Re: Packages of "standard" priority in a fresh cdebootstrapped system as dependencies of packages with higher priorities.

2015-07-25 Thread Jayson Willson

Thank you, now I understand.


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Bug#793404: massive waste of CPU time in debian/rules by inline commands

2015-07-25 Thread Niels Thykier
On 2015-07-24 12:19, Jakub Wilk wrote:
> * Jonas Smedegaard , 2015-07-23, 21:40:
>>> One mistake boost makes is using ":=" instead of plain "=". Contrary
>>> to popular belief, the former almost always causes more evaluation of
>>> $(shell) stuff, specially when dh is involved.
>> Could you elaborate on that?
> 
> dpkg-buildpackage -B will run debian/rules 4 times: once to determine if
> build-arch exist, and once for every target: clean, build(-arch),
> binary-arch.
> 
> dh adds even more debian/rules invocations. It runs it once every target
> (clean, build(-arch), binary-arch), and once for every override.
> 
Indeed - though hardly the common use for override targets, you /can/
exclude a command for free by declaring a /completely/ empty target.

Have a look at:
 $ dh binary --no-act | grep debian/rules | wc -l
 $ dh clean  --no-act | grep debian/rules | wc -l

Which should tell you how many override non-empty targets you have.
Output (of dh  --no-act) is something like:

   dh_testdir
   debian/rules override_dh_auto_configure
   dh_auto_build
   [...]
   dh_installdirs
   debian/rules override_dh_auto_install
   [...]

If your override target is completely empty, the command/target simply
disappears from the list.  Though it does not account for the extra
overhead from dpkg-buildpackage calling build{,-arch,-indep} first in a
separate step.

> So your ":=" variable will be evaluated 4 times, or 7+N times if you use
> dh.
> 
> [...]
> 

It should be doable to reduce the dh side of it to 1+N by caching the
result of make (in a file-based cache).

~Niels


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Bug#793578: ITP: ruby-climate-control -- library to easily manage environment variables

2015-07-25 Thread Balasankar C
Package: wnpp
Severity: wishlist
Owner: Balasankar C 

* Package name: ruby-climate-control
  Version : 0.0.3
  Upstream Author : Joshua Clayton 
* URL : https://github.com/thoughtbot/climate_control
* License : Expat
  Programming Lang: Ruby
  Description : library to easily manage environment variables


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Bug#793585: ITP: ea-utils -- command-line tools for processing biological sequencing data

2015-07-25 Thread Andreas Tille
Package: wnpp
Severity: wishlist
Owner: Andreas Tille 

* Package name: ea-utils
  Version : 1.1.2
  Upstream Author : Erik Aronesty 
* URL : https://code.google.com/p/ea-utils/
* License : MIT
  Programming Lang: C
  Description : command-line tools for processing biological sequencing data
i Ea-utils provides a set of command-line tools for processing biological
 sequencing data, barcode demultiplexing, adapter trimming, etc.
 .
 Primarily written to support an Illumina based pipeline - but should work with
 any FASTQs.
 .
 Main Tools are:
 .
  * fastq-mcf
 Scans a sequence file for adapters, and, based on a log-scaled threshold,
 determines a set of clipping parameters and performs clipping. Also does
 skewing detection and quality filtering.
  * fastq-multx
 Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
 master set fields. Keeps multiple reads in-sync during demultiplexing. Can
 verify that the reads are in-sync as well, and fail if they're not.
  * fastq-join
 Similar to audy's stitch program, but in C, more efficient and supports some
 automatic benchmarking and tuning. It uses the same "squared distance for
 anchored alignment" as other tools.
  * varcall
 Takes a pileup and calculates variants in a more easily parameterized manner
 than some other tools.


This package was prepared by Tim Booth for BioLinux to update the qiime
package.  It is taken over into the Debian Med team and will be maintained
at

   git://anonscm.debian.org/debian-med/ea-utils.git


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Bug#793617: ITP: ruby-parse-cron -- parse cron expressions and calculates the next job occurence

2015-07-25 Thread Dmitry Smirnov
Package: wnpp
Severity: wishlist
X-Debbugs-CC: debian-devel@lists.debian.org 
pkg-ruby-extras-maintain...@lists.alioth.debian.org

   Package name: ruby-parse-cron
Version: 0.1.4
Upstream Author: Michael Siebert 
License: Expat
URL: https://github.com/siebertm/parse-cron
Vcs-Browser: 
https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-parse-cron.git
Description: parse cron expressions and calculate occurrence of next job
 "parse-cron" parses crontab timing specification and determine when the
 next scheduled job should be run.

---

This package is a dependency of Opennebula-4.x.

-- 
Cheers,
 Dmitry Smirnov.

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Re: Facilitating external repositories

2015-07-25 Thread David Kalnischkies
On Thu, Jul 23, 2015 at 10:14:21AM +0200, Wouter Verhelst wrote:
> - Apt will try to download it from a default location in the repository
>   (or perhaps a location specified in the deb822 sources.list file
>   itself).

What the heck is "it" in this sentence? I envision "deb822 sources.list"
file, but reading the location of the file from the file itself seems
a bit hard to pull of in practice…


> - It may be GPG-signed by one or more keys. Apt should have a way of
>   configuring GPG keys that may be allowed to sign sources.list files,
>   preloaded with the set of keys in the Debian keyring. This will allow
>   system administrators in large environments to specify their own set
>   of keys allowed to sign repositories, as well as allowing downstreams
>   to add its own ways of trusting repositories.

Using the Debian keyring as a preload means a) a big package pushed into
the default set of installed packages and b) the update state of this
package: The package can happily contain revoked/expired keys (if
everyone follows the <2 years expire recommendation every key will be
expired well before the end of security support – not even mentioning
LTS and apt can't just --refresh-keys as it can't verify the result).
No longer DDs.  Will not include new DDs. Same for DMs were the active
state can vary faster based on the ping.

There is of course the general problem of if a signature by a 'random'
DD actually assures anything. I mean, I have a key signed by a few DDs,
does that mean I can repropose my key now for an archive? Sounds about
right to me at least. So much for "a trusted path from Debian to [your]
repository" as it is now my man-in-the-middled repository.
(Did I say "I repropose"? That was the blackhat stealing my key of course)

Or did you mean that the DD signs the sources.list file directly? Well,
then my key isn't usable for that right now, but in exchange the DD
might have a slight problem in assuring the correctness of what he is
signing: I am the owner of example.org/debian. Trust me.

If you thought the default CA trust store in a browser is (too) large,
I am not sure what a 1000+ key trust store would be. Sounds for me like
the wet dream of security folks (not)…


Oh, and given that I got you to sign my example.org repo for me, does
that mean you are endorsing my endeavor? I mean, pornview is a normal
image viewer, hotbabe a good cpu monitor and sex my preferred input
method (as a text editor). Any objections? And god forbit that I might
turn (even more) evil.  Or the person I am selling the domain to in
three months… (Or should I say the blackhat who did a hostile take over
of my domain and now ships trojans to everyone with a sources.list
signed by you). But yeah, you are not endorsing me, you just signed
a document to give me root access on every machine you happen to be
a trusted signer on – that is totally different.


Some of this is a problem for an archive signing key as well, but the
difference is that an archive signing key is signing a Release file
which regularly changes, but a sources.list file hardly changes. It
especially doesn't change in the last example with a domain takeover and
there is no poor man's repository version of the web of trust.


If you are adding archive signing keys it must be hundred percent bullet
proof or all of apt-secure is broken. Sure, you are basically automating
what is currently done by hand by many users, but as long as they do it
by hand its their own fault – if you automate it to one-click they will
rightly expect it to be secure.


> - It may possibly add a limitation on the packages that can be
>   downloaded from the given repository (so that a package repository
>   cannot suddenly acquire a package "libc6", accidentally or otherwise).
>   This should allow for wildcards (e.g., in my specific situation this
>   field would contain "libbeid*, eid-*, beid-*")

While a nice feature, hardly a security one as for an attacker it is
only important to know which package to infect. libc6 is of course
installed by everyone, so an "upgrade" in a bugged repository has the
desired effect, but any person with your repository active will also
have one of your packages installed – otherwise they wouldn't have the
repository in the first place, right – so that feature gives a warm
fuzzy feeling at best. Who cares in the end if the package I run my evil
maintainer script with is called 'libc6' or 'eid' …

btw: Who is controlling that whitelist? Lets imagine that your tool
needs in version 2 two new obscure libraries: You will have a hard time
convincing John Doe that he should update the list by hand after apt-get
crapped out with an error message saying that much – on the other hand
Jane Doe will be disappointed if you let apt-get change the list based
on the wishes of the repository. And lets face it: Nobody will be happy
if apt-get is asking a question about this as everyone will be trained
to press 'yes' pretty quickly.

Oh, and what about eid-libc6 

Bug#793644: ITP: hadoop -- Apache Hadoop distributed processing framework

2015-07-25 Thread Emmanuel Bourg
Package: wnpp
Severity: wishlist
Owner: Emmanuel Bourg 

* Package name: hadoop
  Version : 2.6.0
  Upstream Author : The Apache Software Foundation
* URL : http://hadoop.apache.org
* License : Apache-2.0
  Programming Lang: Java
  Description : Apache Hadoop distributed processing framework

Apache Hadoop is a framework for running applications on large cluster built
of commodity hardware. It transparently provides applications both reliability
and data motion. Hadoop implements a computational paradigm named Map/Reduce,
where the application is divided into many small fragments of work, each of
which may be executed or re-executed on any node in the cluster. In addition,
it provides a distributed file system (HDFS) that stores data on the compute
nodes, providing very high aggregate bandwidth across the cluster. Both
MapReduce and the Hadoop Distributed File System are designed so that node
failures are automatically handled by the framework.


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