Search Results: "Aaron M. Ucko"

24 October 2017

Reproducible builds folks: Reproducible Builds: Weekly report #130

Here's what happened in the Reproducible Builds effort between Sunday October 15 and Saturday October 21 2017: Past events Upcoming events New York University sessions A three week session will be held at New York University to work on reproducibilty issues in conjunction with the reproducible builds community. Students from the Application Security course will be working for two weeks to work on the reproducible builds effort. Packages reviewed and fixed, and bugs filed The following reproducible builds-related NMUs were accepted: Patches sent upstream: Reviews of unreproducible packages 41 package reviews have been added, 119 have been updated and 54 have been removed in this week, adding to our knowledge about identified issues. 2 issue types were removed as they were fixed: Weekly QA work During our reproducibility testing, FTBFS bugs have been detected and reported by: diffoscope development strip-nondeterminism development Version 0.039-1 was uploaded to unstable by Chris Lamb. It included contributions already covered by posts of the previous weeks, including: reprotest development tests.reproducible-builds.org Website updates Misc. This week's edition was written by Bernhard M. Wiedemann, Chris Lamb, Holger Levsen, Santiago Torres & reviewed by a bunch of Reproducible Builds folks on IRC & the mailing lists.

1 August 2017

Reproducible builds folks: Reproducible Builds: Weekly report #118

Here's what happened in the Reproducible Builds effort between Sunday July 23 and Saturday July 29 2017: Toolchain development and fixes Packages reviewed and fixed, and bugs filed Reviews of unreproducible packages 4 package reviews have been added, 2 have been updated and 24 have been removed in this week, adding to our knowledge about identified issues. Weekly QA work During our reproducibility testing, FTBFS bugs have been detected and reported by: diffoscope development Misc. This week's edition was written by Chris Lamb, Mattia Rizzolo & reviewed by a bunch of Reproducible Builds folks on IRC & the mailing lists.

3 May 2017

Reproducible builds folks: Reproducible Builds: week 105 in Stretch cycle

Here's what happened in the Reproducible Builds effort between Sunday April 23 and Saturday April 29 2017: Past and upcoming events On April 26th Chris Lamb gave a talk at foss-north 2017 in Gothenburg, Sweden on Reproducible Builds. Between May 5th-7th the Reproducible Builds Hackathon 2017 will take place in Hamburg, Germany. Then on May 26th Bernhard M. Wiedemann will give a talk titled reproducible builds in openSUSE (2017) at the openSUSE Conference 2017 in N rnberg, Germany. Media coverage Already on April 19th Sylvain Beucler wrote a yet another follow-up post Practical basics of reproducible builds 3, after part 1 and part 2 of his series. Toolchain development and fixes Michael Woerister of the Rust project has implemented file maps that affect all path-related compiler information, including "error messages, metadata, debuginfo, and the file!() macro alike". Ximin Luo with support from some other Rust developers and contributors helped steer the final result into something that was compatible with reproducible builds. Many thanks to all involved, especially for the patience of discussing this over several months. Ximin wrote a first-attempt patch to fix R build-path issues. It made 460/477 R packages reproducible, but also caused 3 of these to FTBFS. See randomness_in_r_rdb_rds_databases for details. Bugs filed and patches sent upstream Chris Lamb: Bernhard M. Wiedemann filed a number of patches upstream: Reviews of unreproducible packages 102 package reviews have been added, 64 have been updated and 24 have been removed in this week, adding to our knowledge about identified issues. 3 issue types have been updated: Weekly QA work During our reproducibility testing, FTBFS bugs have been detected and reported by: diffoscope development diffoscope 82 was uploaded to experimental by Chris Lamb. It included contributions from: Changes from previous weeks that were also released with 82: Misc. This week's edition was written by Ximin Luo, Chris Lamb and Holger Levsen & reviewed by a bunch of Reproducible Builds folks on IRC & the mailing lists.

11 April 2017

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

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

12 September 2016

Reproducible builds folks: Reproducible Builds: week 72 in Stretch cycle

What happened in the Reproducible Builds effort between Sunday September 4 and Saturday September 10 2016: Reproducible work in other projects Python 3.6's dictonary type now retains the insertion order. Thanks to themill for the report. In coreboot, Alexander Couzens committed a change to make their release archives reproducible. Patches submitted Reviews of unreproducible packages We've been adding to our knowledge about identified issues. 3 issue types have been added: 1 issue type has been updated: 16 have been have updated: 13 have been removed, not including removed packages: 100s of packages have been tagged with the more generic captures_build_path, and many with captures_kernel_version, user_hostname_manually_added_requiring_further_investigation, user_hostname_manually_added_requiring_further_investigation, captures_shell_variable_in_autofoo_script, etc. Particular thanks to Emanuel Bronshtein for his work here. Weekly QA work FTBFS bugs have been reported by: diffoscope development strip-nondeterminism development tests.reproducible-builds.org: Misc. This week's edition was written by Chris Lamb and Holger Levsen and reviewed by a bunch of Reproducible Builds folks on IRC.

10 March 2016

Lunar: Reproducible builds: week 45 in Stretch cycle

What happened in the reproducible builds effort between February 28th and March 5th:

Toolchain fixes
  • Antonio Terceiro uploaded gem2deb/0.27 that forces generated gemspecs to use the date from debian/changelog.
  • Antonio Terceiro uploaded gem2deb/0.28 that forces generated gemspecs to have their contains file lists sorted.
  • Robert Luberda uploaded ispell/3.4.00-5 which make builds of hashes reproducible.
  • C dric Boutillier uploaded ruby-ronn/0.7.3-4 which will make the output locale agnostic. Original patch by Chris Lamb.
  • Markus Koschany uploaded spring/101.0+dfsg-1. Fixed by Alexandre Detiste.
Ximin Luo resubmitted the patch adding the --clamp-mtime option to Tar on Savannah's bug tracker. Lunar rebased our experimental dpkg on top of the current master branch. Changes in the test infrastructure are required before uploading a new version to our experimental repository. Reiner Herrmann rebased our custom texlive-bin against the latest uploaded version.

Packages fixed The following 77 packages have become reproducible due to changes in their build dependencies: asciidoctor, atig, fuel-astute, jekyll, libphone-ui-shr, linkchecker, maven-plugin-testing, node-iscroll, origami-pdf, plexus-digest, pry, python-avro, python-odf, rails, ruby-actionpack-xml-parser, ruby-active-model-serializers, ruby-activerecord-session-store, ruby-api-pagination, ruby-babosa, ruby-carrierwave, ruby-classifier-reborn, ruby-compass, ruby-concurrent, ruby-configurate, ruby-crack, ruby-css-parser, ruby-cucumber-rails, ruby-delorean, ruby-encryptor, ruby-fakeweb, ruby-flexmock, ruby-fog-vsphere, ruby-gemojione, ruby-git, ruby-grack, ruby-htmlentities, ruby-jekyll-feed, ruby-json-schema, ruby-listen, ruby-markerb, ruby-mathml, ruby-mini-magick, ruby-net-telnet, ruby-omniauth-azure-oauth2, ruby-omniauth-saml, ruby-org, ruby-origin, ruby-prawn, ruby-pygments.rb, ruby-raemon, ruby-rails-deprecated-sanitizer, ruby-raindrops, ruby-rbpdf, ruby-rbvmomi, ruby-recaptcha, ruby-ref, ruby-responders, ruby-rjb, ruby-rspec-rails, ruby-rspec, ruby-rufus-scheduler, ruby-sass-rails, ruby-sass, ruby-sentry-raven, ruby-sequel-pg, ruby-sequel, ruby-settingslogic, ruby-shoulda-matchers, ruby-slack-notifier, ruby-symboltable, ruby-timers, ruby-zip, ticgit, tmuxinator, vagrant, wagon, yard. The following packages became reproducible after getting fixed: Some uploads fixed some reproducibility issues, but not all of them: Patches submitted which have not made their way to the archive yet:
  • #816209 on elog by Reiner Herrmann: use printf instead of echo which is shell-independent.
  • #816214 on python-pip by Reiner Herrmann: removes timestamp from generated Python scripts.
  • #816230 on rows by Reiner Herrmann: tell grep to always treat the input as text.
  • #816232 on eficas by Reiner Herrmann: use printf instead of echo which is shell-independent.
Florent Daigniere and bancfc reported that linux-grsec was currently built with GRKERNSEC_RANDSTRUCT which will prevent reproducible builds with the current packaging.

tests.reproducible-builds.org pbuilder has been updated to the last version to be able to support Build-Depends-Arch and Build-Conflicts-Arch. (Mattia Rizzolo, h01ger) New package sets have been added for Subgraph OS, which is based on Debian Stretch: packages and build dependencies. (h01ger) Two new armhf build nodes have been added (thanks Vagrant Cascadian) and integrated in our Jenkins setup with 8 new armhf builder jobs. (h01ger)

strip-nondeterminism development strip-nondeterminism version 0.016-1 was released on Sunday 28th. It will now normalize the POT-Creation-Date field in GNU Gettext .mo files. (Reiner Herrmann) Several improvements to the packages metadata have also been made. (h01ger, Ben Finney)

Package reviews 185 reviews have been removed, 91 added and 33 updated in the previous week. New issue: fileorder_in_gemspec_files_list. 43 FTBFS bugs were reported by Chris Lamb, Martin Michlmayr, and gregor herrmann.

Misc. After merging the patch from Dhiru Kholia adding support for SOURCE_DATE_EPOCH in rpm, Florian Festi opened a discussion on the rpm-ecosystem mailing list about reproducible builds. On March 4th, Lunar gave an overview of the general reproducible builds effort at the Internet Freedom Festival in Valencia.

5 March 2016

Lunar: Reproducible builds: week 44 in Stretch cycle

What happened in the reproducible builds effort between February 21th and February 27th:

Toolchain fixes Didier Raboud uploaded pyppd/1.0.2-4 which makes PPD generation deterministic. Emmanuel Bourg uploaded plexus-maven-plugin/1.3.8-10 which sorts the components in the components.xml files generated by the plugin. Guillem Jover has implemented stable ordering for members of the control archives in .debs. Chris Lamb submitted another patch to improve reproducibility of files generated by cython.

Packages fixed The following packages have become reproducible due to changes in their build dependencies: dctrl-tools, debian-edu, dvdwizard, dymo-cups-drivers, ekg2, epson-inkjet-printer-escpr, expeyes, fades, foomatic-db, galternatives, gnuradio, gpodder, gutenprint icewm, invesalius, jodconverter-cli latex-mk, libiio, libimobiledevice, libmcrypt, libopendbx, lives, lttnganalyses, m2300w, microdc2, navit, po4a, ptouch-driver, pxljr, tasksel, tilda, vdr-plugin-infosatepg, xaos. The following packages became reproducible after getting fixed: Some uploads fixed some reproducibility issues, but not all of them:

tests.reproducible-builds.org The reproducibly tests for Debian now vary the provider of /bin/sh between bash and dash. (Reiner Herrmann)

diffoscope development diffoscope version 50 was released on February 27th. It adds a new comparator for PostScript files, makes the directory tests pass on slower hardware, and line ordering variations in .deb md5sums files will not be hidden anymore. Version 51 uploaded the next day re-added test data missing from the previous tarball. diffoscope is looking for a new primary maintainer.

Package reviews 87 reviews have been removed, 61 added and 43 updated in the previous week. New issues: captures_shell_variable_in_autofoo_script, varying_ordering_in_data_tar_gz_or_control_tar_gz. 30 new FTBFS have been reported by Chris Lamb, Antonio Terceiro, Aaron M. Ucko, Michael Tautschnig, and Tobias Frost.

Misc. The release team reported on their discussion about the topic of rebuilding all of Stretch to make it self-contained (in respect to reproducibility). Christian Boltz is hoping someone could talk about reproducible builds at the openSUSE conference happening June 22nd-26th in N rnberg, Germany.

4 January 2016

Lunar: Reproducible builds: week 36 in Stretch cycle

What happened in the reproducible builds effort between December 27th and January 2nd: Infrastructure dak now silently accepts and discards .buildinfo files (commit 1, 2), thanks to Niels Thykier and Ansgar Burchardt. This was later confirmed as working by Mattia Rizzolo. Packages fixed The following packages have become reproducible due to changes in their build dependencies: banshee-community-extensions, javamail, mono-debugger-libs, python-avro. The following packages became reproducible after getting fixed: Some uploads fixed some reproducibility issues, but not all of them: Untested changes: reproducible.debian.net The testing distribution (the upcoming stretch) is now tested on armhf. (h01ger) Four new armhf build nodes provided by Vagrant Cascandian were integrated in the infrastructer. This allowed for 9 new armhf builder jobs. (h01ger) The RPM-based build system, koji, is now in unstable and testing. (Marek Marczykowski-G recki, Ximin Luo). Package reviews 131 reviews have been removed, 71 added and 53 updated in the previous week. 58 new FTBFS reports were made by Chris Lamb and Chris West. New issues identified this week: nondeterminstic_ordering_in_gsettings_glib_enums_xml, nondeterminstic_output_in_warnings_generated_by_breathe, qt_translate_noop_nondeterminstic_ordering. Misc. Steven Chamberlain explained in length why reproducible cross-building across architectures mattered, and posted results of his tests comparing a stage1 debootstrapped chroot of linux-i386 once done from official Debian packages, the others cross-built from kfreebsd-amd64.

2 January 2016

Lunar: Reproducible builds: week 33 in Stretch cycle

What happened in the reproducible builds effort between December 6th and December 12th: Toolchain fixes Reiner Herrmann rebased our experimental version of doxygen on version 1.8.9.1-6. Chris Lamb submitted a patch to make the manpages generated by ruby-ronn reproducible by using the locale-agnostic %Y-%m-%d for the dates. Daniel Kahn Gillmor took another shot at the issue of source path captured in DWARF symbols. A patch has been sent for review by GCC upstream to add the ability to read an environment variable with -fdebug-prefix-map. Packages fixed The following 24 packages have become reproducible due to changes in their build dependencies: gkeyfile-sharp, gprbuild, graphmonkey, gthumb, haskell-yi-language, ion, jackson-databind, jackson-dataformat-smile, jackson-dataformat-xml, jnr-ffi, libcommons-net-java, libproxy, maven-shared-utils, monodevelop-database, mydumper, ndesk-dbus, nini, notify-sharp, pixz, protozero, python-rtslib-fb, slurm-llnl, taglib-sharp, tomboy-latex. The following packages became reproducible after getting fixed: Some uploads fixed some reproducibility issues, but not all of them: These uploads might have fixed reproducibility issues but could not be tested yet: Patches submitted which have not made their way to the archive yet: reproducible.debian.net Files created with diffoscope now have diffoscope in their name instead debbindiff. (h01ger) Hostnames of first and second build node are now recorded and shown in the build history. (Mattia Rizzolo) Exchanges have started with F-Droid developers to better understand what would be required to test F-Droid applications. (h01ger) A first small set of Fedora 23 packages is now also being tested while development on a new framework for testing RPMs in general has begun. A new Jenkins job has been added to set up to mock, the build system used by Fedora. Another new job takes care of testing RPMs from Fedora 23 on x86_64. So far only 151 packages from the buildsys-build group are tested (currently all unreproducible), but the plan is to build all 17,000 source packages in Fedora 23 and rawhide. The page presenting the results should also soon be improved. (h01ger, Dhiru Kholia) For Arch Linux, all 2223 packages from the extra repository will also be tested from now on. Packages in extra" are tested every four weeks, while those from core every week. Statistics are now displayed alongside the results. (h01ger) jenkins.debian.net has been updated to jenkins-job-builder version 1.3.0. Many job configurations have been simplified and refactored using features of the new version. This was another milestone for the jenkins.debian.org migration. (Phil Hands, h01ger) diffoscope development Chris Lamb announced try.diffoscope.org: an online service that runs diffoscope on user provided files. Screenshot of try.diffoscope.org Improvements are welcome. The application is licensed under the AGPLv3. On diffoscope itself, most pending patches have now been merged. Expect a release soon! Most of the code implementing parallel processing has been polished. Sadly, unpacking archive is CPU-bound in most cases, so the current thread-only implementation does not offer much gain on big packages. More work is still require to also add concurrent processes. Documentation update Ximin Luo has started to write a specification for buildinfo files that could become a larger platform than the limited set of features that were thought so far for Debian .buildinfo. Package reviews 113 reviews have been removed, 111 added and 56 updated in the previous week. 42 new FTBFS bugs were opened by Chris Lamb and Niko Tyni. New issues identified this week: timestamps_in_documentation_generated_by_docbook_dbtimestamp, timestamps_in_sym_l_files_generated_by_malaga, timestamps_in_edj_files_generated_by_edje_cc. Misc. Chris Lamb presented reproducible builds at skroutz.gr.

8 May 2011

Charles Plessy: GBrowse arrives in Debian

GBrowse, a genome browser, is packaged for Debian since three weeks. It is the result of a work started four years ago, and I am especially grateful to Olivier Sallou for having unblocked and finished the project while I was starting to go round in circles, and to Aaron M. Ucko for repairing the new package, that was not compatible with our build farm. GBrowse and similar software, like IGV, are used for graphical representation of a chromosome and its annotations, such as the gene positions and markers of their activity, and in particular the result of experiments using high throughput DNA sequencing. A Debian Med task is actually dedicated to gather programs for that topic. In a couple of years, it may be possible that any person who wants can sequence his chromosomes, that is, his genome. This will revolution medicine and perhaps break some founding myths. Even if software for the general public will look different, packages like gbrowse are a first step towards a better access of the public to his medical data. Work continues on GBrowse, with the goal of being able to install it with a reference version of the human genome with a command like apt-get install human-genome. The next step will be to update BioPerl, used by GBrowse, to version 1.6.9.