997:           zic     0.9
998:       ziphsmm   1.0.4
R>
Here we index the reverse dependency using the vector we had just computed, and then that new variable to subset the data.table object. Given the aforementioned parsed information from all the DESCRIPTION files, we can learn more:
R> ## likely false entries
R> dat[ RcppRevDep==TRUE, ][NeedsCompilation!="yes", c(1:2,4)]
            Package Version                                                                         Depends
 1:         baitmet   1.0.0                                                           Rcpp, erah (>= 1.0.5)
 2:           bea.R   1.0.1                                                        R (>= 3.2.1), data.table
 3:            brms   1.6.0                     R (>= 3.2.0), Rcpp (>= 0.12.0), ggplot2 (>= 2.0.0), methods
 4: classifierplots   1.3.3                             R (>= 3.1), ggplot2 (>= 2.2), data.table (>= 1.10),
 5:           ctsem   2.3.1                                           R (>= 3.2.0), OpenMx (>= 2.3.0), Rcpp
 6:        DeLorean   1.2.4                                                  R (>= 3.0.2), Rcpp (>= 0.12.0)
 7:            erah   1.0.5                                                               R (>= 2.10), Rcpp
 8:             GxM     1.1                                                                              NA
 9:             hmi   0.6.3                                                                    R (>= 3.0.0)
10:        humarray     1.1 R (>= 3.2), NCmisc (>= 1.1.4), IRanges (>= 1.22.10),\nGenomicRanges (>= 1.16.4)
11:         iNextPD   0.3.2                                                                    R (>= 3.1.2)
12:          joinXL   1.0.1                                                                    R (>= 3.3.1)
13:            mafs   0.0.2                                                                              NA
14:            mlxR   3.1.0                                                           R (>= 3.0.1), ggplot2
15:    RmixmodCombi     1.0              R(>= 3.0.2), Rmixmod(>= 2.0.1), Rcpp(>= 0.8.0), methods,\ngraphics
16:             rrr   1.0.0                                                                    R (>= 3.2.0)
17:        UncerIn2     2.0                          R (>= 3.0.0), sp, RandomFields, automap, fields, gstat
R> 
There are a full seventeen packages which claim to depend on Rcpp while not having any compiled code of their own. That is likely false---but I keep them in my counts, however relunctantly. A CRAN-declared Depends: is a Depends:, after all. Another nice thing to look at is the total number of package that declare that they need compilation:
R> ## number of packages with compiled code
R> dat[ , .(N=.N), by=NeedsCompilation]
   NeedsCompilation    N
1:               no 7625
2:              yes 2832
3:               No    1
R>
Isn't that awesome? It is 2832 out of (currently) 10458, or about 27.1%. Just over one in four. Now the 998 for Rcpp look even better as they are about 35% of all such packages. In order words, a little over one third of all packages with compiled code (which may be legacy C, Fortran or C++) use Rcpp. Wow. Before closing, one shoutout to Dirk Schumacher whose thankr which I made the center of the last post is now on CRAN. As a mighty fine and slim micropackage without external dependencies. Neat.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

14 April 2017

Laura Arjona Reina: Underestimating Debian

I had two issues in the last days that lead me a bit into panic until they got solved. In both cases the issue was external to Debian but I first thought that the problem was in Debian. I m not sure why I had those thoughts, I should be more confident in myself, this awesome operating system, and the community around it! The good thing is that I ll be more confident from now on, and I ve learned that hurry is not a good friend, and I should face my computer problems (and everything in life, probably) with a bit more patience (and backups). Issue 1: Corrupt ext partition in a laptop I have a laptop at home with dual boot Windows 7 + Debian 9 (Stretch). I rarely boot the Windows partition. When I do, I do whatever I need to do/test there, then install updates, and then shutdown the laptop or reboot in Debian to feel happy again when using computers. Some months ago I noticed that booting in Debian was not possible and I was left in an initramfs console that was suggesting to e2fsck /dev/sda6 (my Debian partition). Then I ran e2fsck, say a to fix all the issues found, and the system was booting properly. This issue was a bit scary-looking because of the e2fsck output making screen show random numbers and scrolling quickly for 1 or 2 minutes, until all the inodes or blocks or whatever were fixed. I thought about the disk being faulty, and ran badblocks, but faced the former boot issue again some time after, and then decided to change the disk (then I took the opportunity to make backups, and install a fresh Debian 9 Stretch in the laptop, instead of the Debian 8 stable that was running). The experience with Stretch has been great since then, but some days ago I faced the boot issue again. Then I realised that maybe the issue was appearing when I booted Debian right after using Windows (and this was why it was appearing not very often in my timeline  ). Then I payed more attention to the message that I was receiving in the console
Superblock checksum does not match superblock while trying to open /dev/sda6
 /dev/sda6:
 The superblock could not be read or does not describe a valid ext2/ext3/ext4
 filesystem. If the device is valid and it really contains an ext2/ext3/ext4
 filesystem (and not swap or ufs or something else), then the superblock
 is corrupt, and you might try running e2fsck with an alternate superblock:
 e2fsck -b 8193
 or
 e2fsck -b 32768
and searched about it, and also asked about it to my friends in the redeslibres XMPP chat room  I found this question in the AskUbuntu forum that was exactly my issue (I had ext2fsd installed in Windows). My friends in the XMPP room friendly yelled booo! at me for letting Windows touch my ext partitions (I apologised, it will never happen again!). I now consistently could reproduce the issue (boot Windows, then boot Debian, bang!: initramfs console, e2fsck, reboot Debian, no problem, boot Windows, boot Debian, again the problem, etc). I uninstalled the ext2fsd program and tried to reproduce the issue, and I couldn t reproduce it. So happy end. Issue 2: Accessing Android internal memory to backup files The other issue was with my tablet running Android 4.0.4. It was facing a charge issue, and I wanted to backup the files there before sending it to repair. I connected the tablet with USB to my laptop, and enabled USB debugging. The laptop recognized a MZ604 camera connected, but Dolphin (the file browser of my KDE Plasma desktop) could not show the files. I looked at the settings in the tablet to try to find the setting that allowed me to switch between camera/MTP when connecting with USB, but couldn t find it. I guessed that the tablet was correctly configured because I recall having made a backup some months ago, with no hassle (in Debian 8). I checked that my Debian (9) had installed the needed packages:
 ii kio-mtp 0.75+git20140304-2 amd64 access to MTP devices for applications using the KDE Platform
 ii libmtp-common 1.1.12-1 all Media Transfer Protocol (MTP) common files
 ii libmtp-runtime 1.1.12-1+b1 amd64 Media Transfer Protocol (MTP) runtime tools
 ii libmtp9:amd64 1.1.12-1+b1 amd64 Media Transfer Protocol (MTP) library
So I had no idea about what was going on. Then I suspected some problem in my Debian (maybe I was needing some driver for the Motorola tablet?) and booted Windows 7 to see what happened there. Windows detected a MZ604 device too, but couldn t access the files either (when clicking in the device, no folders were shown). I began to search the internet to see if there were some Motorola drivers out there, and then found the clue to enable the correct settings in the Android device: you need to go to Settings > Storage, and then press the 3-dots button that makes the Menu function, and then appears USB computer connection and there, you can enable Camera or MTP. Very hidden setting! I enabled MTP, and then I could see the folders and files in my Windows system (without need of installing any additional driver), and make my backup. And of course after rebooting and trying in Debian, it worked too. Some outcomes/conclusions Comments? You can comment on this post using this pump.io thread.
Filed under: My experiences and opinion Tagged: Android, Debian, English, KDE, Libre software for Windows

Dirk Eddelbuettel: RcppArmadillo 0.7.800.2.0

armadillo image A new RcppArmadillo version 0.7.800.2.0 is now on CRAN. Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language--and is widely used by (currently) 318 other packages on CRAN -- an increase of 20 just since the last CRAN release of 0.7.600.1.0 in December! Changes in this release relative to the previous CRAN release are as follows:

Changes in RcppArmadillo version 0.7.800.2.0 (2017-04-12)
  • Upgraded to Armadillo release 7.800.2 (Rogue State Redux)
    • The Armadillo license changed to Apache License 2.0
  • The DESCRIPTION file now mentions the Apache License 2.0, as well as the former MPL2 license used for earlier releases.
  • A new file init.c was added with calls to R_registerRoutines() and R_useDynamicSymbols()
  • Symbol registration is enabled in useDynLib
  • The fastLm example was updated

Courtesy of CRANberries, there is a diffstat report. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

13 April 2017

Michal &#268;iha&#345;: Weblate 2.13.1

Weblate 2.13.1 has been released quickly after 2.13. It fixes few minor issues and possible upgrade problem. Full list of changes: If you are upgrading from older version, please follow our upgrading instructions. You can find more information about Weblate on https://weblate.org, the code is hosted on Github. If you are curious how it looks, you can try it out on demo server. You can login there with demo account using demo password or register your own user. Weblate is also being used on https://hosted.weblate.org/ as official translating service for phpMyAdmin, OsmAnd, Aptoide, FreedomBox, Weblate itself and many other projects. Should you be looking for hosting of translations for your project, I'm happy to host them for you or help with setting it up on your infrastructure. Further development of Weblate would not be possible without people providing donations, thanks to everybody who have helped so far! The roadmap for next release is just being prepared, you can influence this by expressing support for individual issues either by comments or by providing bounty for them.

Filed under: Debian English SUSE Weblate 0 comments

12 April 2017

Vincent Bernat: Proper isolation of a Linux bridge

TL;DR: when configuring a Linux bridge, use the following commands to enforce isolation:
# bridge vlan del dev br0 vid 1 self
# echo 1 > /sys/class/net/br0/bridge/vlan_filtering

A network bridge (also commonly called a switch ) brings several Ethernet segments together. It is a common element in most infrastructures. Linux provides its own implementation. A typical use of a Linux bridge is shown below. The hypervisor is running three virtual hosts. Each virtual host is attached to the br0 bridge (represented by the horizontal segment). The hypervisor has two physical network interfaces: Typical use of Linux bridging with virtual machines The main expectation of such a setup is that while the virtual hosts should be able to use resources from the public network, they should not be able to access resources from the infrastructure network (including resources hosted on the hypervisor itself, like a SSH server). In other words, we expect a total isolation between the green domain and the purple one. That s not the case. From any virtual host:
# ip route add 192.168.14.3/32 dev eth0
# ping -c 3 192.168.14.3
PING 192.168.14.3 (192.168.14.3) 56(84) bytes of data.
64 bytes from 192.168.14.3: icmp_seq=1 ttl=59 time=0.644 ms
64 bytes from 192.168.14.3: icmp_seq=2 ttl=59 time=0.829 ms
64 bytes from 192.168.14.3: icmp_seq=3 ttl=59 time=0.894 ms
--- 192.168.14.3 ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 2033ms
rtt min/avg/max/mdev = 0.644/0.789/0.894/0.105 ms

Why? There are two main factors of this behavior:
  1. A bridge can accept IP traffic. This is a useful feature if you want Linux to act as a bridge and provide some IP services to bridge users (a DHCP relay or a default gateway). This is usually done by configuring the IP address on the bridge device: ip addr add 192.0.2.2/25 dev br0.
  2. An interface doesn t need an IP address to process incoming IP traffic. Additionally, by default, Linux accepts to answer ARP requests independently from the incoming interface.

Bridge processing After turning an incoming Ethernet frame into a socket buffer, the network driver transfers the buffer to the netif_receive_skb() function. The following actions are executed:
  1. copy the frame to any registered global or per-device taps (e.g. tcpdump),
  2. evaluate the ingress policy (configured with tc),
  3. hand over the frame to the device-specific receive handler, if any,
  4. hand over the frame to a global or device-specific protocol handler (e.g. IPv4, ARP, IPv6).
For a bridged interface, the kernel has configured a device-specific receive handler, br_handle_frame(). This function won t allow any additional processing in the context of the incoming interface, except for STP and LLDP frames or if brouting is enabled1. Therefore, the protocol handlers are never executed in this case. After a few additional checks, Linux will decide if the frame has to be locally delivered:
  • the entry for the target MAC in the FDB is marked for local delivery, or
  • the target MAC is a broadcast or a multicast address.
In this case, the frame is passed to the br_pass_frame_up() function. A VLAN-related check is optionally performed. The socket buffer is attached to the bridge interface (br0) instead of the physical interface (eth0), is evaluated by Netfilter and sent back to netif_receive_skb(). It will go through the four steps a second time.

IPv4 processing When a device doesn t have a protocol-independent receive handler, a protocol-specific handler will be used:
# cat /proc/net/ptype
Type Device      Function
0800          ip_rcv
0011          llc_rcv [llc]
0004          llc_rcv [llc]
0806          arp_rcv
86dd          ipv6_rcv
Therefore, if the Ethernet type of the incoming frame is 0x800, the socket buffer is handled by ip_rcv(). Among other things, the three following steps will happen:
  • If the frame destination address is not the MAC address of the incoming interface, not a multicast one and not a broadcast one, the frame is dropped ( not for us ).
  • Netfilter gets a chance to evaluate the packet (in a PREROUTING chain).
  • The routing subsystem will decide the destination of the packet in ip_route_input_slow(): is it a local packet, should it be forwarded, should it be dropped, should it be encapsulated? Notably, the reverse-path filtering is done during this evaluation in fib_validate_source().
Reverse-path filtering (also known as uRPF, or unicast reverse-path forwarding, RFC 3704) enables Linux to reject traffic on interfaces which it should never have originated: the source address is looked up in the routing tables and if the outgoing interface is different from the current incoming one, the packet is rejected.

ARP processing When the Ethernet type of the incoming frame is 0x806, the socket buffer is handled by arp_rcv().
  • Like for IPv4, if the frame is not for us, it is dropped.
  • If the incoming device has the NOARP flag, the frame is dropped.
  • Netfilter gets a chance to evaluate the packet (configuration is done with arptables).
  • For an ARP request, the values of arp_ignore and arp_filter may trigger a drop of the packet.

IPv6 processing When the Ethernet type of the incoming frame is 0x86dd, the socket buffer is handled by ipv6_rcv().
  • Like for IPv4, if the frame is not for us, it is dropped.
  • If IPv6 is disabled on the interface, the packet is dropped.
  • Netfilter gets a chance to evaluate the packet (in a PREROUTING chain).
  • The routing subsystem will decide the destination of the packet. However, unlike IPv4, there is no reverse-path filtering2.

Workarounds There are various methods to fix the situation. We can completely ignore the bridged interfaces: as long as they are attached to the bridge, they cannot process any upper layer protocol (IPv4, IPv6, ARP). Therefore, we can focus on filtering incoming traffic from br0. It should be noted that for IPv4, IPv6 and ARP protocols, the MAC address check can be circumvented by using the broadcast MAC address.

Protocol-independent workarounds The four following fixes will indistinctly drop IPv4, ARP and IPv6 packets.

Using VLAN-aware bridge Linux 3.9 introduced the ability to use VLAN filtering on bridge ports. This can be used to prevent any local traffic:
# echo 1 > /sys/class/net/br0/bridge/vlan_filtering
# bridge vlan del dev br0 vid 1 self
# bridge vlan show
port    vlan ids
eth0     1 PVID Egress Untagged
eth2     1 PVID Egress Untagged
eth3     1 PVID Egress Untagged
eth4     1 PVID Egress Untagged
br0     None
This is the most efficient method since the frame is dropped directly in br_pass_frame_up().

Using ingress policy It s also possible to drop the bridged frame early after it has been re-delivered to netif_receive_skb() by br_pass_frame_up(). The ingress policy of an interface is evaluated before any handler. Therefore, the following commands will ensure no local delivery (the source interface of the packet is the bridge interface) happens:
# tc qdisc add dev br0 handle ffff: ingress
# tc filter add dev br0 parent ffff: u32 match u8 0 0 action drop
In my opinion, this is the second most efficient method.

Using ebtables Just before re-delivering the frame to netif_receive_skb(), Netfilter gets a chance to issue a decision. It s easy to configure it to drop the frame:
# ebtables -A INPUT --logical-in br0 -j DROP
However, to the best of my knowledge, this part of Netfilter is known to be inefficient.

Using namespaces Isolation can also be obtained by moving all the bridged interfaces into a dedicated network namespace and configure the bridge inside this namespace:
# ip netns add bridge0
# ip link set netns bridge0 eth0
# ip link set netns bridge0 eth2
# ip link set netns bridge0 eth3
# ip link set netns bridge0 eth4
# ip link del dev br0
# ip netns exec bridge0 brctl addbr br0
# for i in 0 2 3 4; do
>    ip netns exec bridge0 brctl addif br0 eth$i
>    ip netns exec bridge0 ip link set up dev eth$i
> done
# ip netns exec bridge0 ip link set up dev br0
The frame will still wander a bit inside the IP stack, wasting some CPU cycles and increasing the possible attack surface. But ultimately, it will be dropped.

Protocol-dependent workarounds Unless you require multiple layers of security, if one of the previous workarounds is already applied, there is no need to apply one of the protocol-dependent fix below. It s still interesting to know them because it is not uncommon to already have them in place.

ARP The easiest way to disable ARP processing on a bridge is to set the NOARP flag on the device. The ARP packet will be dropped as the very first step of the ARP handler.
# ip link set arp off dev br0
# ip l l dev br0
8: br0: <BROADCAST,MULTICAST,NOARP,UP,LOWER_UP> mtu 1500 qdisc noqueue state UP mode DEFAULT group default qlen 1000
    link/ether 50:54:33:00:00:04 brd ff:ff:ff:ff:ff:ff
arptables can also drop the packet quite early:
# arptables -A INPUT -i br0 -j DROP
Another way is to set arp_ignore to 2 for the given interface. The kernel will only answer to ARP requests whose target IP address is configured on the incoming interface. Since the bridge interface doesn t have any IP address, no ARP requests will be answered.
# sysctl -qw net.ipv4.conf.br0.arp_ignore=2
Disabling ARP processing is not a sufficient workaround for IPv4. A user can still insert the appropriate entry in its neighbor cache:
# ip neigh replace 192.168.14.3 lladdr 50:54:33:00:00:04 dev eth0
# ping -c 1 192.168.14.3
PING 192.168.14.3 (192.168.14.3) 56(84) bytes of data.
64 bytes from 192.168.14.3: icmp_seq=1 ttl=49 time=1.30 ms
--- 192.168.14.3 ping statistics ---
1 packets transmitted, 1 received, 0% packet loss, time 0ms
rtt min/avg/max/mdev = 1.309/1.309/1.309/0.000 ms
As the check on the target MAC address is quite loose, they don t even need to guess the MAC address:
# ip neigh replace 192.168.14.3 lladdr ff:ff:ff:ff:ff:ff dev eth0
# ping -c 1 192.168.14.3
PING 192.168.14.3 (192.168.14.3) 56(84) bytes of data.
64 bytes from 192.168.14.3: icmp_seq=1 ttl=49 time=1.12 ms
--- 192.168.14.3 ping statistics ---
1 packets transmitted, 1 received, 0% packet loss, time 0ms
rtt min/avg/max/mdev = 1.129/1.129/1.129/0.000 ms

IPv4 The earliest place to drop an IPv4 packet is with Netfilter3:
# iptables -t raw -I PREROUTING -i br0 -j DROP
If Netfilter is disabled, another possibility is to enable strict reverse-path filtering for the interface. In this case, since there is no IP address configured on the interface, the packet will be dropped during the route lookup:
# sysctl -qw net.ipv4.conf.br0.rp_filter=1
Another option is the use of a dedicated routing rule. Compared to the reverse-path filtering option, the packet will be dropped a bit earlier, still during the route lookup.
# ip rule add iif br0 blackhole

IPv6 Linux provides a way to completely disable IPv6 on a given interface. The packet will be dropped as the very first step of the IPv6 handler:
# sysctl -qw net.ipv6.conf.br0.disable_ipv6=1
Like for IPv4, it s possible to use Netfilter or a dedicated routing rule.

About the example In the above example, the virtual host get ICMP replies because they are routed through the infrastructure network to Internet (e.g. the hypervisor has a default gateway which also acts as a NAT router to Internet). This may not be the case. If you want to check if you are vulnerable despite not getting an ICMP reply, look at the guest neighbor table to check if you got an ARP reply from the host:
# ip route add 192.168.14.3/32 dev eth0
# ip neigh show dev eth0
192.168.14.3 lladdr 50:54:33:00:00:04 REACHABLE
If you didn t get a reply, you could still have issues with IP processing. Add a static neighbor entry before checking the next step:
# ip neigh replace 192.168.14.3 lladdr ff:ff:ff:ff:ff:ff dev eth0
To check if IP processing is enabled, check the bridge host s network statistics:
# netstat -s   grep "ICMP messages"
    15 ICMP messages received
    15 ICMP messages sent
    0 ICMP messages failed
If the counters are increasing, it is processing incoming IP packets. One-way communication still allows a lot of bad things, like DoS attacks. Additionally, if the hypervisor happens to also act as a router, the reach is extended to the whole infrastructure network, potentially exposing weak devices (e.g. PDU) exposing an SNMP agent. If one-way communication is all that s needed, the attacker can also spoof its source IP address, bypassing IP-based authentication.

  1. A frame can be forcibly routed (L3) instead of bridged (L2) by brouting the packet. This action can be triggered using ebtables.
  2. For IPv6, reverse-path filtering needs to be implemented with Netfilter, using the rpfilter match.
  3. If the br_netfilter module is loaded, net.bridge.bridge-nf-call-ipatbles sysctl has to be set to 0. Otherwise, you also need to use the physdev match to not drop IPv4 packets going through the bridge.

Michal &#268;iha&#345;: Weblate 2.13

Weblate 2.13 has been released today pretty much on the schedule. The most important change being more fine grained access control and some smaller UI improvements. There are other new features and bug fixes as well. Full list of changes: If you are upgrading from older version, please follow our upgrading instructions. You can find more information about Weblate on https://weblate.org, the code is hosted on Github. If you are curious how it looks, you can try it out on demo server. You can login there with demo account using demo password or register your own user. Weblate is also being used on https://hosted.weblate.org/ as official translating service for phpMyAdmin, OsmAnd, Aptoide, FreedomBox, Weblate itself and many other projects. Should you be looking for hosting of translations for your project, I'm happy to host them for you or help with setting it up on your infrastructure. Further development of Weblate would not be possible without people providing donations, thanks to everybody who have helped so far! The roadmap for next release is just being prepared, you can influence this by expressing support for individual issues either by comments or by providing bounty for them.

Filed under: Debian English Gammu phpMyAdmin SUSE Weblate 0 comments

11 April 2017

Riku Voipio: Deploying OBS

Open Build Service from SuSE is web service building deb/rpm packages. It has recently been added to Debian, so finally there is relatively easy way to set up PPA style repositories in Debian. Relative as in "there is a learning curve, but nowhere near the complexity of replicating Debian's internal infrastructure". OBS will give you both repositories and build infrastructure with a clickety web UI and command line client (osc) to manage. See Hectors blog for quickstart instructions. Things to learned while setting up OBSMe coming from Debian background, and OBS coming from SuSE/RPM world, there are some quirks that can take by surprise. Well done packagingUsually web services are a tough fit for Distros. The cascade of weird dependencies and build systems where the only practical way to build an "open source" web service is by replicating the upstream CI scripts. Not in case of OBS. Being done by distro people shows. OBS does automatic rebuilds of reverse dependenciesAka automatic binNMUs when you update a library. This however means you need lots of build power around. OBS has it's own dependency resolver on the server that recalculate what packages need rebuilding when - workers just get a list of packages to install for build-depends. This a major divergence from Debian, where sbuild handles dependencies client side. The OBS dependency handler doesn't handle virtual packages* / alternative build-deps like Debian - you may have to add a specific "Prefer: foo-dev" into the OBS project config to solve alternative choices. OBS server and worker do http requests in both directionsOn startup workers connect to OBS server, open a TCP port and wait requests coming OBS. Having connections both directions is a bit of hassle firewall-wise. On the bright side, no need to setup uploads via FTP here.. Signing repositories is complicatedWith Debian 9.0 making signed repositories pretty much mandatory, OBS makes signing rather complicated. obs-signd isn't included in Debian, since it depends on gnupg patch that hasn't been upstreamed. Fortunately I found a workaround. OBS signs release files with /usr/bin/sign -d /path/to/release. Where replacing the obs-signd provided sign command your own script is easy ;) Git integration is rather bolted-on than integratedOBS provides a method to integrate with git using services. - There is no clickety UI to link to git repo, instead you make an xml file called _service with osc. There is no way to have debian/ tree in git. The upstream community is friendlyIncluding the happiest thanks from an upstream I've seen recently. SummaryAll in all rather satisfied with OBS. If you have a home-grown jenkins etc based solution for building DEB/RPM packages, you should definitely consider OBS. For simpler uses, no need to install OBS yourself, openSUSE public OBS will happily build Debian packages for you. *How useful are virtual packages anymore? "foo-defaults" packages seem to be the go-to solution for most real usecases anyways.

Antoine Beaupr : A report from Netconf: Day 1

As is becoming traditional, two times a year the kernel networking community meets in a two-stage conference: an invite-only, informal, two-day plenary session called Netconf, held in Toronto this year, and a more conventional one-track conference open to the public called Netdev. I was invited to cover both conferences this year, given that Netdev was in Montreal (my hometown), and was happy to meet the crew of developers that maintain the network stack of the Linux kernel. This article covers the first day of the conference which consisted of around 25 Linux developers meeting under the direction of David Miller, the kernel's networking subsystem maintainer. Netconf has no formal sessions; although some people presented slides, interruptions are frequent (indeed, encouraged) and the focus is on hashing out issues that are blocked on the mailing list and getting suggestions, ideas, solutions, and feedback from their peers.

Removing ndo_select_queue() One of the first discussions that elicited a significant debate was the ndo_select_queue() function, a key component of the Linux polling system that determines when and how to send packets on a network interface (see netdev_pick_tx and friends). The general question was whether the use of ndo_select_queue() in drivers is a good idea. Alexander Duyck explained that Intel people were considering using ndo_select_queue() for receive/transmit queue matching. Intel drivers do not currently use the hook provided by the Linux kernel and it turns out no one is happy with ndo_select_queue(): the heuristics it uses don't really please anyone. The consensus (including from Duyck himself) seemed to be that it should just not be used anymore, or at least not used for that specific purpose. The discussion turned toward the wireless network stack, which uses it extensively, but for other purposes. Johannes Berg explained that the wireless stack uses ndo_select_queue() for traffic classification, for example to get voice traffic through even if the best-effort queue is backed up. The wireless stack could stop using it by doing flow control completely inside the wireless stack, which already uses the fq_codel flow-control mechanism for other purposes, so porting away from ndo_select_queue() seems possible there. The problem then becomes how to update all the drivers to change that behavior, which would be a lot of work. Still, it seems people are moving away from a generic ndo_select_queue() interface to stack-specific or even driver-specific (in the case of Intel) queue management interfaces.

refcount_t followup There was a followup discussion on the integration of the refcount_t type into the network stack, which we covered recently. This type is meant to be an in-kernel defense against exploits based on overflowing or underflowing an object's reference count. The consensus seems to be that having refcount_t used for debugging is acceptable, but it cannot be enabled by default. An issue that was identified is that the networking developers are fairly sure that introducing refcount_t would have a severe impact on performance, but they do not have benchmarks to prove it, something Miller identified as a problem that needs to be worked on. Miller then expressed some openness to the idea of having it as a kernel configuration option. A similar discussion happened, on the second day, regarding the KASan memory error detector which was covered when it was introduced in 2014. Eric Dumazet warned that there could be a lot of issues that cannot be detected by KASan because of the way the network stack often bypasses regular memory-allocation routines for performance reasons. He also noted that this can sometimes mean the stack may go over the regular 10% memory limit (the tcp_mem parameter, described in the tcp(7) man page) for certain operations, especially when rebuilding out of order packets with lots of parallel TCP connections. Therefore it was proposed that these special memory recycling tricks could be optionally disabled, at run or compile-time, to instrument proper memory tracking. Dumazet argued this was a situation similar to refcount_t in that we need a way to disable high performance to make the network stack easier to debug with KAsan. The problem with optional parameters is that they are often disabled in production or even by default, which, in turn, means that critical bugs cannot actually be found because the code paths are not tested. When I asked Dumazet about this, he explained that Google performs integration testing of new kernels before putting them in production, and those toggles could be enabled there to find and fix those bugs. But he agreed that certain code paths are then not tested until the code gets deployed in production. So it seems the status quo remains: security folks wants to improve the reliability of the kernel, but the network folks can't afford the performance cost. Yet it was clear in the discussions that the team cares about security issues and wants those issues to be fixed; the impact of some of the solutions is just too big.

Lightweight wireless management packet access Berg explained that some users need to have high-performance access to certain management frames in the wireless stack and wondered how to best expose those to user space. The wireless stack already allows users to clone a network interface in "monitor" mode, but this has a big performance cost, as the radiotap header needs to be constructed from scratch and the packet header needs to be copied. As wireless improves and the bandwidth rises to gigabit levels, this can become significant bottleneck for packet sniffers or reporting software that need to know precisely what's going on over the air outside of the regular access point client operation. It seems the proper way to do this is with an eBPF program. As Miller summarized, just add another API call that allows loading a BPF program into the kernel and then those users can use a BPF filtering point to get the statistics they need. This will require an extra hook in the wireless stack, but it seems like this is the way that will be taken to implement this feature.

VLAN 0 inconsistencies Hannes Frederic Sowa brought up the seemingly innocuous question of "how do we handle VLAN 0?" In theory, VLAN 0 means "no VLAN". But the Linux kernel currently handles this differently depending on whether the VLAN module is loaded and whether a VLAN 0 interface was created. Sometimes the VLAN tag is stripped, sometimes not. It turns out the semantics of this were accidentally changed last time there was a change here and this was originally working but is now broken. Sowa therefore got the go-ahead to fix this to make the behavior consistent again.

Loopy fun Then it came the turn of Jamal Hadi Salim, the maintainer of the kernel's traffic-control (tc) subsystem. The first issue he brought up is a problem in the tc REDIRECT action that can create infinite loops within the kernel. The problem can be easily alleviated when loops are created on the same interface: checks can be added that just drop packets coming from the same device and rate-limit logging to avoid a denial-of-service (DoS) condition. The more serious problem occurs when a packet is forwarded from (say) interface eth0 to eth1 which then promptly redirects it from eth1 back to eth0. Obviously, this kind of problem can only be created by a user with root access so, at first glance, those issues don't seem that serious: admins can shoot themselves in the foot, so what? But things become a little more serious when you consider the container case, where an untrusted user has root access inside a container and should have constrained resource limitations. Such a loop could allow this user to deploy an effective DoS attack against a whole group of containers running on the same machine. Even worse, this endless loop could possibly turn into a deadlock in certain scenarios, as the kernel could try to transmit the packet on the same device it originated from and block, progressively filling the queues and eventually completely breaking network access. Florian Westphal argued that a container can already create DoS conditions, for example by doing a ping flood. According to Salim, this whole problem was created when two bits used for tracking such packets were reclaimed from the skb structure used to represent packets in the kernel. Those bits were a simple TTL (time to live) field that was incremented on each loop and dropped after a pre-determined limit was reached, breaking infinite loops. Salim asked everyone if this should be fixed or if we should just forget about this issue and move on. Miller proposed to keep a one-behind state for the packet, fixing the simplest case (two interfaces). The general case, however, would requite a bitmap of all the interfaces to be scanned, which would impose a large overhead. Miller said an attempt to fix this should somehow be made. The root of the problem is that the network maintainers are trying to reduce the size of the skb structure, because it's used in many critical paths of the network stack. Salim's position is that, without the TTL fields, there is no way to fix the general case here, and this constitutes a security issue. So either the bits need to be brought back, or we need to live with the inherent DoS threat.

Dumping large statistics sets Another issue Salim brought up was the question of how to export large statistics sets from the kernel. It turns out that some use cases may end up dumping a lot of data. Salim mentioned a real-world tc use case that calls for reading six-million entries. The current netlink-based API provides a way to get only 20 entries at a time, which means it takes forever to dump the state of all those policy actions. Salim has a patch that changes the dump size be eight times the NLMSG_GOOD_SIZE, which improves performance by an order of magnitude already, although there are issues with checking the user-space buffer size there. But a more complete solution is needed. What Salim proposed was a way to ask only for the states that changed since the last dump was requested. He has a patch to add a last_access field to the netlink_callback structure used by netlink_dump() to output data; that raised the question of how to actually use that field. Since Salim fetches that data every five seconds, he figured he could just tell the kernel to return all the nodes that changed in that period. But then if the dump takes more than five seconds to complete, the next dump may be missing states that changed during the extra delay. An alternative mechanism would be for the user-space utility to keep the time stamp it requested and use that as a delta for the next dump. It turns out this is a larger problem than just tc. Dumazet mentioned this was an issue with fq_codel classes: he would even like to be able to dump those statistics faster than every five seconds. Roopa Prabhu mentioned that Cumulus also has similar problems dumping stats from bridges, so clearly a more generic solution is needed here. There is, however, a fundamental problem with dumping large statistics sets from the kernel: those statistics are constantly changing while the dump is created and unless versioning or locking mechanisms are used which would slow things down the data returned is bound to be only an approximation of reality. Salim promised to send a set of RFC patches to further discussions regarding this issue, but during the following Netdev conference, Berg published a patch to fix this ten-year-old issue, which brought cheers from the audience.
The author would like to thank the Netconf and Netdev organizers for travel to, and hosting assistance in, Toronto. Many thanks to Berg, Dumazet, Salim, and Sowa for their time taken for a technical review of this article. Note: this article first appeared in the Linux Weekly News.

Reproducible builds folks: Reproducible Builds: week 102 in Stretch cycle

Here's what happened in the Reproducible Builds effort between Sunday April 2 and Saturday April 8 2017: Media coverage Toolchain development and fixes Reviews of unreproducible packages 27 package reviews have been added, 14 have been updated and 17 have been removed in this week, adding to our knowledge about identified issues. Weekly QA work During our reproducibility testing, FTBFS bugs have been detected and reported by: tests.reproducible-builds.org Misc. This week's edition was written by Chris Lamb, Vagrant Cascadian & reviewed by a bunch of Reproducible Builds folks on IRC & the mailing lists.

10 April 2017

Michal &#268;iha&#345;: New free software projects on Hosted Weblate

Hosted Weblate provides also free hosting for free software projects. Finally I got to processing requests a bit faster, so there are just few new projects. This time, the newly hosted projects include: If you want to support this effort, please donate to Weblate, especially recurring donations are welcome to make this service alive. You can do them on Liberapay or Bountysource.

Filed under: Debian English Weblate 0 comments

9 April 2017

Sam Hartman: When "when" is too hard a question: SQLAlchemy, Python datetime, and ISO8601

A new programmer asked on a work chat room how timezones are handled in databases. He asked if it was a good idea to store things in UTC. The senior programmers all laughed as we told some of our horror stories with timezones. Yes, UTC is great; if only it were that simple.
About a week later I was designing the schema for a blue sky project I'm implementing. I had to confront time in all its Pythonic horror.
Let's start with the datetime.datetime class. Datetime objects optionally include a timezone. If no timezone is present, several methods such as timestamp treat the object as a local time in the system's timezone. The timezone method returns a POSIX timestamp, which is always expressed in UTC, so knowing the input timezone is important. The now method constructs such an object from the current time.
However other methods act differently. The utcnow method constructs a datetime object that has the UTC time, but is not marked with a timezone. So, for example datetime.fromtimestamp(datetime.utcnow().timestamp()) produces the wrong result unless your system timezone happens to have the same offset as UTC.
It's also possible to construct a datetime object that includes a UTC time and is marked as having a UTC time. The utcnow method never does this, but you can pass the UTC timezone into the now method and get that effect. As you'd expect, the timestamp method returns the correct result on such a datetime.
Now enter SQLAlchemy, one of the more popular Python ORMs. Its DATETIME type has an argument that tries to request a column capable of storing a a timezone from the underlying database. You aren't guaranteed to get this though; some databases don't provide that functionality. With PostgreSQL, I do get such a column, although something in SQLAlchemy is not preserving the timezones (although it is correctly adjusting the time). That is, I'll store a UTC time in an object, flush it to my session, and then read back the same time represented in my local timezone (marked as my local timezone). You'd think this would be safe.
Enter SQLite. SQLite makes life hard for people wanting to store time; it seems to want to store things as strings. That's fairly incompatible with storing a timezone and doing any sort of comparisons on dates. SQLAlchemy does not try to store a timezone in SQLite. It just trims any timezone information from the datetime. So, if I do something like
d = datetime.now(timezone.utc)
obj.date_col = d
session.add(obj)
session.flush()
assert obj.date_col == d # fails
assert obj.date_col.timestamp() == d.timestamp() # fails
assert d == obj.date_col.replace(tzinfo = timezone.utc) # finally succeeds

There are some unfortunate consequences of this. If you mark your datetimes with timezone information (even if it is always the same timezone), whether two datetimes representing the same datetime compare equal depends on whether objects have been flushed to the session yet. If you don't mark your objects with timezones, then you may not store timezone information on other databases.
At least if you use only the methods we've discussed so far, you're reasonably safe if you use local time everywhere in your application and don't mark your datetimes with timezones. That's undesirable because as our new programmer correctly surmised, you really should be using UTC. This is particularly true if users of your database might span multiple timezones.
You can use UTC time and not mark your objects as UTC. This will give the wrong data with a database that actually does support timezones, but will sort of work with SQLite. You need to be careful never to convert your datetime objects into POSIX time as you'll get the wrong result.
It turns out that my life was even more complicated because parts of my project serialize data into JSON. For that serialization, I've chosen ISO 8601. You've probably seen that format: '2017-04-09T18:17:27.340410+00:00. Datetime provides the convenient isoformat method to print timestamps in the ISO 8601 format. If the datetime has a timezone indication, it is included in the ISO formatted string. If not, then no timezone indication is included. You know how I mentioned that datetime takes a string without a timezone marker as local time? Yeah, well, that's not what 8601 does: UTC all the way, baby! And at least the parser in the iso8601 module will always include timezone markers. So, if you use datetime to print a timestamp without a timezone marker and then read that back in to construct a new datetime on the deserialization side, then you'll get the wrong time. OK, so mark things with timezones then. Well, if you use local time, then the time you get depends on whether you print the ISO string before or after session flush (before or after SQLAlchemy trims the timezone information as it goes to SQLite).
It turns out that I had the additional complication of one side of my application using SQLite and one side using PostgreSQL. Remember how I mentioned that something between SQLAlchemy and PostgreSQL was recasting my times in local timezone (although keeping the time the same)? Well, consider how that's going to work. I serialize with the timezone marker on the PostgreSQL side. I get a ISO8601 localtime marked with the correct timezone marker. I deserialize on the SQLite side. Before session flush, I get a local time marked as localtime. After session flush, I get a local time with no marking. That's bad. If I further serialize on the SQLite side, I'll get that local time incorrectly marked as UTC. Moreover, all the times being locally generated on the SQLite side are UTC, and as we explored, SQLite really only wants one timezone in play.
I eventually came up with the following approach:

  1. If I find myself manipulating a time without a timezone marking, assert that its timezone is UTC not localtime.

  2. Always use UTC for times coming into the system.

  3. If I'm generating an ISO 8601 time from a datetime that has a timezone marker in a timezone other than UTC, represent that time as a UTC-marked datetime adjusting the time for the change in timezone.


This is way too complicated. I think that both datetime and SQLAlchemy's SQLite time handling have a lot to answer for. I think SQLAlchemy's core time handling may also have some to answer for, but I'm less sure of that.

Antoine Beaupr : Contribute your skills to Debian in Montreal, April 14 2017

Join us in Montreal, on April 14 2017, and we will find a way in which you can help Debian with your current set of skills! You might even learn one or two things in passing (but you don't have to). Debian is a free operating system for your computer. An operating system is the set of basic programs and utilities that make your computer run. Debian comes with dozens of thousands of packages, precompiled software bundled up for easy installation on your machine. A number of other operating systems, such as Ubuntu and Tails, are based on Debian. The upcoming version of Debian, called Stretch, will be released later this year. We need you to help us make it awesome :) Whether you're a computer user, a graphics designer, or a bug triager, there are many ways you can contribute to this effort. We also welcome experience in consensus decision-making, anti-harassment teams, and package maintenance. No effort is too small and whatever you bring to this community will be appreciated. Here's what we will be doing:

Goals and principles This is a work in progress, and a statement of intent. Not everything is organized and confirmed yet. We want to bring together a heterogeneous group of people. This goal will guide our handling of sponsorship requests, and will help us make decisions if more people want to attend than we can welcome properly. In other words: if you're part of a group that is currently under-represented in computer communities, we would like you to be able to attend. We are committed to providing a friendly, safe and welcoming environment for all, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion, nationality, or other similar personal characteristic. Attending this event requires reading and respecting the Debian Code of Conduct, that sets the standards in terms of behaviour for the whole event, including communication (public and private) before, while and after. The space where this event will take place is unfortunately not accessible to wheelchairs. Food (including vegetarian options) should be provided for lunch. If you have any specific needs regarding food, please let us know when registering, and we will do our best.

What we will be doing This will be an informal session to confirm and fix bugs in Debian. If you have never worked with Debian packages, this is a good opportunity to learn about packaging and bugtracker usage. Bugs flagged as Release Critical are blocking the release of the upcoming version of Debian. To fix them, it helps to make sure the bug report documents the up-to-date status of the bug, and of its resolution. One does not need to be a programmer to do this work! For example, you can try and reproduce bugs in software you use... or in software you will discover. This helps package maintainers better focus their work. We will also try to actually fix bugs by testing patches and uploading fixes into Debian itself. Antoine Beaupr , a seasoned Debian developer, will be available to sponsor uploads and teach people about basic Debian packaging skills.

Where? When? How to register? See https://wiki.debian.org/BSP/2017/04/ca/Montreal for the exact address and time.

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