Search Results: "nate"

24 March 2017

Gunnar Wolf: Dear lazyweb: How would you visualize..?

Dear lazyweb, I am trying to get a good way to present the categorization of several cases studied with a fitting graph. I am rating several vulnerabilities / failures according to James Cebula et. al.'s paper, A taxonomy of Operational Cyber Security Risks; this is a somewhat deep taxonomy, with 57 end items, but organized in a three levels deep hierarchy. Copying a table from the cited paper (click to display it full-sized): My categorization is binary: I care only whether it falls within a given category or not. My first stab at this was to represent each case using a star or radar graph. As an example: As you can see, to a "bare" star graph, I added a background color for each top-level category (blue for actions of people, green for systems and technology failures), red for failed internal processes and gray for external events), and printed out only the labels for the second level categories; for an accurate reading of the graphs, you have to refer to the table and count bars. And, yes, according to the Engineering Statistics Handbook:
Star plots are helpful for small-to-moderate-sized multivariate data sets. Their primary weakness is that their effectiveness is limited to data sets with less than a few hundred points. After that, they tend to be overwhelming.
I strongly agree with the above statement And stating that "a few hundred points" can be understood is even an overstatement. 50 points are just too much. Now, trying to increase usability for this graph, I came across the Sunburst diagram. One of the proponents for this diagram, John Stasko, has written quite a bit about it. Now... How to create my beautiful Sunburst diagram? That's a tougher one. Even though the page I linked to in the (great!) Data visualization catalogue presents even some free-as-in-software tools to do this... They are Javascript projects that will render their beautiful plots (even including an animation)... To the browser. I need them for a static (i.e. to be printed) document. Yes, I can screenshot and all, but I want them to be automatically generated, so I can review and regenerate them all automatically. Oh, I could just write JSON and use SaaS sites such as Aculocity to do the heavy-lifting, but if you know me, you will understand why I don't want to. So... I set out to find a Gunnar-approved way to display the information I need. Now, as the Protovis documentation says, an icicle is simply a sunburst transformed from polar to cartesian coordinates... But I came to a similar conclusion: The tools I found are not what I need. OK, but an icicle graph seems much simpler to produce I fired up my Emacs, and started writing using Ruby, RMagick and RVG... I decided to try a different way. This is my result so far: So... What do you think? Does this look right to you? Clearer than the previous one? Worst? Do you have any idea on how I could make this better? Oh... You want to tell me there is something odd about it? Well, yes, of course! I still need to tweak it quite a bit. Would you believe me if I told you this is not really a left-to-right icicle graph, but rather a strangely formatted Graphviz non-directed graph using the dot formatter? I can assure you you don't want to look at my Graphviz sources... But in case you insist... Take them and laugh. Or cry. Of course, this file comes from a hand-crafted template, but has some autogenerated bits to it. I have still to tweak it quite a bit to correct several of its usability shortcomings, but at least it looks somewhat like what I want to achieve. Anyway, I started out by making a "dear lazyweb" question. So, here it goes: Do you think I'm using the right visualization for my data? Do you have any better suggestions, either of a graph or of a graph-generating tool? Thanks! [update] Thanks for the first pointer, Lazyweb! I found a beautiful solution; we will see if it is what I need or not (it is too space-greedy to be readable... But I will check it out more thoroughly). It lays out much better than anything I can spew out by myself Writing it as a mindmap using TikZ directly from within LaTeX, I get the following result:

Dirk Eddelbuettel: RApiDatetime 0.0.1

Very happy to announce a new package of mine is now up on the CRAN repository network: RApiDatetime. It provides six entry points for C-level functions of the R API for Date and Datetime calculations: asPOSIXlt and asPOSIXct convert between long and compact datetime representation, formatPOSIXlt and Rstrptime convert to and from character strings, and POSIXlt2D and D2POSIXlt convert between Date and POSIXlt datetime. These six functions are all fairly essential and useful, but not one of them was previously exported by R. Hence the need to put them together in the this package to complete the accessible API somewhat. These should be helpful for fellow package authors as many of us have either our own partial copies of some of this code, or rather farm back out into R to get this done. As a simple (yet real!) illustration, here is an actual Rcpp function which we could now cover at the C level rather than having to go back up to R (via Rcpp::Function()):
    inline Datetime::Datetime(const std::string &s, const std::string &fmt)  
        Rcpp::Function strptime("strptime");    // we cheat and call strptime() from R
        Rcpp::Function asPOSIXct("as.POSIXct"); // and we need to convert to POSIXct
        m_dt = Rcpp::as<double>(asPOSIXct(strptime(s, fmt)));
        update_tm();
     
I had taken a first brief stab at this about two years ago, but never finished. With the recent emphasis on C-level function registration, coupled with a possible use case from anytime I more or less put this together last weekend. It currently builds and tests fine on POSIX-alike operating systems. If someone with some skill and patience in working on Windows would like to help complete the Windows side of things then I would certainly welcome help and pull requests. For questions or comments please use the issue tracker off 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.

23 March 2017

Simon McVittie: GTK hackfest 2017: D-Bus communication with containers

At the GTK hackfest in London (which accidentally became mostly a Flatpak hackfest) I've mainly been looking into how to make D-Bus work better for app container technologies like Flatpak and Snap. The initial motivating use cases are: At the moment, Flatpak runs a D-Bus proxy for each app instance that has access to D-Bus, connects to the appropriate bus on the app's behalf, and passes messages through. That proxy is in a container similar to the actual app instance, but not actually the same container; it is trusted to not pass messages through that it shouldn't pass through. The app-identification mechanism works in practice, but is Flatpak-specific, and has a known race condition due to process ID reuse and limitations in the metadata that the Linux kernel maintains for AF_UNIX sockets. In practice the use of X11 rather than Wayland in current systems is a much larger loophole in the container than this race condition, but we want to do better in future. Meanwhile, Snap does its sandboxing with AppArmor, on kernels where it is enabled both at compile-time (Ubuntu, openSUSE, Debian, Debian derivatives like Tails) and at runtime (Ubuntu, openSUSE and Tails, but not Debian by default). Ubuntu's kernel has extra AppArmor features that haven't yet gone upstream, some of which provide reliable app identification via LSM labels, which dbus-daemon can learn by querying its AF_UNIX socket. However, other kernels like the ones in openSUSE and Debian don't have those. The access-control (AppArmor mediation) is implemented in upstream dbus-daemon, but again doesn't work portably, and is not sufficiently fine-grained or flexible to do some of the things we'll likely want to do, particularly in dconf. After a lot of discussion with dconf maintainer Allison Lortie and Flatpak maintainer Alexander Larsson, I think I have a plan for fixing this. This is all subject to change: see fd.o #100344 for the latest ideas. Identity model Each user (uid) has some uncontained processes, plus 0 or more containers. The uncontained processes include dbus-daemon itself, desktop environment components such as gnome-session and gnome-shell, the container managers like Flatpak and Snap, and so on. They have the user's full privileges, and in particular they are allowed to do privileged things on the user's session bus (like running dbus-monitor), and act with the user's full privileges on the system bus. In generic information security jargon, they are the trusted computing base; in AppArmor jargon, they are unconfined. The containers are Flatpak apps, or Snap apps, or other app-container technologies like Firejail and AppImage (if they adopt this mechanism, which I hope they will), or even a mixture (different app-container technologies can coexist on a single system). They are containers (or container instances) and not "apps", because in principle, you could install com.example.MyApp 1.0, run it, and while it's still running, upgrade to com.example.MyApp 2.0 and run that; you'd have two containers for the same app, perhaps with different permissions. Each container has an container type, which is a reversed DNS name like org.flatpak or io.snapcraft representing the container technology, and an app identifier, an arbitrary non-empty string whose meaning is defined by the container technology. For Flatpak, that string would be another reversed DNS name like com.example.MyGreatApp; for Snap, as far as I can tell it would look like example-my-great-app. The container technology can also put arbitrary metadata on the D-Bus representation of a container, again defined and namespaced by the container technology. For instance, Flatpak would use some serialization of the same fields that go in the Flatpak metadata file at the moment. Finally, the container has an opaque container identifier identifying a particular container instance. For example, launching com.example.MyApp twice (maybe different versions or with different command-line options to flatpak run) might result in two containers with different privileges, so they need to have different container identifiers. Contained server sockets App-container managers like Flatpak and Snap would create an AF_UNIX socket inside the container, bind() it to an address that will be made available to the contained processes, and listen(), but not accept() any new connections. Instead, they would fd-pass the new socket to the dbus-daemon by calling a new method, and the dbus-daemon would proceed to accept() connections after the app-container manager has signalled that it has called both bind() and listen(). (See fd.o #100344 for full details.) Processes inside the container must not be allowed to contact the AF_UNIX socket used by the wider, uncontained system - if they could, the dbus-daemon wouldn't be able to distinguish between them and uncontained processes and we'd be back where we started. Instead, they should have the new socket bind-mounted into their container's XDG_RUNTIME_DIR and connect to that, or have the new socket set as their DBUS_SESSION_BUS_ADDRESS and be prevented from connecting to the uncontained socket in some other way. Those familiar with the kdbus proposals a while ago might recognise this as being quite similar to kdbus' concept of endpoints, and I'm considering reusing that name. Along with the socket, the container manager would pass in the container's identity and metadata, and the method would return a unique, opaque identifier for this particular container instance. The basic fields (container technology, technology-specific app ID, container ID) should probably be added to the result of GetConnectionCredentials(), and there should be a new API call to get all of those plus the arbitrary technology-specific metadata. When a process from a container connects to the contained server socket, every message that it sends should also have the container instance ID in a new header field. This is OK even though dbus-daemon does not (in general) forbid sender-specified future header fields, because any dbus-daemon that supported this new feature would guarantee to set that header field correctly, the existing Flatpak D-Bus proxy already filters out unknown header fields, and adding this header field is only ever a reduction in privilege. The reasoning for using the sender's container instance ID (as opposed to the sender's unique name) is for services like dconf to be able to treat multiple unique bus names as belonging to the same equivalence class of contained processes: instead of having to look up the container metadata once per unique name, dconf can look it up once per container instance the first time it sees a new identifier in a header field. For the second and subsequent unique names in the container, dconf can know that the container metadata and permissions are identical to the one it already saw. Access control In principle, we could have the new identification feature without adding any new access control, by keeping Flatpak's proxies. However, in the short term that would mean we'd be adding new API to set up a socket for a container without any access control, and having to keep the proxies anyway, which doesn't seem great; in the longer term, I think we'd find ourselves adding a second new API to set up a socket for a container with new access control. So we might as well bite the bullet and go for the version with access control immediately. In principle, we could also avoid the need for new access control by ensuring that each service that will serve contained clients does its own. However, that makes it really hard to send broadcasts and not have them unintentionally leak information to contained clients - we would need to do something more like kdbus' approach to multicast, where services know who has subscribed to their multicast signals, and that is just not how dbus-daemon works at the moment. If we're going to have access control for broadcasts, it might as well also cover unicast. The plan is that messages from containers to the outside world will be mediated by a new access control mechanism, in parallel with dbus-daemon's current support for firewall-style rules in the XML bus configuration, AppArmor mediation, and SELinux mediation. A message would only be allowed through if the XML configuration, the new container access control mechanism, and the LSM (if any) all agree it should be allowed. By default, processes in a container can send broadcast signals, and send method calls and unicast signals to other processes in the same container. They can also receive method calls from outside the container (so that interfaces like org.freedesktop.Application can work), and send exactly one reply to each of those method calls. They cannot own bus names, communicate with other containers, or send file descriptors (which reduces the scope for denial of service). Obviously, that's not going to be enough for a lot of contained apps, so we need a way to add more access. I'm intending this to be purely additive (start by denying everything except what is always allowed, then add new rules), not a mixture of adding and removing access like the current XML policy language. There are two ways we've identified for rules to be added: Initially, many contained apps would work in the first way (and in particular sockets=session-bus would add a rule that allows almost everything), while over time we'll probably want to head towards recommending more use of the second. Related topics Access control on the system bus We talked about the possibility of using a very similar ruleset to control access to the system bus, as an alternative to the XML rules found in /etc/dbus-1/system.d and /usr/share/dbus-1/system.d. We didn't really come to a conclusion here. Allison had the useful insight that the XML rules are acting like a firewall: they're something that is placed in front of potentially-broken services, and not part of the services themselves (which, as with firewalls like ufw, makes it seem rather odd when the services themselves install rules). D-Bus system services already have total control over what requests they will accept from D-Bus peers, and if they rely on the XML rules to mediate that access, they're essentially rejecting that responsibility and hoping the dbus-daemon will protect them. The D-Bus maintainers would much prefer it if system services took responsibility for their own access control (with or without using polkit), because fundamentally the system service is always going to understand its domain and its intended security model better than the dbus-daemon can. Analogously, when a network service listens on all addresses and accepts requests from elsewhere on the LAN, we sometimes work around that by protecting it with a firewall, but the optimal resolution is to get that network service fixed to do proper authentication and access control instead. For system services, we continue to recommend essentially this "firewall" configuration, filling in the $ variables as appropriate:
<busconfig>
    <policy user="$ the daemon uid under which the service runs ">
        <allow own="$ the service's bus name "/>
    </policy>
    <policy context="default">
        <allow send_destination="$ the service's bus name "/>
    </policy>
</busconfig>
We discussed the possibility of moving towards a model where the daemon uid to be allowed is written in the .service file, together with an opt-in to "modern D-Bus access control" that makes the "firewall" unnecessary; after some flag day when all significant system services follow that pattern, dbus-daemon would even have the option of no longer applying the "firewall" (moving to an allow-by-default model) and just refusing to activate system services that have not opted in to being safe to use without it. However, the "firewall" also protects system bus clients, and services like Avahi that are not bus-activatable, against unintended access, which is harder to solve via that approach; so this is going to take more thought. For system services' clients that follow the "agent" pattern (BlueZ, polkit, NetworkManager, Geoclue), the correct "firewall" configuration is more complicated. At some point I'll try to write up a best-practice for these. New header fields for the system bus At the moment, it's harder than it needs to be to provide non-trivial access control on the system bus, because on receiving a method call, a service has to remember what was in the method call, then call GetConnectionCredentials() to find out who sent it, then only process the actual request when it has the information necessary to do access control. Allison and I had hoped to resolve this by adding new D-Bus message header fields with the user ID, the LSM label, and other interesting facts for access control. These could be "opt-in" to avoid increasing message sizes for no reason: in particular, it is not typically useful for session services to receive the user ID, because only one user ID is allowed to connect to the session bus anyway. Unfortunately, the dbus-daemon currently lets unknown fields through without modification. With hindsight this seems an unwise design choice, because header fields are a finite resource (there are 255 possible header fields) and are defined by the D-Bus Specification. The only field that can currently be trusted is the sender's unique name, because the dbus-daemon sets that field, overwriting the value in the original message (if any). To make it safe to rely on the new fields, we would have to make the dbus-daemon filter out all unknown header fields, and introduce a mechanism for the service to check (during connection to the bus) whether the dbus-daemon is sufficiently new that it does so. If connected to an older dbus-daemon, the service would not be able to rely on the new fields being true, so it would have to ignore the new fields and treat them as unset. The specification is sufficiently vague that making new dbus-daemons filter out unknown header fields is a valid change (it just says that "Header fields with an unknown or unexpected field code must be ignored", without specifying who must ignore them, so having the dbus-daemon delete those fields seems spec-compliant). This all seemed fine when we discussed it in person; but GDBus already has accessors for arbitrary header fields by numeric ID, and I'm concerned that this might mean it's too easy for a system service to be accidentally insecure: It would be natural (but wrong!) for an implementor to assume that if g_message_get_header (message, G_DBUS_MESSAGE_HEADER_FIELD_SENDER_UID) returned non-NULL, then that was guaranteed to be the correct, valid sender uid. As a result, fd.o #100317 might have to be abandoned. I think more thought is needed on that one. Unrelated topics As happens at any good meeting, we took the opportunity of high-bandwidth discussion to cover many useful things and several useless ones. Other discussions that I got into during the hackfest included, in no particular order: More notes are available from the GNOME wiki. Acknowledgements The GTK hackfest was organised by GNOME and hosted by Red Hat and Endless. My attendance was sponsored by Collabora. Thanks to all the sponsors and organisers, and the developers and organisations who attended.

22 March 2017

Mike Hommey: When the memory allocator works against you, part 2

This is a followup to the When the memory allocator works against you post from a few days ago. You may want to read that one first if you haven t, and come back. In case you don t or didn t read it, it was all about memory consumption during a git clone of the mozilla-central mercurial repository using git-cinnabar, and how the glibc memory allocator is using more than one would expect. This post is going to explore how/why it s happening. I happen to have written a basic memory allocation logger for Firefox, so I used it to log all the allocations happening during a git clone exhibiting the runaway memory increase behavior (using a python that doesn t use its own allocator for small allocations). The result was a 6.5 GB log file (compressed with zstd ; 125 GB uncompressed!) with 2.7 billion calls to malloc, calloc, free, and realloc, recorded across (mostly) 2 processes (the python git-remote-hg process and the native git-cinnabar-helper process ; there are other short-lived processes involved, but they do less than 5000 calls in total). The vast majority of those 2.7 billion calls is done by the python git-remote-hg process: 2.34 billion calls. We ll only focus on this process. Replaying those 2.34 billion calls with a program that reads the log allowed to reproduce the runaway memory increase behavior to some extent. I went an extra mile and modified glibc s realloc code in memory so it doesn t call memcpy, to make things faster. I also ran under setarch x86_64 -R to disable ASLR for reproducible results (two consecutive runs return the exact same numbers, which doesn t happen with ASLR enabled). I also modified the program to report the number of live allocations (allocations that haven t been freed yet), and the cumulated size of the actually requested allocations (that is, the sum of all the sizes given to malloc, calloc, and realloc calls for live allocations, as opposed to what the memory allocator really allocated, which can be more, per malloc_usable_size). RSS was not tracked because the allocations are never filled to make things faster, such that pages for large allocations are never dirty, and RSS doesn t grow as much because of that. Full disclosure: it turns out the system bytes and in-use bytes numbers I had been collecting in the previous post were smaller than what they should have been, and were excluding memory that the glibc memory allocator would have mmap()ed. That however doesn t affect the trends that had been witnessed. The data below is corrected. (Note that in the graph above and the graphs that follow, the horizontal axis represents the number of allocator function calls performed) While I was here, I figured I d check how mozjemalloc performs, and it has a better behavior (although it has more overhead). What doesn t appear on this graph, though, is that mozjemalloc also tells the OS to drop some pages even if it keeps them mapped (madvise(MADV_DONTNEED)), so in practice, it is possible the actual RSS decreases too. And jemalloc 4.5: (It looks like it has better memory usage than mozjemalloc for this use case, but its stats are being thrown off at some point, I ll have to investigate) Going back to the first graph, let s get a closer look at what the allocations look like when the system bytes number is increasing a lot. The highlights in the following graphs indicate the range the next graph will be showing. So what we have here is a bunch of small allocations (small enough that they don t seem to move the requested line ; most under 512 bytes, so under normal circumstances, they would be allocated by python, a few between 512 and 2048 bytes), and a few large allocations, one of which triggers a bump in memory use. What can appear weird at first glance is that we have a large allocation not requiring more system memory, later followed by a smaller one that does. What the allocations actually look like is the following:

void *ptr0 = malloc(4850928); // #1391340418
void *ptr1 = realloc(some_old_ptr, 8000835); // #1391340419
free(ptr0); // #1391340420
ptr1 = realloc(ptr1, 8000925); // #1391340421
/* ... */
void *ptrn = malloc(879931); // #1391340465
ptr1 = realloc(ptr1, 8880819); // #1391340466
free(ptrn); // #1391340467
As it turns out, inspecting all the live allocations at that point, while there was a hole large enough to do the first two reallocs (the second actually happens in place), at the point of the third one, there wasn t a large enough hole to fit 8.8MB. What inspecting the live allocations also reveals, is that there is a large number of large holes between all the allocated memory ranges, presumably coming from previous similar patterns. There are, in fact, 91 holes larger than 1MB, 24 of which are larger than 8MB. It s the accumulation of those holes that can t be used to fulfil larger allocations that makes the memory use explode. And there aren t enough small allocations happening to fill those holes. In fact, the global trend is for less and less memory to be allocated, so, smaller holes are also being poked all the time. Really, it s all a straightforward case of memory fragmentation. The reason it tends not to happen with jemalloc is that jemalloc groups allocations by sizes, which the glibc allocator doesn t seem to be doing. The following is how we got a hole that couldn t fit the 8.8MB allocation in the first place:

ptr1 = realloc(ptr1, 8880467); // #1391324989; ptr1 is 0x5555de145600
/* ... */
void *ptrx = malloc(232); // #1391325001; ptrx is 0x5555de9bd760 ; that is 13 bytes after the end of ptr1.
/* ... */
free(ptr1); // #1391325728; this leaves a hole of 8880480 bytes at 0x5555de145600.
All would go well if ptrx was free()d, but it looks like it s long-lived. At least, it s still allocated by the time we reach the allocator call #1391340466. And since the hole is 339 bytes too short for the requested allocation, the allocator has no other choice than request more memory to the system. What s bothering, though, is that the allocator chose to allocate ptrx in the space following ptr1, when it allocated similarly sized buffers after allocating ptr1 and before allocating ptrx in completely different places, and while there are plenty of holes in the allocated memory where it could fit. Interestingly enough, ptrx is a 232 bytes allocation, which means under normal circumstances, python itself would be allocating it. In all likeliness, when the python allocator is enabled, it s allocations larger than 512 bytes that become obstacles to the larger allocations. Another possibility is that the 256KB fragments that the python allocator itself allocates to hold its own allocations become the obstacles (my original hypothesis). I think the former is more likely, though, putting back the blame entirely on glibc s shoulders. Now, it looks like the allocation pattern we have here is suboptimal, so I re-ran a git clone under a debugger to catch when a realloc() for 8880819 bytes happens (the size is peculiar enough that it only happened once in the allocation log). But doing that with a conditional breakpoint is just too slow, so I injected a realloc wrapper with LD_PRELOAD that sends a SIGTRAP signal to the process, so that an attached debugger can catch it. Thanks to the support for python in gdb, it was then posible to pinpoint the exact python instructions that made the realloc() call (it didn t come as a surprise ; in fact, that was one of the places I had in mind, but I wanted definite proof):

new = ''
end = 0
# ...
for diff in RevDiff(rev_patch):
    new += data[end:diff.start]
    new += diff.text_data
    end = diff.end
    # ...
new += data[end:]
What happens here is that we re creating a mercurial manifest we got from the server in patch form against a previous manifest. So data contains the original manifest, and rev_patch the patch. The patch essentially contains instructions of the form replace n bytes at offset o with the content c . The code here just does that in the most straightforward way, implementation-wise, but also, it turns out, possibly the worst way. So let s unroll this loop over a couple iterations:
new = ''
This allocates an empty str object. In fact, this doesn t actually allocate anything, and only creates a pointer to an interned representation of an empty string.
new += data[0:diff.start]
This is where things start to get awful. data is a str, so data[0:diff.start] creates a new, separate, str for the substring. One allocation, one copy. Then appends it to new. Fortunately, CPython is smart enough, and just assigns data[0:diff.start] to new. This can easily be verified with the CPython REPL:
>>> foo = ''
>>> bar = 'bar'
>>> foo += bar
>>> foo is bar
True
(and this is not happening because the example string is small here ; it also happens with larger strings, like 'bar' * 42000) Back to our loop:
new += diff.text_data
Now, new is realloc()ated to have the right size to fit the appended text in it, and the contents of diff.text_data is copied. One realloc, one copy. Let s go for a second iteration:
new += data[diff.end:new_diff.start]
Here again, we re doing an allocation for the substring, and one copy. Then new is realloc()ated again to append the substring, which is an additional copy.
new += new_diff.text_data
new is realloc()ated yet again to append the contents of new_diff.text_data. We now finish with:
new += data[new_diff.end:]
which, again creates a substring from the data, and then proceeds to realloc()ate new one freaking more time. That s a lot of malloc()s and realloc()s to be doing After modifying the code to implement the first and fifth items, memory usage during a git clone of mozilla-central looks like the following (with the python allocator enabled): (Note this hasn t actually landed on the master branch yet) Compared to what it looked like before, this is largely better. But that s not the only difference: the clone was also about 1000 seconds faster. That s more than 15 minutes! But that s not all so surprising when you know the volumes of data handled here. More insight about this coming in an upcoming post. But while the changes outlined above make the glibc allocator behavior less likely to happen, it doesn t totally obliviate it. In fact, it seems it is still happening by the end of the manifest import phase. We re still allocating increasingly large temporary buffers because the size of the imported manifests grows larger and larger, and every one of them is the result of patching a previous one. The only way to avoid those large allocations creating holes would be to avoid doing them in the first place. My first attempt at doing that, keeping manifests as lists of lines instead of raw buffers, worked, but was terribly slow. So slow, in fact, that I had to stop a clone early and estimated the process would likely have taken a couple days. Iterating over multiple generators at the same time, a lot, kills performance, apparently. I ll have to try with significantly less of that.

Dirk Eddelbuettel: anytime 0.2.2

A bugfix release of the anytime package arrived at CRAN earlier today. This is tenth release since the inaugural version late last summer, and the second (bugfix / feature) release this year. anytime is a very focused package aiming to do just one thing really well: to convert anything in integer, numeric, character, factor, ordered, ... format to either POSIXct or Date objects -- and to do so without requiring a format string. See the anytime page, or the GitHub README.md for a few examples. This releases addresses an annoying bug related to British TZ settings and the particular impact of a change in 1971, and generalizes input formats to accept integer or numeric format in two specific ranges. Details follow below:

Changes in anytime version 0.2.2 (2017-03-21)
  • Address corner case of integer-typed (large) values corresponding to POSIXct time (PR #57 closing ##56)
  • Add special case for Europe/London and 31 Oct 1971 BST change to avoid a one-hour offset error (#58 fixing #36 and #51)
  • Address another corner case of numeric values corresponding to Date types which are now returned as Date
  • Added file init.c with calls to R_registerRoutines() and R_useDynamicSymbols(); already used .registration=TRUE in useDynLib in NAMESPACE

Courtesy of CRANberries, there is a comparison to the previous release. More information is on the anytime page. For questions or comments use the issue tracker off 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.

21 March 2017

Reproducible builds folks: Reproducible Builds: week 99 in Stretch cycle

Here's what happened in the Reproducible Builds effort between Sunday March 12 and Saturday March 18 2017: Upcoming events Reproducible Builds Hackathon Hamburg 2017 The Reproducible Builds Hamburg Hackathon 2017, or RB-HH-2017 for short is a 3 day hacking event taking place May 5th-7th in the CCC Hamburg Hackerspace located inside Frappant, as collective art space located in a historical monument in Hamburg, Germany. The aim of the hackathon is to spent some days working on Reproducible Builds in every distribution and project. The event is open to anybody interested on working on Reproducible Builds issues, with or without prior experience! Accomodation is available and travel sponsorship may be available by agreement. Please register your interest as soon as possible. Reproducible Builds Summit Berlin 2016 This is just a quick note, that all the pads we've written during the Berlin summit in December 2016 are now online (thanks to Holger), nicely complementing the report by Aspiration Tech. Request For Comments for new specification: BUILD_PATH_PREFIX_MAP Ximin Luo posted a draft version of our BUILD_PATH_PREFIX_MAP specification for passing build-time paths between high-level and low-level build tools. This is meant to help eliminate irreproducibility caused by different paths being used at build time. At the time of writing, this affects an estimated 15-20% of 25000 Debian packages. This is a continuation of an older proposal SOURCE_PREFIX_MAP, which has been updated based on feedback on our patches from GCC upstream, attendees of our Berlin 2016 summit, and participants on our mailing list. Thanks to everyone that contributed! The specification also contains runnable source code examples and test cases; see our git repo. Please comment on this draft ASAP - we plan to release version 1.0 of this in a few weeks. Toolchain changes Packages reviewed and fixed, and bugs filed Chris Lamb: Reviews of unreproducible packages 5 package reviews have been added, 274 have been updated and 800 have been removed in this week, adding to our knowledge about identified issues. 1 issue type has been added: Weekly QA work During our reproducibility testing, FTBFS bugs have been detected and reported by: diffoscope development diffoscope 79 and 80 were uploaded to experimental by Chris Lamb. It included contributions from: Chris Lamb: Maria Glukhova: strip-nondeterminism development strip-nondeterminism 0.032-1 was uploaded to unstable by Chris Lamb. It included contributions from: Chris Lamb: tests.reproducible-builds.org Misc. This week's edition was written by Ximin Luo, Holger Levsen and Chris Lamb & reviewed by a bunch of Reproducible Builds folks on IRC & the mailing lists.

Tanguy Ortolo: Bad support of ZIP archives with extra fields

For sharing multiple files, it is often convenient to pack them into an archive, and the most widely supported format to do so is probably ZIP. Under *nix, you can archive a directory with Info-ZIP:
% zip -r something.zip something/
(When you have several files, it is recommended to archive them in a directory, to avoid cluttering the directory where people will extract them.)Unsupported ZIP archive Unfortunately, while we would expect ZIP files to be widely supported, I found out that this is not always the case, and I had many recipients failing to open them under operating systems such as iOS. Avoid extra fields That issue seems to be linked to the usage of extra file attributes, that are enabled by default, in order to store Unix file metadata. The field designed to store such extra attributes was designed from the beginning so each implementation can take into account attributes it supports and ignore any other ones, but some buggy ZIP implementation appear not to function at all with them. Therefore, unless you actually need to preserve Unix file metadata, you should avoid using extra fields. With Info-ZIP, you would have to add the option -X:
% zip -rX something.zip something/

19 March 2017

Dirk Eddelbuettel: Rcpp 0.12.10: Some small fixes

The tenth update in the 0.12.* series of Rcpp just made it to the main CRAN repository providing GNU R with by now over 10,000 packages. Windows binaries for Rcpp, as well as updated Debian packages will follow in due course. This 0.12.10 release follows the 0.12.0 release from late July, the 0.12.1 release in September, the 0.12.2 release in November, the 0.12.3 release in January, the 0.12.4 release in March, the 0.12.5 release in May, the 0.12.6 release in July, the 0.12.7 release in September, the 0.12.8 release in November, and the 0.12.9 release in January --- making it the fourteenth release at the steady and predictable bi-montly release frequency. Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 975 packages on CRAN depend on Rcpp for making analytical code go faster and further. That is up by sixtynine packages over the two months since the last release -- or just over a package a day! The changes in this release are almost exclusively minor bugfixes and enhancements to documentation and features: James "coatless" Balamuta rounded out the API, I aki Ucar fixed a bug concerning one-character output, Jeroen Ooms allowed for finalizers on XPtr objects, Nathan Russell corrected handling of lower (upper) triangular matrices, Dan Dillon and I dealt with Intel compiler quirks for his algorithm.h header, and I added a C++17 plugin along with some (overdue!) documentation regarding the various C++ standards that are supported by Rcpp (which is in essence whatever your compiler supports, i.e., C++98, C++11, C++14 all the way to C++17 but always keep in mind what CRAN and different users may deploy).

Changes in Rcpp version 0.12.10 (2017-03-17)
  • Changes in Rcpp API:
    • Added new size attribute aliases for number of rows and columns in DataFrame (James Balamuta in #638 addressing #630).
    • Fixed single-character handling in Rstreambuf (I aki Ucar in #649 addressing #647).
    • XPtr gains a parameter finalizeOnExit to enable running the finalizer when R quits (Jeroen Ooms in #656 addressing #655).
  • Changes in Rcpp Sugar:
    • Fixed sugar functions upper_tri() and lower_tri() (Nathan Russell in #642 addressing #641).
    • The algorithm.h file now accomodates the Intel compiler (Dirk in #643 and Dan in #645 addressing issue #640).
  • Changes in Rcpp Attributes
    • The C++17 standard is supported with a new plugin (used eg for g++-6.2).
  • Changes in Rcpp Documentation:
    • An overdue explanation of how C++11, C++14, and C++17 can be used was added to the Rcpp FAQ.

Thanks to CRANberries, you can also look at a diff to the previous release. As always, even fuller details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. A local directory has source and documentation too. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

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 March 2017

Antonio Terceiro: Patterns for Testing Debian Packages

At the and of 2016 I had the pleasure to attend the 11th Latin American Conference on Pattern Languages of Programs, a.k.a SugarLoaf PLoP. PLoP is a series of conferences on Patterns (as in Design Patterns ), a subject that I appreciate a lot. Each of the PLoP conferences but the original main big conference has a funny name. SugarLoaf PLoP is called that way because its very first edition was held in Rio de Janeiro, so the organizers named it after a very famous mountain in Rio. The name stuck even though a long time has passed since it was held in Rio for the last time. 2016 was actually the first time SugarLoaf PLoP was held outside of Brazil, finally justifying the Latin American part of its name. I was presenting a paper I wrote on patterns for testing Debian packages. The Debian project funded my travel expenses through the generous donations of its supporters. PLoP s are very fun conferences with a relaxed atmosphere, and is amazing how many smart (and interesting!) people gather together for them. My paper is titled Patterns for Writing As-Installed Tests for Debian Packages , and has the following abstract:
Large software ecosystems, such as GNU/Linux distributions, demand a large amount of effort to make sure all of its components work correctly invidually, and also integrate correctly with each other to form a coherent system. Automated Quality Assurance techniques can prevent issues from reaching end users. This paper presents a pattern language originated in the Debian project for automated software testing in production-like environments. Such environments are closer in similarity to the environment where software will be actually deployed and used, as opposed to the development environment under which developers and regular Continuous Integration mechanisms usually test software products. The pattern language covers the handling of issues arising from the difference between development and production-like environments, as well as solutions for writing new, exclusive tests for as-installed functional tests. Even though the patterns are documented here in the context of the Debian project, they can also be generalized to other contexts.
In practical terms, the paper documents a set of patterns I have noticed in the last few years, when I have been pushing the Debian Continous Integration project. It should be an interesting read for people interested in the testing of Debian packages in their installed form, as done with autopkgtest. It should also be useful for people from other distributions interested in the subject, as the issues are not really Debian-specific. I have recently finished the final version of the paper, which should be published in the ACM Digital Library at any point now. You can download a copy of the paper in PDF. Source is also available, if you are into markdown, LaTeX, makefiles and this sort of thing. If everything goes according to plan, I should be presenting a talk on this at the next Debconf in Montreal.

15 March 2017

Dirk Eddelbuettel: RcppEigen 0.3.2.9.1

A new maintenance release 0.3.2.9.1 of RcppEigen, still based on Eigen 3.2.9 is now on CRAN and is now going into Debian soon. This update ensures that RcppEigen and the Matrix package agree on their #define statements for the CholMod / SuiteSparse library. Thanks to Martin Maechler for the pull request. I also added a file src/init.c as now suggested (soon: requested) by the R CMD check package validation. The complete NEWS file entry follows.

Changes in RcppEigen version 0.3.2.9.1 (2017-03-14)
  • Synchronize CholMod header file with Matrix package to ensure binary compatibility on all platforms (Martin Maechler in #42)
  • Added file init.c with calls to R_registerRoutines() and R_useDynamicSymbols(); also use .registration=TRUE in useDynLib in NAMESPACE

Courtesy of CRANberries, there is also a diffstat report for the most recent release.

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

Michal &#268;iha&#345;: Life of free software project

During last week I've noticed several interesting posts about challenges being free software maintainer. After being active in open source for 16 years I can share much of the feelings I've read and I can also share my dealings with the things. First of all let me link some of the other posts on the topic: I guess everybody involved in in some popular free software project knows it - there is much more work to be done than people behind the project can handle. It really doesn't matter it those are bug reports, support requests, new features or technical debt, it's simply too much of that. If you are the only one behind the project it can feel even more pressing. There can be several approaches how to deal with that, but you have to choose what you prefer and what is going to work for you and your project. I've used all of the below mentioned approaches on some of the projects, but I don't think there is a silver bullet. Finding more people Obviously if you can not cope with the work, let's find more people to do the work. Unfortunately it's not that easy. Sometimes people come by, contribute few patches, but it's not that easy to turn them into regular contributor. You should encourage them to stay and to care about the part of the project they have touched. You can try to attract completely new contributors through programs as Google Summer of Code (GSoC) or Outreachy, but that has it's own challenges as well. With phpMyAdmin we're participating regularly in GSoC (we've only missed last year as we were not chosen by Google that year) and it indeed helps to bring new people on the board. Many of them even stay around your project (currently 3 of 5 phpMyAdmin team members are former GSoC students). But I think this approach really works only for bigger organizations. You can also motivate people by money. It's way which is not really much used on free software projects, partly because lack of funding (I'll get to that later) and partly because it doesn't necessarily bring long time contributors, just cash hunters. I've been using Bountysource for some of my projects (Weblate and Gammu) and so far it mostly works other way around - if somebody posts bounty on the issue, it means it's quite important for him to get that fixed, so I use that as indication for myself. On attracting new developers it never really worked well, even when I've tried to post bounties to some easy to fix issues, where newbies could learn our code base and get paid for that. These issues stayed opened for months and in the end I've fixed them myself because they annoyed me. Don't care too much I think this is most important aspect - you simply can never fix all the problems. Let's face it and work according to that. There can be various levels of don't caring. I find it always better to try to encourage people to fix their problem, but you can't expect big success rate in that, so you might find it not worth of the time. What I currently do: If you still can't handle that, you should consider abandoning the project as well. Does it bring something to you other than frustration of not completed work? I know it can be hard decision, in the end it is your child, but sometimes it's the best think you can do. Get paid to do the work Are you doing your fulltime job and then work on free software on nights or weekends? It can probably work for some time, but unless you find some way to make these two match, you will lack free time to relax and spend with friends or family. There are several options to make these work together. You can find job where doing free software will be natural part of it. This worked for me pretty well at SUSE, but I'm sure there are more companies where it will work. It can happen that the job will not cover all your free software activities, but this still helps. You can also make your project to become your employer. This can be sometimes challenging to make volunteers and paid contractors to work on one project, but I think this can be handled. Such setup currently works currently quite well for phpMyAdmin (we will announce second contractor soon) and works quite well for me with Weblate as well. Funding free software projects Once your project is well funded, you can fix many problems by money. You can pay yourself to do the work, hire additional developers, get better infrastructure or travel to conferences to spread word about it. But the question is how to get to the point of being well funded. There are several crowdfunding platforms which can help you with that (Liberapay, Bountysource salt, Gratipay or Snowdrift to mention some). You can also administer the funding yourself or using some legal entity such as Software Freedom Conservancy which handles this for phpMyAdmin. But the most important thing is to persuade people and companies to give back. You know there are lot of companies relying on your project, but how to make them fund the project? I really don't know, I still struggle with this as I don't want to be too pushy in asking for money, but I'd really like to see them to give back. What kind of works is giving your sponsors logo / link placement on your website. If your website is well ranked, you can expect to get quite a lot of SEO sponsors and the question is where to draw a line what you still find acceptable. Obviously the most willing to pay companies will have nothing to do with what you do and they just want to get the link. The industry you can expect is porn, gambling, binary options and various MFA sites. You will get some legitimate sponsors related to your project as well. We felt we've gone too far with phpMyAdmin last year and we've stricten the rules recently, but the outcome is still not visible on our website (as we've just limited new sponsors, but existing contracts will be honored). Another option is to monetize your project more directly. You can offer consulting services or provide it as a service (this is what I currently do with Weblate). It really depends on the product if you can build customer base on that or not, but certainly this is not something what would work well for all projects. Thanks for reading this and I hope it's not too chaotic, as I've moved parts there and back while writing and I'm afraid it got too long in the end.

Filed under: Debian English Gammu phpMyAdmin SUSE Weblate 0 comments

13 March 2017

Sean Whitton: Initial views of 5th edition DnD

I ve been playing in a 5e campaign for around two months now. In the past ten days or so I ve been reading various source books and Internet threads regarding the design of 5th edition. I d like to draw some comparisons and contrasts between 5th edition, and the 3rd edition family of games (DnD 3.5e and Paizo s Pathfinder, which may be thought of as 3.75e). The first thing I d like to discuss is that wizards and clerics are no longer Vancian spellcasters. In rules terms, this is the idea that individual spells are pieces of ammunition. Spellcasters have a list of individual spells stored in their heads, and as they cast spells from that list, they cross off each item. Barring special rules about spontaneously converting prepared spells to healing spells, for clerics, the only way to add items back to the list is to take a night s rest. Contrast this with spending points from a pool of energy in order to use an ability to cast a fireball. Then the limiting factor on using spells is having enough points in your mana pool, not having further castings of the spell waiting in memory. One of the design goals of 5th edition was to reduce the dominance of spellcasters at higher levels of play. The article to which I linked in the previous paragraph argues that this rebalancing requires the removal of Vancian magic. The idea, to the extent that I ve understood it, is that Vancian magic is not an effective restriction on spellcaster power levels, so it is to be replaced with other restrictions adding new restrictions while retaining the restrictions inherent in Vancian magic would leave spellcasters crippled. A further reason for removing Vancian magic was to defeat the so-called five minute adventuring day . The compat ability of a party that contains higher level Vancian spellcasters drops significantly once they ve fired off their most powerful combat spells. So adventuring groups would find themselves getting into a fight, and then immediately retreating to fully rest up in order to get their spells back. This removes interesting strategic and roleplaying possibilities involving the careful allocation of resources, and continuing to fight as hit points run low. There are some other related changes. Spell components are no longer used up when casting a spell. So you can use one piece of bat guano for every fireball your character ever casts, instead of each casting requiring a new piece. Correspondingly, you can use a spell focus, such as a cool wand, instead of a pouch full of material components since the pouch never runs out, there s no mechanical change if a wizard uses an arcane focus instead. 0th level spells may now be cast at will (although Pathfinder had this too). And there are decent 0th level attack spells, so a spellcaster need not carry a crossbow or shortbow in order to have something to do on rounds when it would not be optimal to fire off one of their precious spells. I am very much in favour of these design goals. The five minute adventuring day gets old fast, and I want it to be possible for the party to rely on the cool abilities of non-spellcasters to deal with the challenges they face. However, I am concerned about the flavour changes that result from the removal of Vancian magic. These affect wizards and clerics differently, so I ll take each case in turn. Firstly, consider wizards. In third edition, a wizard had to prepare and cast Read Magic (the only spell they could prepare without a spellbook), and then set about working through their spellbook. This involved casting the spells they wanted to prepare, up until the last few triggering words or gestures that would cause the effect of the spell to manifest. They would commit these final parts of the spell to memory. When it came to casting the spell, the wizard would say the final few words and make the required gestures, and bring out relevant material components from their component pouch. The completed spell would be ripped out of their mind, to manifest its effect in the world. We see that the casting of a spell is a highly mentally-draining activity it rips the spell out of the caster s memory! not to be undertaken lightly. Thus it is natural that a wizard would learn to use a crossbow for basic damage-dealing. Magic is not something that comes very naturally to the wizard, to be deployed in combat as readily as the fighter swings their sword. They are not a superhero or video game character, pew pew ing their way to victory. This is a very cool starting point upon which to roleplay an academic spellcaster, not really available outside of tabletop games. I see it as a distinction between magical abilities and real magic. Secondly, consider clerics. Most of the remarks in the previous paragraph apply, suitably reworked to be in terms of requesting certain abilities from the deity to whom the cleric is devoted. Additionally, there is the downgrading of the importance of the cleric s healing magic in 5th edition. Characters can heal themselves by taking short and long rests. Previously, natural healing was very slow, so a cleric would need to convert all their remaining magic to healing spells at the end of the day, and hope that it was enough to bring the party up to fighting shape. Again, this made the party of adventurers seem less like superheroes or video game characters. Magic had a special, important and unique role, that couldn t be replaced by the abilities of other classes.
There are some rules in the back of the DMG Slow Natural Healing , Healing Kit Dependency , Lingering Wounds which can be used to make healing magic more important. I m not sure how well they would work without changes to the cleric class.
I would like to find ways to restore the feel and flavour of Vancian clerics and wizards to 5th edition, without sacrificing the improvements that have been made that let other party members do cool stuff too. I hope it is possible to keep magic cool and unique without making it dominate the game. It would be easy to forbid the use of arcane foci, and say that material component pouches run out if the party do not visit a suitable marketplace often enough. This would not have a significant mechanical effect, and could enhance roleplaying possibilities. I am not sure how I could deal with the other issues I ve discussed without breaking the game. The second thing I would like to discuss is bounded accuracy. Under this design principle, the modifiers to dice rolls grow much more slowly. The gain of hit points remains unbounded. Under third edition, it was mechanically impossible for a low-level monster to land a hit on a higher-level adventurer, rendering them totally useless even in overwhelming numbers. With bounded accuracy, it s always possible for a low-level monster to hit a PC, even if they do insigificant damage. That means that multiple low-level monsters pose a threat. This change opens up many roleplaying opportunities by keeping low-level character abilities relevant, as well as monster types that can remain involves in stories without giving them implausible new abilities so they don t fall far behind the PCs. However, I m a little worried that it might make high level player characters feel a lot less powerful to play. I want to cease a be a fragile adventurer and become a world-changing hero at later levels, rather than forever remain vulnerable to the things that I was vulnerable to at the start of the game. This desire might just be the result of the video games which I played growing up. In the JRPGs I played and in Diablo II, enemies in earlier areas of the map were no threat at all once you d levelled up by conquering higher-level areas. My concerns about bounded accuracy might just be that it clashes with my own expectations of how fantasy heroes work. A good DM might be able to avoid these worries entirely. The final thing I d like to discuss is the various simplifications to the rules of 5th edition, when it is compared with 3rd edition and Pathfinder. Attacks of opportunity are only provoked when leaving a threatened square; you can go ahead and cast a spell when in melee with someone. There is a very short list of skills, and party members are much closer to each other in skills, now that you can t pump more and more ranks into one or two abilities. Feats as a whole are an optional rule. At first I was worried about these simplifications. I thought that they might make character building and tactics in combat a lot less fun. However, I am now broadly in favour of all of these changes, for two reasons. Firstly, they make the game so much more accessible, and make it far more viable to play without relying on a computer program to fill in the boxes on your character sheet. In my 5th edition group, two of us have played 3rd edition games, and the other four have never played any tabletop games before. But nobody has any problems figuring out their modifiers because it is always simply your ability bonus or penalty, plus your proficiency bonus if relevant. And advantage and disadvantage is so much more fun than getting an additional plus or minus two. Secondly, these simplifications downplay the importance of the maths, which means it is far less likely to be broken. It is easier to ensure that a smaller core of rules is balanced than it is to keep in check a larger mass of rules, constantly being supplemented by more and more addon books containing more and more feats and prestige classes. That means that players make their characters cool by roleplaying them in interesting ways, not making them cool by coming up with ability combos and synergies in advance of actually sitting down to play. Similarly, DMs can focus on flavouring monsters, rather than writing up longer stat blocks. I think that this last point reflects what I find most worthwhile about tabletop RPGs. I like characters to encounter cool NPCs and cool situations, and then react in cool ways. I don t care that much about character creation. (I used to care more about this, but I think it was mainly because of interesting options for magic items, which hasn t gone away.) The most important thing is exercising group creativity while actually playing the game, rather than players and DMs having to spend a lot of time preparing the maths in advance of playing. Fifth edition enables this by preventing the rules from getting in the way, because they re broken or overly complex. I think this is why I love Exalted: stunting is vital, and there is social combat. I hope to be able to work out a way to restore Vancian magic, but even without that, on balance, fifth edition seems like a better way to do group storytelling about fantasy heroes. Hopefully I will have an opportunity to DM a 5th edition campaign. I am considering disallowing all homebrew and classes and races from supplemental books. Stick to the well-balanced core rules, and do everything else by means of roleplaying and flavour. This is far less gimmicky, if more work for unimaginative players (such as myself!). Some further interesting reading:

12 March 2017

Steve Kemp: How I started programming

I've written parts of this story in the past, but never in one place and never in much detail. So why not now? In 1982 my family moved house, so one morning I went to school and at lunch-time I had to walk home to a completely different house. We moved sometime towards the end of the year, and ended up spending lots of money replacing the windows of the new place. For people in York I was born in Farrar Street, Y010 3BY, and we moved to a place on Thief Lane, YO1 3HS. Being named as it was I "ironically" stole at least two street-signs and hung them on my bedroom wall. I suspect my parents were disappointed. Anyway the net result of this relocation, and the extra repairs meant that my sisters and I had a joint Christmas present that year, a ZX Spectrum 48k. I tried to find pictures of what we received but unfortunately the web doesn't remember the precise bundle. All together though we received: I know we also received Horace and the Spiders, and I have vague memories of some other things being included, including a Space Invaders clone. No doubt my parents bought them separately. Highlights of my Spectrum-gaming memories include R-Type, Strider, and the various "Dizzy" games. Some of the latter I remember very fondly. Unfortunately this Christmas was pretty underwhelming. We unpacked the machine, we cabled it up to the family TV-set - we only had the one, after all - and then proceeded to be very disappointed when nothing we did resulted in a successful game! It turns out our cassette-deck was not good enough. Being back in the 80s the shops were closed over Christmas, and my memory is that it was around January before we received a working tape-player/recorder, such that we could load games. Happily the computer came with manuals. I read one, skipping words and terms I didn't understand. I then read the other, which was the spiral-bound orange book. It contained enough examples and decent wording that I learned to write code in BASIC. Not bad for an 11/12 year old. Later I discovered that my local library contained "computer books". These were colourful books that promised "The Mystery of Silver Mounter", or "Write your own ADVENTURE PROGRAMS". But were largely dry books that contained nothing but multi-page listings of BASIC programs to type in. Often with adjustments that had to be made for your own computer-flavour (BASIC varying between different systems).
If you want to recapture the magic scroll to the foot of this Osbourne page and you can download them!
Later I taught myself Z80 Assembly Language, partly via the Spectrum manual and partly via such books as these two (which I still own 30ish years later): Pretty much the only reason I continued down this path is because I wanted infinite/extra lives in the few games I owned. (Which were largely pirated via the schoolboy network of parents with cassette-copiers.) Eventually I got some of my l33t POKES printed in magazines, and received free badges from the magazines of the day such as Your Sinclair & Sinclair User. For example I was "Hacker of the Month" in the Your Sinclair issue 67 , Page 32, apparently because I "asked so nicely in my letter". Terrible scan is terrible: Anyway that takes me from 1980ish to 1984. The only computer I ever touched was a Spectrum. Friends had other things, and there were Sega consoles, but I have no memories of them. Suffice it to say that later when I first saw a PC (complete with Hercules graphics, hard drives, and similar sourcery, running GEM IIRC) I was pleased that Intel assembly was "similar" to Z80 assembly - and now I know the reason why. Some time in the future I might document how I got my first computer job. It is hillarious. As was my naivete.

9 March 2017

Petter Reinholdtsen: Detecting NFS hangs on Linux without hanging yourself...

Over the years, administrating thousand of NFS mounting linux computers at the time, I often needed a way to detect if the machine was experiencing NFS hang. If you try to use df or look at a file or directory affected by the hang, the process (and possibly the shell) will hang too. So you want to be able to detect this without risking the detection process getting stuck too. It has not been obvious how to do this. When the hang has lasted a while, it is possible to find messages like these in dmesg:
nfs: server nfsserver not responding, still trying
nfs: server nfsserver OK
It is hard to know if the hang is still going on, and it is hard to be sure looking in dmesg is going to work. If there are lots of other messages in dmesg the lines might have rotated out of site before they are noticed. While reading through the nfs client implementation in linux kernel code, I came across some statistics that seem to give a way to detect it. The om_timeouts sunrpc value in the kernel will increase every time the above log entry is inserted into dmesg. And after digging a bit further, I discovered that this value show up in /proc/self/mountstats on Linux. The mountstats content seem to be shared between files using the same file system context, so it is enough to check one of the mountstats files to get the state of the mount point for the machine. I assume this will not show lazy umounted NFS points, nor NFS mount points in a different process context (ie with a different filesystem view), but that does not worry me. The content for a NFS mount point look similar to this:
[...]
device /dev/mapper/Debian-var mounted on /var with fstype ext3
device nfsserver:/mnt/nfsserver/home0 mounted on /mnt/nfsserver/home0 with fstype nfs statvers=1.1
        opts:   rw,vers=3,rsize=65536,wsize=65536,namlen=255,acregmin=3,acregmax=60,acdirmin=30,acdirmax=60,soft,nolock,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=129.240.3.145,mountvers=3,mountport=4048,mountproto=udp,local_lock=all
        age:    7863311
        caps:   caps=0x3fe7,wtmult=4096,dtsize=8192,bsize=0,namlen=255
        sec:    flavor=1,pseudoflavor=1
        events: 61063112 732346265 1028140 35486205 16220064 8162542 761447191 71714012 37189 3891185 45561809 110486139 4850138 420353 15449177 296502 52736725 13523379 0 52182 9016896 1231 0 0 0 0 0 
        bytes:  166253035039 219519120027 0 0 40783504807 185466229638 11677877 45561809 
        RPC iostats version: 1.0  p/v: 100003/3 (nfs)
        xprt:   tcp 925 1 6810 0 0 111505412 111480497 109 2672418560317 0 248 53869103 22481820
        per-op statistics
                NULL: 0 0 0 0 0 0 0 0
             GETATTR: 61063106 61063108 0 9621383060 6839064400 453650 77291321 78926132
             SETATTR: 463469 463470 0 92005440 66739536 63787 603235 687943
              LOOKUP: 17021657 17021657 0 3354097764 4013442928 57216 35125459 35566511
              ACCESS: 14281703 14290009 5 2318400592 1713803640 1709282 4865144 7130140
            READLINK: 125 125 0 20472 18620 0 1112 1118
                READ: 4214236 4214237 0 715608524 41328653212 89884 22622768 22806693
               WRITE: 8479010 8494376 22 187695798568 1356087148 178264904 51506907 231671771
              CREATE: 171708 171708 0 38084748 46702272 873 1041833 1050398
               MKDIR: 3680 3680 0 773980 993920 26 23990 24245
             SYMLINK: 903 903 0 233428 245488 6 5865 5917
               MKNOD: 80 80 0 20148 21760 0 299 304
              REMOVE: 429921 429921 0 79796004 61908192 3313 2710416 2741636
               RMDIR: 3367 3367 0 645112 484848 22 5782 6002
              RENAME: 466201 466201 0 130026184 121212260 7075 5935207 5961288
                LINK: 289155 289155 0 72775556 67083960 2199 2565060 2585579
             READDIR: 2933237 2933237 0 516506204 13973833412 10385 3190199 3297917
         READDIRPLUS: 1652839 1652839 0 298640972 6895997744 84735 14307895 14448937
              FSSTAT: 6144 6144 0 1010516 1032192 51 9654 10022
              FSINFO: 2 2 0 232 328 0 1 1
            PATHCONF: 1 1 0 116 140 0 0 0
              COMMIT: 0 0 0 0 0 0 0 0
device binfmt_misc mounted on /proc/sys/fs/binfmt_misc with fstype binfmt_misc
[...]
The key number to look at is the third number in the per-op list. It is the number of NFS timeouts experiences per file system operation. Here 22 write timeouts and 5 access timeouts. If these numbers are increasing, I believe the machine is experiencing NFS hang. Unfortunately the timeout value do not start to increase right away. The NFS operations need to time out first, and this can take a while. The exact timeout value depend on the setup. For example the defaults for TCP and UDP mount points are quite different, and the timeout value is affected by the soft, hard, timeo and retrans NFS mount options. The only way I have been able to get working on Debian and RedHat Enterprise Linux for getting the timeout count is to peek in /proc/. But according to Solaris 10 System Administration Guide: Network Services, the 'nfsstat -c' command can be used to get these timeout values. But this do not work on Linux, as far as I can tell. I asked Debian about this, but have not seen any replies yet. Is there a better way to figure out if a Linux NFS client is experiencing NFS hangs? Is there a way to detect which processes are affected? Is there a way to get the NFS mount going quickly once the network problem causing the NFS hang has been cleared? I would very much welcome some clues, as we regularly run into NFS hangs.

7 March 2017

Dirk Eddelbuettel: RProtoBuf 0.4.9

RProtoBuf provides R bindings for the Google Protocol Buffers ("Protobuf") data encoding and serialization library used and released by Google, and deployed as a language and operating-system agnostic protocol by numerous projects. The RProtoBuf 0.4.9 release is the fourth and final update this weekend following the request by CRAN to not use package= in .Call() when PACKAGE= is really called for. Some of the code in RProtoBuf 0.4.9 had this bug; some other entry points had neither (!!). With the ongoing drive to establish proper registration of entry points, a few more issues were coming up, all of which are now addressed. And we had some other unreleased minor cleanup, so this made for a somewhat longer (compared to the other updates this weekend) NEWS list:

Changes in RProtoBuf version 0.4.9 (2017-03-06)
  • A new file init.c was added with calls to R_registerRoutines() and R_useDynamicSymbols()
  • Symbol registration is enabled in useDynLib
  • Several missing PACKAGE= arguments were added to the corresponding .Call invocations
  • Two (internal) C++ functions were renamed with suffix _cpp to disambiguate them from R functions with the same name
  • All of above were part of #26
  • Some editing corrections were made to the introductory vignette (David Kretch in #25)
  • The 'configure.ac' file was updated, and renamed from the older converntion 'configure.in', along with 'src/Makevars'. (PR #24 fixing #23)

CRANberries also provides a diff to the previous release. The RProtoBuf page has an older package vignette, a 'quick' overview vignette, a unit test summary vignette, and the pre-print for the JSS paper. Questions, comments etc should go to the GitHub issue tracker off 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.

Dirk Eddelbuettel: RVowpalWabbit 0.0.9

The RVowpalWabbit package update is the third of four upgrades requested by CRAN, following RcppSMC 0.1.5 and RcppGSL 0.3.2. This package being somewhat raw, the change was simple and just meant converting the single entry point to using Rcpp Attributes -- which addressed the original issue in passing. No new code or features were added. We should mention that is parallel work ongoing in a higher-level package interfacing the vw binary -- rvw -- as well as plan to redo this package via the external libraries. In that sounds interesting to you, please get in touch. More information is on the RVowpalWabbit 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.

5 March 2017

Dirk Eddelbuettel: RcppGSL 0.3.2

The RcppGSL package provides an interface from R to the GNU GSL using the Rcpp package. RcppGSL release 0.3.2 is one of several maintenance releases this weekend to fix an issue flagged by CRAN: calls to .Call() sometimes used package= where PACKAGE= was meant. This came up now while the registration mechanism is being reworked. So RcppGSL was updated too, and we took the opportunity to bring several packaging aspects up to the newest standards, including support for the soon-to-be required registration of routines. No new code or features were added. The NEWS file entries follow below:

Changes in version 0.3.2 (2017-03-04)
  • In the fastLm function, .Call now uses the correct PACKAGE= argument
  • Added file init.c with calls to R_registerRoutines() and R_useDynamicSymbols(); also use .registration=TRUE in useDynLib in NAMESPACE
  • The skeleton configuration for created packages was updated.

Courtesy of CRANberries, a summary of changes to the most recent release is available. More information is on the RcppGSL page. Questions, comments etc should go to the issue tickets 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.

Dirk Eddelbuettel: RcppSMC 0.1.5

RcppSMC provides Rcpp-based bindings to R for them Sequential Monte Carlo Template Classes (SMCTC) by Adam Johansen described in his JSS article. RcppSMC release 0.1.5 is one of several maintenance releases this weekend to fix an issue flagged by CRAN: calls to .Call() sometimes used package= where PACKAGE= was meant. This came up now while the registration mechanism is being reworked. Hence RcppSMC was updated, and we took the opportunity to bring several packaging aspects up to the newest standards, including support for the soon-to-be required registration of routines. No new code or features were added. The NEWS file entries follow below:

Changes in RcppSMC version 0.1.5 (2017-03-03)
  • Correct .Call to use PACKAGE= argument
  • DESCRIPTION, NAMESPACE, README.md changes to comply with current R CMD check levels
  • Added file init.c with calls to R_registerRoutines() and R_useDynamicSymbols()
  • Updated .travis.yml file for continuous integration

Courtesy of CRANberries, there is a diffstat report for this release. More information is on the RcppSMC 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.

Shirish Agarwal: To say or not to say

Voltaire For people who are visually differently-abled, the above reads To learn who rules over you, simply find out who you are not allowed to criticize Voltaire wrote this either in late 16th century or early 17th century and those words were as apt in those times, as it is in these turbulent times as well. Update 05/03 According to @bla these words are attributable to a neo-nazi and apparently a child abuser. While I don t know the context in which it was shared, it describes the environment in which we are perfectly. Please see his comment for a link and better understanding. The below topic requires a bit of maturity, so if you are easily offended, feel free not to read further. While this week-end I was supposed to share about the recent Science Day celebrations that we did last week Science Day celebrations at GMRT Would explore it probably next week. This week the attempt is to share thoughts which had been simmering at the back of my mind for more than 2 weeks or more and whose answers are not clear to me. My buttons were pressed when Martin f. Kraft shared about a CoC violation and the steps taken therein. While it is easy to say with 20:20 hind-sight to say that the gentleman acted foolishly, I don t really know the circumstances to pass the judgement so quickly. In reality, while I didn t understand the joke in itself, I have to share some background by way of anecdotes as to why it isn t so easy for me to give a judgement call. a. I don t know the topics chosen by stand-up comedians in other countries, in India, most of the stand-up acts are either about dating or sex or somewhere in-between, which is lovingly given the name Leela (dance of life) in Indian mythology. I have been to several such acts over the years at different events, different occasions and 99.99% of the time I would see them dealing with pedophilia, necrophilia and all sorts of deviants in sexuality and people laughing wildly, but couple of times when the comedian shared the term sex with people, educated, probably more than a few world-travelled middle to higher-middle class people were shocked into silence. I had seen this not in once but 2-3 times in different environments and was left wondering just couple of years back Is sex such a bad word that people get easily shocked ? Then how is it that we have 1.25 billion + people in India. There had to be some people having sex. I don t think that all 1.25 billion people are test-tube babies. b. This actually was what lead to my quandary last year when my sharing of My Experience with Debian which I had carefully prepared for newbies, seeing seasoned debian people, I knew my lame observations wouldn t cut ice with them and hence had to share my actual story which involved a bit of porn. I was in two minds whether or not to say it till my eyes caught a t-shirt on which it was said We make porn or something to that effect. That helped me share my point. c. Which brings me to another point, it seems it is becoming increasingly difficult to talk about anything either before apologizing to everyone and not really knowing who will take offence at what and what the repercussions might be. In local sharings, I always start with a blanket apology that if I say something that offends you, please let me know afterwards so I can work on it. As the term goes You can t please everyone and that is what happens. Somebody sooner or later would take offence at something and re-interpret it in ways which I had not thought of. Charlie Chaplin - King of self-deprecating humor From the little sharings and interactions I have been part of, I find people take offence at the most innocuous things. For instance, one of the easy routes of not offending anyone is to use self-deprecating humour (or so I thought) either of my race, caste, class or even my issues with weight and each of the above would offend somebody. Charlie Chaplin didn t have those problems. If somebody is from my caste, I m portraying the caste in a certain light, a certain slant. If I m talking about weight issues, then anybody who is like me (fat) feels that the world is laughing at them rather than at me or they will be discriminated against. While I find the last point a bit valid, it leaves with me no tools and no humour. I neither have the observational powers or the skills that Kapil Sharma has and have to be me. While I have no clue what to do next, I feel the need to also share why humour is important in any sharing.- a. Break When any speaker uses humour, the idea is to take a break from a serious topic. It helps to break the monotony of the talk especially if the topic is full of jargon talk and new concepts. A small comedic relief brings the attendees attention back to the topic as it tends to wander in a long monotonous talk. b. Bridge Some of the better speakers use one or more humourous anecdote to explain and/or bridge the chasm between two different concepts. Some are able to produce humour on the fly while others like me have to rely on tried and tested methods. There is one another thing as well, humour is seems to be a mixture of social, cultural and political context and its very easy to have it back-fired upon you. For instance, I attempted humour on refugees, probably not the best topic to try humour in the current political climate, and predictably, it didn t go down well. I had to share and explain about Robin Williams slightly dark yet humorous tale in Moscow on the Hudson The film provides comedy and pathos in equal measure. You are left identifying with Vladimir Ivanoff (Robin Williams character) especially in the last scene where he learns of his grand-mother dying and he remembers her and his motherland, Russia and plays a piece on his saxophone as a tribute both to his grand-mother and the motherland. Apparently, in the height of the cold war, if a Russian defected to United States (land of Satan and other such terms used) you couldn t return to Russia. The movie, seen some years back left a deep impact on me. For all the shortcomings and ills that India has, even if I could, would and could I be happy anywhere else ? The answers are not so easy. With most NRI s (Non-Resident Indians) who emigrated for good did it not so much for themselves but for their children. So the children would hopefully have a better upbringing, better facilities, better opportunities than they would have got here. I talked to more than a few NRI s and while most of them give standardized answers, talking awhile and couple of beers or their favourite alcohol later, you come across deeply conflicted human beings whose heart is in India and their job, profession and money interests compel them to be in the country where they are serving. And Indian movies further don t make it easy for the Indian populace when trying to integrate into a new place. Some of the biggest hits of yesteryear s were about having the distinct Indian culture in their new country while the message of most countries is integration. I know of friends who are living in Germany who have to struggle through their German in order to be counted as a citizen, the same I guess is true of other countries as well, not just the language but the customs as well. They also probably struggle with learning more than one language and having an amalgamation of values which somehow they and their children have to make sense of. I was mildly shocked last week to learn that Mishi Choudary had to train people in the U.S. to differentiate between Afghan turban styles of wearing and the Punjabi style of wearing the turban. A simple search on Afghani turban and Punjabi turban reveals that there are a lot of differences between the two cultures. In fact, the way they talk, the way they walk, there are lots that differentiate the two cultures. The second shocking video was of an African-American man racially abusing an Indian-American girl. At first, I didn t believe it till I saw the video on facebook. My point through all that is it seems humour, that clean, simple exercise which brings a smile to you and uplifts the spirit doesn t seem to be as easy as it once was. Comments, suggestions, criticisms all are welcome.
Filed under: Miscellenous Tagged: #Elusive, #Fear, #hind-sight, #Humour, #immigrant, #integration, #Mishi Choudary, #refugee, #Robin Williams, #self-deprecating, #SFLC, #two-minds

4 March 2017

Simon Josefsson: GPS on Replicant 6

I use Replicant on my main Samsung S3 mobile phone. Replicant is a fully free Android distribution. One consequence of the fully free means that some functionality is not working properly, because the hardware requires non-free software. I am in the process of upgrading my main phone to the latest beta builds of Replicant 6. Getting GPS to work on Replicant/S3 is not that difficult. I have made the decision that I am willing to compromise on freedom a bit for my Geocaching hobby. I have written before how to get GPS to work on Replicant 4.0 and GPS on Replicant 4.2. When I upgraded to Wolfgang s Replicant 6 build back in September 2016, it took some time to figure out how to get GPS to work. I prepared notes on non-free firmware on Replicant 6 which included a section on getting GPS to work. Unfortunately, that method requires that you build your own image and has access to the build tree. Which is not for everyone. This writeup explains how to get GPS to work on a Replicant 6 without building your own image. Wolfgang already explained how to add all other non-free firmware to Replicant 6 but it did not cover GPS. The reason is that GPS requires non-free software to run on your main CPU. You should understand the consequences of this before proceeding! The first step is to download a Replicant 6.0 image, currently they are available from the replicant 6.0 forum thread. Download the replicant-6.0-i9300.zip file and flash it to your phone as usual. Make sure everything (except GPS of course) works, after loading other non-free firmware (Wifi, Bluetooth etc) using "./firmwares.sh i9300 all" that you may want. You can install the Geocaching client c:geo via fdroid by adding fdroid.cgeo.org as a separate repository. Start the app and verify that GPS does not work. Keep the replicant-6.0-i9300.zip file around, you will need it later. The tricky part about GPS is that the daemon is started through the init system of Android, specified by the file /init.target.rc. Replicant ships with the GPS part commented out. To modify this file, we need to bring out our little toolbox. Modifying the file on the device itself will not work, the root filesystem is extracted from a ramdisk file on every boot. Any changes made to the file will not be persistent. The file /init.target.rc is stored in the boot.img ramdisk, and that is the file we need to modify to make a persistent modification. First we need the unpackbootimg and mkbootimg tools. If you are lucky, you might find them pre-built for your operating system. I am using Debian and I couldn t find them easily. Building them from scratch is however not that difficult. Assuming you have a normal build environment (i.e., apt-get install build-essentials) try the following to build the tools. I was inspired by a post on unpacking and editing boot.img for some of the following instructions.
git clone https://github.com/CyanogenMod/android_system_core.git
cd android_system_core/
git checkout cm-13.0 
cd mkbootimg/
gcc -o ./mkbootimg -I ../include ../libmincrypt/*.c ./mkbootimg.c
gcc -o ./unpackbootimg -I ../include ../libmincrypt/*.c ./unpackbootimg.c
sudo cp mkbootimg unpackbootimg /usr/local/bin/
You are now ready to unpack the boot.img file. You will need the replicant ZIP file in your home directory. Also download the small patch I made for the init.target.rc file: https://gitlab.com/snippets/1639447. Save the patch as replicant-6-gps-fix.diff in your home directory.
mkdir t
cd t
unzip ~/replicant-6.0-i9300.zip 
unpackbootimg -i ./boot.img
mkdir ./ramdisk
cd ./ramdisk/
gzip -dc ../boot.img-ramdisk.gz   cpio -imd
patch < ~/replicant-6-gps-fix.diff 
Assuming the patch applied correctly (you should see output like "patching file init.target.rc" at the end) you will now need to put the ramdisk back together.
find . ! -name .   LC_ALL=C sort   cpio -o -H newc -R root:root   gzip > ../new-boot.img-ramdisk.gz
cd ..
mkbootimg --kernel ./boot.img-zImage \
--ramdisk ./new-boot.img-ramdisk.gz \
--second ./boot.img-second \
--cmdline "$(cat ./boot.img-cmdline)" \
--base "$(cat ./boot.img-base)" \
--pagesize "$(cat ./boot.img-pagesize)" \
--dt ./boot.img-dt \
--ramdisk_offset "$(cat ./boot.img-ramdisk_offset)" \
--second_offset "$(cat ./boot.img-second_offset)" \
--tags_offset "$(cat ./boot.img-tags_offset)" \
--output ./new-boot.img
Reboot your phone to the bootloader:
adb reboot bootloader
Then flash the new boot image back to your phone:
heimdall flash --BOOT new-boot.img
The phone will restart. To finalize things, you need the non-free GPS software components glgps, gps.exynos4.so and gps.cer. Before I used a complicated method involving sdat2img.py to extract these files from a CyanogenMod 13.x archive. Fortunately, Lineage OS is now offering downloads containing the relevant files too. You will need to download some files, extract them, and load them onto your phone.
wget https://mirrorbits.lineageos.org/full/i9300/20170125/lineage-14.1-20170125-experimental-i9300-signed.zip
mkdir lineage
cd lineage
unzip ../lineage-14.1-20170125-experimental-i9300-signed.zip
adb root
adb wait-for-device
adb remount
adb push system/bin/glgps /system/bin/
adb push system/lib/hw/gps.exynos4.vendor.so /system/lib/hw/gps.exynos4.so
adb push system/bin/gps.cer /system/bin/
Now reboot your phone and start c:geo and it should find some satellites. Congratulations!

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