Bug#881900: stretch-pu: package libofx/1:0.9.10-2+deb9u1

[Dylan Aïssi]

Hi Adam,

2017-11-19 23:38 GMT+01:00 Adam D. Barratt <a...@adam-barratt.org.uk>:
>
> Flagged for acceptance.
>

Thanks. I just opened a similar bug for libofx in Jessie (#882132).

Best,
Dylan

Bug#882132: jessie-pu: package libofx/1:0.9.10-1+deb8u1

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
Tags: jessie
User: release.debian@packages.debian.org
Usertags: pu

Dear release team,
Upstream has fixed 2 CVE (CVE-2017-2816 and CVE-2017-14731), these 2
CVE are non-dsa. I already backported patches to
unstable/testing/stretch (#881900) and now I would like to fix the
Jessie version. Please find attached a debdiff.

Best,
Dylan


libofx_0.9.10-1+deb8u1.debdiff
Description: Binary data

Bug#881900: stretch-pu: package libofx/1:0.9.10-2+deb9u1

[Dylan Aïssi]

Hi Adam,

2017-11-18 19:31 GMT+01:00 Adam D. Barratt <a...@adam-barratt.org.uk>:
>
> Please go ahead.
>
> Adam

Thanks, uploaded.

Best,
Dylan

Bug#881900: stretch-pu: package libofx/1:0.9.10-2+deb9u1

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian@packages.debian.org
Usertags: pu

Dear release team,
Upstream has fixed 2 CVE (CVE-2017-2816 and CVE-2017-14731), these 2
CVE are non-dsa. I already backported patches to unstable/testing and
now I would like to fix the Stretch and Jessie versions. Please find
attached a debdiff for Stretch.

Best,
Dylan


libofx_0.9.10-2+deb9u1.debdiff
Description: Binary data

Bug#877442: marked as pending

[Dylan Aïssi]

Hi Moritz,

2017-11-14 21:33 GMT+01:00 Moritz Muehlenhoff <j...@debian.org>:
>
> There's still the possibility to fix this via a stable point update
> [1], so I was wondering whether anything of that sort is planned by
> you.
>

Thanks for the hint. Now, it is ongoing [1].

Best,
Dylan

[1] https://bugs.debian.org/881900

Bug#882132: jessie-pu: package libofx/1:0.9.10-1+deb8u1

[Dylan Aïssi]

Hi Adam,

2017-12-02 13:05 GMT+01:00 Adam D. Barratt <a...@adam-barratt.org.uk>:
>
> Please go ahead.
>

Thanks, uploaded.

Best,
Dylan

Bug#899401: ITP: r-cran-metamix -- GNU R bayesian mixture analysis for metagenomic community profiling

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian R Packages Maintainers 

Package name: r-cran-metamix
URL: https://cran.r-project.org/package=metaMix
License: GPL-3
Description: GNU R bayesian mixture analysis for metagenomic community profiling
 Resolves complex metagenomic mixtures by analysing deep sequencing
 data, using a mixture model based approach. The use of parallel Monte
 Carlo Markov chains for the exploration of the species space enables
 the identification of the set of species more likely to contribute to
 the mixture.

This package will be maintained by the Debian R Packages Maintainers at:
https://salsa.debian.org/r-pkg-team/r-cran-metamix

Bug#899400: ITP: bolt-lmm -- Efficient large cohorts genome-wide Bayesian mixed-model association testing

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: bolt-lmm
URL: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/
License: GPL-3+
Description: Efficient large cohorts genome-wide Bayesian mixed-model
association testing
 The BOLT-LMM software package currently consists of two main algorithms, the
 BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
 algorithm for variance components analysis (i.e., partitioning of
 SNP-heritability and estimation of genetic correlations).

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/bolt-lmm

Bug#901871: ITP: photoflare -- Simple but powerful Cross Platform Image Editor

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Dylan Aïssi 

Package name: photoflare
URL: http://photoflare.io/
License: GPL-3+
Description: Simple but powerful Cross Platform Image Editor
 This is an effort to bring quick, simple but powerful image editing to the
 masses. PhotoFlare is inspired by the image editor currently only available
 on Microsoft Windows – PhotoFiltre. However, it will not be a straight clone.
 It is being built from the ground up to be much improved and cross platform
 too!

Bug#900764: ITP: minimac4 -- Fast Imputation Based on State Space Reduction HMM

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: minimac4
URL: https://genome.sph.umich.edu/wiki/Minimac4
License: GPL-3
Description: Fast Imputation Based on State Space Reduction HMM
 Minimac4 is a lower memory and more computationally efficient implementation
 of "minimac2/3". It is an algorithm for genotypic imputation that works on
 phased genotypes (say from MaCH).
 .
 Minimac4 is designed to handle very large reference panels in a more
 computationally efficient way with no loss of accuracy. This algorithm
 analyzes only the unique sets of haplotypes in small genomic segments, thereby
 saving on time\-complexity, computational memory but no loss in degree of
 accuracy.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/minimac4

Bug#900765: ITP: libstatgen -- processing and analyzing next generation sequencing and genotyping data library

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: libstatgen
URL: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
License: GPL-3+
Description: processing and analyzing next generation sequencing and
genotyping data library
 libStatGen is a library for statistical genetic programs. It includes some:
 A. General Operation Classes including: File/Stream I/O, String processing
  and Parameter Parsing.
 B. Statistical Genetic Specific Classes including: Handling Common file
  formats (Accessors to get/set values, Indexed access to BAM files) and
  some utility classes, including: 1. Cigar: interpretation and mapping
  between query and reference. 2. Pileup: structured access to data by
  individual reference position.

This library is a dependency of minimac4 (#900764).

The package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/libstatgen/

Bug#900759:

[Dylan Aïssi]

tag 900759 pending
thanks

Fixed in git.

Bug#858947: Processed: retitle to RFP: plink2 -- whole-genome association analysis toolset

[Dylan Aïssi]

Hi Andreas,

2018-07-02 9:52 GMT+02:00 Andreas Tille :
> I wonder whether plink2[1] will simply replace plink1.9 and this
> RFP could be closed.

Plink2 will not be compatible with plink1 and plink1.9, so for
reproducibility and compatibility we need to keep them in Debian.
I still plan to package plink2 but I am waiting for a more stable
version to finish the package. I don't want to propose an alpha
version, maybe I will wait at least until a beta version.

Best,
Dylan

Bug#902405: RFS: photoflare/1.5.4-1

[Dylan Aïssi]

Package: sponsorship-requests
Severity: normal

Dear mentors,

I am looking for a sponsor for my package "photoflare"

* Package name: photoflare
  Version : 1.5.4-1
  Upstream Author : Dylan Coakley
* URL : http://photoflare.io/
* License : GPL-3+
  Section : graphics

It builds those binary packages:

photoflare - Simple but powerful Image Editor

To access further information about this package, please visit the
following URL:

  https://mentors.debian.net/package/photoflare


Alternatively, one can download the package with dget using this command:

dget -x 
https://mentors.debian.net/debian/pool/main/p/photoflare/photoflare_1.5.4-1.dsc

Changes since the last upload:

  * Initial release. (Closes: #901871, LP: #1711644)

Regards,
Dylan Aïssi

Bug#884379: libjung-java has changed build system

[Dylan Aïssi]

Hi Andreas,

I had a look at it and it seems that we need maven-release-plugin
which is not yet packaged [1]. If I find time, I will try to package
it.

Best,
Dylan

[1] https://bugs.debian.org/573393

Bug#890451: Generate a skeleton of README.source about rda and rdata files

[Dylan Aïssi]

Package: dh-r
Severity: wishlist


Hi,

dh-make-R (and dh-update-R) could generate (and update) a
README.source file or at least a skeleton with relevant information
for .rda (and *.Rda, *.rdata, *.Rdata, etc.) files, see [2] for more
information. Andreas already wrote a shell script [2] to do this.

Best,
Dylan

[1] https://lintian.debian.org/tags/r-data-without-readme-source.html
[2] https://lists.debian.org/debian-science/2017/10/msg00070.html

Bug#890969: ITP: r-cran-factominer -- Multivariate Exploratory Data Analysis and Data Mining

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: r-cran-factominer
URL: https://cran.r-project.org/package=FactoMineR
License: GPL-2+
Description: Multivariate Exploratory Data Analysis and Data Mining
 Exploratory data analysis methods to summarize, visualize and describe
 datasets. The main principal component methods are available, those with
 the largest potential in terms of applications: principal component
 analysis (PCA) when variables are quantitative, correspondence analysis
 (CA) and multiple correspondence analysis (MCA) when variables are
 categorical, Multiple Factor Analysis when variables are structured in
 groups, etc. and hierarchical cluster analysis.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-factominer.git

Bug#890971: ITP: r-cran-leaps -- Regression Subset Selection

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: r-cran-leaps
URL: https://cran.r-project.org/package=leaps
License: GPL-2+
Description: Regression Subset Selection
 Regression subset selection, including exhaustive search.

This is a dependency of r-cran-factominer (#890969). The package will
be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-leaps.git

Bug#890970: ITP: r-cran-flashclust -- Implementation of optimal hierarchical clustering

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: r-cran-flashclust
URL: https://cran.r-project.org/package=flashClust
License: GPL-2+
Description: Implementation of optimal hierarchical clustering
 Fast implementation of hierarchical clustering

This is a dependency of r-cran-factominer (#890969). The package will
be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-flashclust.git

Bug#891080: Generate a skeleton of debian/upstream/metadata using upstream inst/CITATION

[Dylan Aïssi]

Package: dh-r
Severity: wishlist


Hi,

dh-make-R (and dh-update-R) could generate (and update) a
d/upstream/metadata file or at least a skeleton with relevant
information from the upstream inst/CITATION file. Lintian will now
emit an (experimental) tag when the metadata file is missing [1].

Best,
Dylan

[1] https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html

Bug#815234: lintian: Detect Rdata files with embedded code

[Dylan Aïssi]

Hi Chris,

On Tue, 30 Jan 2018 13:33:28 +0530 Chris Lamb <la...@debian.org> wrote:
>
> > determine if any code is embedded in the file
>
> So, how does one do this? :)
>

Not sure but maybe this [1] could be useful here.


Best,
Dylan


[1] http://search.cpan.org/dist/Statistics-R-IO/

Bug#891326: ITP: jheatchart -- Heat map charting library for Java

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: jheatchart
URL: http://www.javaheatmap.com/
License: LGPL-3+
Description: Heat map charting library for Java
 The JHeatChart library provides a simple API for generating Java heat maps.
 Output heat maps as .png, .jpg or .gif images. Generate Image objects for
 further processing. Show generated Image in a Swing JPanel. Fully customisable
 colours, dimensions, fonts etc. Linear, logarithmic and exponential
 colour scales.

This is a dependency of ChromHMM. This package will be maintained by
the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/jheatchart.git

Bug#891231: lintian: Improve r-data-without-readme-source by comparing r-data filenames to README.source contents

[Dylan Aïssi]

Package: lintian
Version: 2.5.76
Severity: wishlist

Hi,
To improve the check r-data-without-readme-source and to avoid unmaintained
README.source, lintian could check if the filename of all .RData files from
a package are referenced into the README.source.

A simple example where it could be useful is: a new version of a package
contains a new binary R data file, but if the maintainer does not update
the README.source, lintian will no emits any tag whereas this binary is not
properly describe.

Best,
Dylan

Bug#891476: ITP: r-cran-prettyr -- Pretty Descriptive Stats

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: r-cran-prettyr
URL: https://cran.r-project.org/package=prettyR
License: GPL-2+
Description: Pretty Descriptive Stats
 Functions for conventionally formatting descriptive stats,
 reshaping data frames and formatting R output as HTML.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-prettyr.git

Bug#904835: ITP: r-cran-ranger -- Fast Implementation of Random Forests

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian R Packages Maintainers 

Package name: r-cran-ranger
URL: https://cran.r-project.org/package=ranger
License: GPL-3+
Description: Fast Implementation of Random Forests
 A fast implementation of Random Forests, particularly suited for high
 dimensional data. Ensembles of classification, regression, survival and
 probability prediction trees are supported. Data from genome-wide association
 studies can be analyzed efficiently. In addition to data frames, datasets of
 class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix')
 can be directly analyzed.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-ranger.git

Bug#905164: ITP: r-cran-reticulate -- R interface to Python modules, classes, and functions

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian R Packages Maintainers 

Package name: r-cran-reticulate
URL: https://cran.r-project.org/package=reticulate
License: Apache-2.0
Description: R interface to Python modules, classes, and functions
 Interface to Python modules, classes, and functions. When calling into
 Python, R data types are automatically converted to their equivalent Python
 types. When values are returned from Python to R they are converted back to R
 types.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-reticulate.git

Bug#904985: lintian: Check for R packages wrongly set Architecture to any instead all

[Dylan Aïssi]

Package: lintian
Version: 2.5.94
Severity: wishlist

Hi,
A common mistake in R packaging is to set Architecture to any instead
all [1]. Only R packages with "NeedsCompilation: yes" in their
DESCRIPTION files (Debian Control File format) must be marked any [1].
So, all R packages (r-cran- or r-bioc- or r-other-) with this field
set to "no" must be marked as all and not any.

I fixed a batch of deb R packages but to avoid new one incorrectly
marked any, a lintian test would be great.

Best,
Dylan

[1] https://qa.debian.org/bls/bytag/I-no-compiler-commands.html
[2] 
https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#The-DESCRIPTION-file

Bug#908159: emacs: Saving clipboard to X clipboard manager takes forever on exit

[Dylan Thurston]

Package: emacs
Version: 1:25.2+1-11
Severity: normal

Emacs takes a long time on exit, with the status message "Saving
clipboard to X clipboard manager". Eventually there's a message sent
to stderr:

dpt@tulip:~$ emacs -Q
Error saving to X clipboard manager.
If the problem persists, set 'x-select-enable-clipboard-manager' to nil.

To reproduce, start 'emacs -Q', type some text and cut it, and then
exit with C-x C-c.

Similar behaviour seems to occur when closing an emacsclient window
with C-x # as well.

-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.17.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) (ignored: LC_ALL 
set to en_US.UTF-8), LANGUAGE=en_US.utf8 (charmap=UTF-8) (ignored: LC_ALL set 
to en_US.UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages emacs depends on:
ii  emacs-gtk  1:25.2+1-11

emacs recommends no packages.

emacs suggests no packages.

-- no debconf information

Bug#903728: ITP: python-colormath -- Abstracts common color math operations

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: python-colormath
URL: https://pypi.org/project/colormath/
License: BSD-3-clause
Description: Abstracts common color math operations
 python-colormath is a simple Python module that spares the user from directly
 dealing with color math. Some features include: Support for a wide range of
 color spaces. A good chunk of the CIE spaces, RGB, HSL/HSV, CMY/CMYK, and many
 more. Conversions between the various color spaces. For example, XYZ to sRGB,
 Spectral to XYZ, CIE Lab to Adobe RGB. Calculation of color difference. All
 CIE Delta E functions, plus CMC. Chromatic adaptations (changing illuminants).
 RGB to hex and vice-versa. 16-bit RGB support.

This package is a dependency of MultiQC.

It will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/python-colormath/

Bug#903730: ITP: python-spectra -- Easy color scales and color conversion

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: python-spectra
URL: https://pypi.org/project/spectra/
License: Expat
Description: Easy color scales and color conversion for Python
 Spectra is a Python library that makes color math, color scales, and
 color-space conversion easy. Support for: Color scales, Color ranges, Color
 blending, Brightening/darkening colors, Saturating/desaturating colors,
 Conversion to/from multiple color spaces.

This package is a dependency of MultiQC.

It will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/python-spectra/

Bug#903732: ITP: python-lzstring -- LZ-based compression algorithm

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: python-lzstring
URL: https://pypi.org/project/lzstring/
License: Expat
Description: LZ-based compression algorithm for Python
 python-lzstring is a simple Python module that compression data using LZ-based
 algorithm.

This package is a dependency of MultiQC.

It will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/python-lzstring/

Bug#892284: ITP: ChromHMM -- Chromatin state discovery and characterization

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
 Owner: Debian Med Packaging Team 

Package name: chromhmm
URL: http://compbio.mit.edu/ChromHMM/
License: GPL-3+
Description: Chromatin state discovery and characterization
 ChromHMM is software for learning and characterizing chromatin states.
 ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of
 various histone modifications to discover de novo the major re-occuring
 combinatorial and spatial patterns of marks. ChromHMM is based on a
 multivariate Hidden Markov Model that explicitly models the presence or
 absence of each chromatin mark. The resulting model can then be used to
 systematically annotate a genome in one or more cell types. By automatically
 computing state enrichments for large-scale functional and annotation datasets
 ChromHMM facilitates the biological characterization of each state. ChromHMM
 also produces files with genome-wide maps of chromatin state annotations that
 can be directly visualized in a genome browser.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/chromhmm.git/

Bug#879248: r-cran-nmf: detecting number of cores

[Dylan Aïssi]

Hi Michael,

2018-03-12 8:44 GMT+01:00 Michael Cree <mc...@orcon.net.nz>:
> How about the attached patch?  Should detection of number of cores
> fail it sets the number of cores to be one.  With this patch
> r-cran-nmf builds successfully on Alpha.

Thanks for this patch. But, I think if we really want to fix this
issue in our package before than upstream releases a fixed version, we
should probably use the same way as upstream.
That is to backport these 2 commits [1-2].

Best,
Dylan

[1] https://github.com/renozao/NMF/commit/063cdcb102
[2] https://github.com/renozao/NMF/commit/6996bce01e

Bug#891808: ITP: r-bioc-impute -- Imputation for microarray data

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: r-bioc-impute
URL: https://bioconductor.org/packages/impute/
License: GPL-2
Description: Imputation for microarray data
 R package which provide a function to perform imputation for
 microarray data (currently KNN only).

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-bioc-impute.git

Bug#892481: r-cran-testthat: autopkgtest failure

[Dylan Aïssi]

Hi Graham,

On Fri, 9 Mar 2018 15:24:45 +0200 Graham Inggs <gin...@debian.org> wrote:
>
> By changing the locale from C to C.UTF-8, similar to what I did in
> r-cran-urltools [3], there is only one test failure remaining:

Thanks. Done.

>
>  > test_check("testthat")
> ── 1. Error: returns local path when called from
> tools::testInstalledPackages (@
> cannot change working directory
> 1: setwd("test-path-installed/testthat-tests/testthat") at
> testthat/test-test-path.R:11
>
> ══ testthat results
> ═══
> OK: 449 SKIPPED: 2 FAILED: 1
> 1. Error: returns local path when called from
> tools::testInstalledPackages (@test-test-path.R#11)
>
> It is a new test, not a regression, so skipping it may be a valid option.
>

I am not sure how to proceed here. Is there a simple way to skip this
test except to patch the relevant file and to use the skip function?

Best,
Dylan

Bug#879248:

[Dylan Aïssi]

Hi Andreas,

2018-03-09 10:40 GMT+01:00 Andreas Tille <andr...@an3as.eu>:
>
> How did you guessed the version number 0.23.4?  There are no release
> tags on Github - at least I can not find any?  Somehow issue #106 is
> mentioning removal from CRAN so may be we can expect some properly
> versioned NMF with correct fix soon.  I'm not sure whether we should
> add the patch above as quilt patch meanwhile.
>

Some commits after this one, upstream updated DESCRIPTION with this
unreleased version [1].
It is unclear how they release new versions, so I will keep an eye on
#106 and maybe ask them to release something >=0.23.4.
I agree with you, probably useless to backport the patch. I mentioned
it, only to keep a trace.

Best,
Dylan

[1] https://github.com/renozao/NMF/commit/b26e3e3189

Bug#879248:

[Dylan Aïssi]

It seems to be fixed in 0.23.4 but not yet on CRAN.

https://github.com/renozao/NMF/commit/6996bce01e

Bug#896142: ITP: ChromImpute -- Large-scale systematic epigenome imputation

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: chromimpute
URL: http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/
License: GPL-2
Description: Large-scale systematic epigenome imputation
 ChromImpute is software for large-scale systematic epigenome imputation.
 ChromImpute takes an existing compendium of epigenomic data and uses it to
 predict signal tracks for mark-sample combinations not experimentally mapped
 or to generate a potentially more robust version of data sets that have been
 mapped experimentally. ChromImpute bases its predictions on features from
 signal tracks of other marks that have been mapped in the target sample and
 the target mark in other samples with these features combined using an
 ensemble of regression trees.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/chromimpute.git/

Bug#882555: r-cran-ddalpha: FTBFS on m68k: no boost::math::Rlog1p

[Dylan Aïssi]

Hi Aaron,

On Thu, 23 Nov 2017 16:54:33 -0500 "Aaron M. Ucko" <u...@debian.org> wrote:
> The build of r-cran-ddalpha for m68k (admittedly not a release
> architecture) failed:
>
>   g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG  
> -I"/usr/lib/R/site-library/Rcpp/include"-fpic  -g -O2 
> -fdebug-prefix-map=/build/r-base-vkBOGA/r-base-3.4.2.20171120=. 
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
> -D_FORTIFY_SOURCE=2 -g -c Polynomial.cpp -o Polynomial.o
>   In file included from 
> /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:72:0,
>from /usr/lib/R/site-library/Rcpp/include/Rcpp.h:27,
>from stdafx.h:27,
>from Polynomial.cpp:14:
>   /usr/include/boost/math/special_functions/log1p.hpp: In static member 
> function 'static void boost::math::detail::log1p_initializer<T, Policy, 
> tag>::init::do_init(const mpl_::int_<64>&)':
>   /usr/share/R/include/Rmath.h:76:15: error: 'Rlog1p' is not a member of 
> 'boost::math'
>#define log1p Rlog1p
>  ^
>   /usr/share/R/include/Rmath.h:76:15: note: suggested alternative: 'log1p'
>   /usr/lib/R/etc/Makeconf:168: recipe for target 'Polynomial.o' failed
>   make[1]: *** [Polynomial.o] Error 1
>
> Could you please take a look?

This package was built correctly for m68k on 2018-03-23 [1].
Can we close this bug?

Best,
Dylan

[1] https://buildd.debian.org/status/logs.php?pkg=r-cran-ddalpha=m68k

Bug#887680: r-cran-git2r: FTBFS on m68k: missing value where TRUE/FALSE needed

[Dylan Aïssi]

Hi Aaron,

On Thu, 18 Jan 2018 21:05:31 -0500 "Aaron M. Ucko" <u...@debian.org> wrote:
> The build of r-cran-git2r for m68k (admittedly not a release
> architecture) failed:
>
>   Error in if (nc[currentIndex] == 0L) upperBlockIndex <- c(upperBlockIndex,  
> :
> missing value where TRUE/FALSE needed
>   ERROR: installing package DESCRIPTION failed for package 'git2r'
>
> Could you please take a look?
>

This package was built correctly for m68k on 2018-02-27 [1].
Can we close this bug?

Best,
Dylan

[1] https://buildd.debian.org/status/logs.php?pkg=r-cran-git2r=m68k

Bug#887682: r-cran-utf8: FTBFS on m68k: missing value where TRUE/FALSE needed

[Dylan Aïssi]

Hi Aaron,

On Thu, 18 Jan 2018 21:33:47 -0500 "Aaron M. Ucko" <u...@debian.org> wrote:
> The build of r-cran-utf8 for m68k (admittedly not a release
> architecture) failed:
>
>   Error in if (any(i)) x[i] <- paste0(x[i], "\n", indentString) :
> missing value where TRUE/FALSE needed
>   ERROR: installing package indices failed
>
> This is the same mysterious error message as with r-cran-git2r, just
> in a different context; there may well be a bug in R itself here.
>
> Could you please take a look?

This package was built correctly for m68k on 2018-02-27 [1].
Can we close this bug?

Best,
Dylan

[1] https://buildd.debian.org/status/logs.php?pkg=r-cran-utf8=m68k

Bug#894747: lintian: Re-enable YAML parsing for d/upstream/metadata files

[Dylan Aïssi]

Package: lintian
Version: 2.5.80
Severity: wishlist
Control: block 731340 by -1

Hi,

Currently, the lintian checks for validity of d/u/metadata are
disabled since 2.5.50.4 [1] due to a security problem [2]
(CVE-2017-8829), but now we can safety use YAML::XS with the
$LoadBlessed option [3]. I wondering if we can re-enable the
d/u/metadata checks in lintian using the safety method?

Best,
Dylan

[1] 
https://anonscm.debian.org/git/lintian/lintian.git/commit/checks/upstream-metadata.pm?id=6119d49c3b
[2] https://bugs.debian.org/861958
[3] https://bugs.debian.org/862373#59

Bug#893827: ITP: bioSyntax -- Syntax highlighting for computational biology

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: biosyntax
URL: https://biosyntax.org/
License: GPL-3
Description: Syntax Highlighting for Computational Biology (gedit)
 Syntax highlighting for computational biology to bring you intuitively close
 to your data. BioSyntax supports .sam, .flagstat, .vcf, .fasta, .fastq, .faidx
 , .clustal, .pdb, .gtf, .bed files & more.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/biosyntax.git/

Bug#892038: ITP: r-cran-ggsci -- Scientific Journal and Sci-Fi Themed Color Palettes

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 
X-Debbugs-Cc: debia...@lists.debian.org

Package name: r-cran-ggsci
URL: https://cran.r-project.org/package=ggsci
License: GPL-3
Description: Scientific Journal and Sci-Fi Themed Color Palettes
 A collection of 'ggplot2' color palettes inspired by
 plots in scientific journals, data visualization libraries,
 science fiction movies, and TV shows.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-ggsci.git

Bug#892039: ITP: r-cran-bigmemory -- Manage Massive Matrices with Shared Memory and Memory-Mapped Files

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 
X-Debbugs-Cc: debia...@lists.debian.org

Package name: r-cran-bigmemory
URL: https://cran.r-project.org/package=bigmemory
License: LGPL-3 or Apache-2
Description: Manage Massive Matrices with Shared Memory and Memory-Mapped Files
 Create, store, access, and manipulate massive matrices.
 Matrices are allocated to shared memory and may use memory-mapped
 files.  Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
 'bigalgebra' provide advanced functionality.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-bigmemory.git

Bug#892040: ITP: r-cran-bigmemory.sri -- A shared resource interface for Bigmemory Project packages

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 
X-Debbugs-Cc: debia...@lists.debian.org

Package name: r-cran-bigmemory.sri
URL: https://cran.r-project.org/package=bigmemory.sri
License: LGPL-3 or Apache-2
Description: A shared resource interface for Bigmemory Project packages
 This package provides a shared resource interface for the bigmemory and
 synchronicity packages.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-bigmemory.sri.git

Bug#660165: Source package names for R libraries (and others)

[Dylan Aïssi]

Hi Chris,

2018-02-26 15:24 GMT+01:00 Chris Lamb <la...@debian.org>:
> Again, not sure what this has to do with tests or the reference to
> "recommendation" :)  (Did you reply to the right bug here?)

Yes :-) , I tried to give an example (ok a bad one) how to have the
same source and binary names for R packages could be beneficial. Or
rather how a source name beginning by with r-* could be beneficial
today (i.e. it will activate some tests).

It should probably be better to forget my previous email :-).

Best,
Dylan

Bug#891231: lintian: Improve r-data-without-readme-source by comparing r-data filenames to README.source contents

[Dylan Aïssi]

Hi Chris,

2018-02-23 17:22 GMT+01:00 Chris Lamb <la...@debian.org>:
>> To improve the check r-data-without-readme-source and to avoid unmaintained
>> README.source, lintian could check if the filename of all .RData files from
>> a package are referenced into the README.source.
>
> Good idea!
>
>> A simple example where it could be useful is: a new version of a package
>> contains a new binary R data file, but if the maintainer does not update
>> the README.source, lintian will no emits any tag whereas this binary is not
>> properly described.
>
> Sounds like we want something a bit more machine-readable than README.source.
> Is it legal to add fields to a DEP-5 debian/copyright for this? If not,
> I wonder if a debian/source/rdata with some field (or similar) could work?

I'm not sure if d/copyright could be a correct place for this, but
d/source/rdata sounds nice. Anyway this should be discussed with the
team (we still don't have a place for discussion #886854 excepted to
spam Debian Med and Debian Science teams). We should also probably
have a tool to generate (at least) a skeleton of this file (#890451 in
CC) to avoid a manual editing :-).

> An example from the R maintainers (especially including a violating case)
> would be extremely useful.

Let's wait and see what the team will decide before to go further.

Best,
Dylan

Bug#660165:

[Dylan Aïssi]

Hi,

Just my two cents, all Debian R packages without r-*** source package
name don't profit of the R autodep8 tests. So, increase the
application of this "recommendation" will also increase number of
automatic tested R packages.

Best,
Dylan

Bug#891734: ITP: r-cran-gee -- Generalized Estimation Equation Solver

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

Package name: r-cran-gee
URL: https://cran.r-project.org/package=gee
License: GPL-2
Description: Generalized Estimation Equation Solver
 R package which provide a function to solve a Generalized Estimation
 Equation Model.

The package will be maintained by the Debian R Packages Team at:
https://salsa.debian.org/r-pkg-team/r-cran-gee.git

Bug#911809: ITP: r-cran-ini -- Read and Write '.ini' Files

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-ini
  Version : 0.3.1
  Upstream Author : David Valentim Dias
* URL : https://cran.r-project.org/package=ini
* License : GPL-3
  Programming Lang: GNU R
  Description : Read and Write '.ini' Files
 Parse simple '.ini' configuration files to an structured list. Users
 can manipulate this resulting list with lapply() functions. This same
 structured list can be used to write back to file after modifications.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-ini

Bug#912177: ITP: r-cran-rcmdcheck -- Run 'R CMD check' from 'R' and Capture Results

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-rcmdcheck
  Version : 1.3.0
  Upstream Author : Mango Solutions, Gábor Csárdi, RStudio
* URL : https://cran.r-project.org/package=rcmdcheck
* License : MIT
  Programming Lang: GNU R
  Description : Run 'R CMD check' from 'R' and Capture Results
 Run 'R CMD check' from 'R' programmatically, and capture the
 results of the individual checks.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-rcmdcheck

Bug#912158: ITP: r-cran-remotes -- R Package Installation from Remote Repositories

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-remotes
  Version : 2.0.1
  Upstream Author : Gábor Csárdi,
* URL : https://cran.r-project.org/package=remotes
* License : GPL-2+
  Programming Lang: GNU R
  Description : R Package Installation from Remote Repositories,
Including 'GitHub'
 Download and install R packages stored in 'GitHub',
 'BitBucket', or plain 'subversion' or 'git' repositories. This package
 is a lightweight replacement of the 'install_*' functions in 'devtools'.
 Indeed most of the code was copied over from 'devtools'.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-remotes

Bug#912138: ITP: r-cran-sessioninfo -- R Session Information

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-sessioninfo
  Version : 1.1.0
  Upstream Author : Gábor Csárdi, R core, Hadley Wickham, Winston
Chang, Robert M Flight, Kirill Müller, Jim Hester
* URL : https://cran.r-project.org/package=sessioninfo
* License : GPL-2
  Programming Lang: GNU R
  Description : R Session Information
 Query and print information about the current R session.
 It is similar to 'utils::sessionInfo()', but includes more information
 about packages, and where they were installed from.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-sessioninfo

Bug#912534: ITP: r-cran-selectr -- Translate CSS Selectors to XPath Expressions

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-selectr
  Version : 0.4
  Upstream Author : Simon Potter, Simon Sapin, Ian Bicking
* URL : https://cran.r-project.org/package=selectr
* License : BSD-3-clause
  Programming Lang: GNU R
  Description : Translate CSS Selectors to XPath Expressions
 Translates a CSS3 selector into an equivalent XPath
 expression. This allows us to use CSS selectors when working with
 the XML package as it can only evaluate XPath expressions. Also
 provided are convenience functions useful for using CSS selectors on
 XML nodes. This package is a port of the Python package 'cssselect'
 (<https://cssselect.readthedocs.io/>).

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-selectr

Bug#911982: ITP: r-cran-clisymbols -- Unicode Symbols at the R Prompt

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-clisymbols
  Version : 1.2.0
  Upstream Author : Gábor Csárdi, Sindre Sorhus
* URL : https://cran.r-project.org/package=clisymbols
* License : MIT
  Programming Lang: GNU R
  Description : Unicode Symbols at the R Prompt
 A small subset of Unicode symbols, that are useful
 when building command line applications. They fall back to
 alternatives on terminals that do not support Unicode.
 Many symbols were taken from the 'figures' 'npm' package
 (see <https://github.com/sindresorhus/figures>).

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-clisymbols

Bug#911984: ITP: r-cran-xopen -- Open System Files, 'URLs', Anything

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-xopen
  Version : 1.0.0
  Upstream Author : Gábor Csárdi
* URL : https://cran.r-project.org/package=xopen
* License : MIT
  Programming Lang: GNU R
  Description : Open System Files, 'URLs', Anything
 Cross platform solution to open files, directories or 'URLs'
 with their associated programs.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-xopen

Bug#911989: ITP: r-cran-usethis -- Automate Package and Project Setup

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-usethis
  Version : 1.4.0
  Upstream Author : Hadley Wickham, Jennifer Bryan, RStudio
* URL : https://cran.r-project.org/package=usethis
* License : GPL-3
  Programming Lang: GNU R
  Description : Automate Package and Project Setup
 Automate package and project setup tasks that are otherwise
 performed manually. This includes setting up unit testing, test
 coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
 projects, and more.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-usethis

Bug#912716: ITP: r-cran-reprex -- Prepare Reproducible Example Code via the Clipboard

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-reprex
  Version : 0.2.1
  Upstream Author : Jennifer Bryan, Jim Hester, David Robinson, Hadley
Wickham, RStudio
* URL : https://cran.r-project.org/package=reprex
* License : MIT
  Programming Lang: GNU R
  Description : Prepare Reproducible Example Code via the Clipboard
 Convenience wrapper that uses the 'rmarkdown' package to render
 small snippets of code to target formats that include both code and output.
 The goal is to encourage the sharing of small, reproducible, and runnable
 examples on code-oriented websites, such as <https://stackoverflow.com> and
 <https://github.com>, or in email. The user's clipboard is the default source
 of input code and the default target for rendered output. 'reprex' also
 extracts clean, runnable R code from various common formats, such as
 copy/paste from an R session.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-reprex

Bug#912728: ITP: r-cran-tidyverse -- Easily Install and Load the 'Tidyverse'

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-tidyverse
  Version : 1.2.1
  Upstream Author : Hadley Wickham, RStudio
* URL : https://cran.r-project.org/package=tidyverse
* License : GPL-3
  Programming Lang: GNU R
  Description : Easily Install and Load the 'Tidyverse'
 The 'tidyverse' is a set of packages that work in harmony
 because they share common data representations and 'API' design. This
 package is designed to make it easy to install and load multiple
 'tidyverse' packages in a single step. Learn more about the 'tidyverse'
 at <https://tidyverse.org>.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-tidyverse

Bug#912741: ITP: r-cran-biocmanager -- Access the Bioconductor Project Package Repository

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-biocmanager
  Version : 1.30.3
  Upstream Author : Martin Morgan, Marcel Ramos
* URL : https://cran.r-project.org/package=BiocManager
* License : Artistic-2.0
  Programming Lang: GNU R
  Description : Access the Bioconductor Project Package Repository
 A convenient tool to install and update Bioconductor packages.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-biocmanager

Bug#912609: ITP: r-cran-rvest -- Easily Harvest (Scrape) Web Pages

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-rvest
  Version : 0.3.2
  Upstream Author : Hadley Wickham, RStudio
* URL : https://cran.r-project.org/package=rvest
* License : GPL-3
  Programming Lang: GNU R
  Description : Easily Harvest (Scrape) Web Pages
 Wrappers around the 'xml2' and 'httr' packages to make it easy to
 download, then manipulate, HTML and XML.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-rvest

Bug#911914: ITP: r-cran-clipr -- Read and Write from the System Clipboard

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-clipr
  Version : 0.4.1
  Upstream Author : Matthew Lincoln,
* URL : https://cran.r-project.org/package=clipr
* License : GPL-3
  Programming Lang: GNU R
  Description : Read and Write from the System Clipboard
 Simple utility functions to read from and write to the Windows,
 OS X, and X11 clipboards.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-clipr

Bug#911913: ITP: r-cran-gh -- Minimal client to access the 'GitHub' 'API'

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

* Package name: r-cran-gh
  Version : 1.0.1
  Upstream Author : Gábor Csárdi
* URL : https://cran.r-project.org/package=gh
* License : MIT
  Programming Lang: GNU R
  Description : Minimal client to access the 'GitHub' 'API'.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-gh

Bug#913305: [R-pkg-team] Bug#913305: r-bioc-s4vectors breaks multiple autopkgtests

[Dylan Aïssi]

Hi,

Le ven. 9 nov. 2018 à 16:45, Graham Inggs  a écrit :
>
> Hi
>
> On 2018/11/09 16:40, Paul Gevers wrote:
> > If the answer to my question above is "those packages are broken", then
> > my next question is, if it is somehow possible to let the package
> > dependency framework know that this is a transition?
>
> In my opinion, r-bioc-s4vectors needs a bunch of additional breaks, as I
> did in 0.18.1-3 and 0.18.1-4.  This eased the migration somewhat in Ubuntu.
>

As it's not recommended mixing BioC packages from different BioC
releases, maybe we can introduce (for next BioC release?) a mechanism
similar to the virtual r-api-3.5 package i.e. r-api-bioc-3.8 (provided
by r-bioc-biocgenerics).
This could avoid to spend other people's time to open bugs like this
one or #913527.

Best,
Dylan

Bug#910351: New version available on CRAN, need to rename this package

[Dylan Aïssi]

Package: r-other-hms-dbmi-spp
Version: 1.15.2-1
Severity: wishlist

https://cran.r-project.org/package=spp

Bug#909334: ITP: openrazer -- OpenRazer peripheral drivers

[Dylan Aïssi]

Package: wnpp
Severity: wishlist
Owner: Dylan Aïssi 

Package name: openrazer
URL: https://openrazer.github.io/
License: GPL-2+
Description: OpenRazer peripheral drivers
 OpenRazer is a collection of GNU/Linux drivers for the Razer devices.
 Supported devices include keyboards, mice, mouse-mats, headsets and
 various other devices.

Current packaging take place at:
https://salsa.debian.org/daissi-guest/openrazer

Bug#889582: Update libmtp package in Debian (new upstream releases)

[Dylan Aïssi]

Hi Alessio,

The last libmtp version packaged in Debian is quite old (2017-04), 3
new versions were released since. Do you intend to update the Debian
package before the freeze?

If you don't have time, I can help you to update the package.

Best,
Dylan

Bug#889582: Update libmtp package in Debian (new upstream releases)

[Dylan Aïssi]

Hi Alessio,

Le lun. 21 janv. 2019 à 02:23, Alessio Treglia  a écrit :
> On Fri, 18 Jan 2019 at 16:39, Dylan Aïssi  wrote:
> > If you don't have time, I can help you to update the package.
>
> Please go ahead.

Thanks :-)

Last questions:
- Should I do a NMU or co-maint is fine for you?
- Since the old git repo is gone with alioth, I have created a new one
with gbp --debsnap [1], is it ok if I move it to the debian group in
salsa (i.e. [2])?

Best,
Dylan

[1] https://salsa.debian.org/daissi/libmtp
[2] https://salsa.debian.org/debian/libmtp

Bug#884379: Trying to upgrade libjung-free-java

[Dylan Aïssi]

Hi Andreas,

Le mar. 8 janv. 2019 à 15:22, Andreas Tille  a écrit :
> I try to upgrade libjung-free-java[1].

The upstream build system has been completely rewrite and now it seems
to use maven-release which is not packaged in Debian (RFP: #573393).
So, I tried to package maven-release but unfortunately I was not able to do it.

Best,
Dylan

Bug#884379: Trying to upgrade libjung-free-java

[Dylan Aïssi]

Le mer. 23 janv. 2019 à 09:55, Andreas Tille  a écrit :
>
> Did you published your attempt somewhere (suggested is
> salsa:java-team/maven-release)?
>

Trying to remember what I did 1 year ago. I did not push my attempt
because it was very embryonic and I was not able to deal with all the
java stuff.

Best,
Dylan

Bug#916333: ITP: dav1d -- fast and small AV1 video stream decoder

[Dylan Aïssi]

Package: wnpp
Owner: Debian Multimedia Maintainers 
Severity: wishlist

Package name: dav1d
Version: 0.1.0
Upstream Author: VideoLan
URL: https://code.videolan.org/videolan/dav1d
License: BSD-2-clause
Description: fast and small AV1 video stream decoder
 dav1d is an AOMedia Video 1 (AV1) cross-platform decoder and focused on speed
 and correctness.
 .
 dav1d supports the following features:
  * support for all features of the AV1 bitstream
  * support for all bitdepth, 8, 10 and 12bits
  * support for all chroma subsamplings 4:2:0, 4:2:2, 4:4:4 and grayscale
  * full acceleration for AVX-2 64bits processors
  * partial acceleration for SSSE3 processors
  * partial acceleration for NEON processors

This package is maintained by Debian Multimedia Team at
  https://salsa.debian.org/multimedia-team/dav1d

Bug#914731:

[Dylan Aïssi]

Hi Graham,

Another R package autopkgtest (r-cran-metamix) fails with this error:
> libmpi.so: cannot open shared object file: No such file or directory

This seems to be induced by one of them dependency: r-cran-rmpi which
is not loadable in R. Maybe a new occurrence of #861748 [1] ?

[1] https://bugs.debian.org/861748

Best,
Dylan

Bug#914731:

[Dylan Aïssi]

Hummm, it worked on my own autopkgtest instance.
I will investigate it again.

Bug#915376: ITP: r-bioc-zlibbioc -- (Virtual) zlibbioc Bioconductor package

[Dylan Aïssi]

Package: wnpp
Owner: Dylan Aïssi 
Severity: wishlist

Package name: r-bioc-zlibbioc
Version: 1.28.0
Upstream Author: Martin Morgan
URL: https://bioconductor.org/packages/zlibbioc/
License: Artistic-2.0
Programming Lang: GNU R
Description: (Virtual) zlibbioc Bioconductor package
 zlibbioc provides the zlib library to the Bioconductor environment.
 This is useless on Debian as we have a packaged zlib. So, to avoid to patch
 all Bioconductor packages which required zlibbioc, zlibbioc is packaged as an
 empty shell depending on zlib1g-dev (similar mechanism to r-cran-bh).

This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-bioc-zlibbioc

Bug#891080:

[Dylan Aïssi]

tag 891080 pending
thanks

There is now a script for that:
https://salsa.debian.org/r-pkg-team/dh-r/blob/master/scripts/convert_citation2metadata

Bug#915717: Some bioconductor packages FTBFS because of missing 'git_branch' field

[Dylan Aïssi]

Package: dh-r
Version: 20181123
Severity: important

Some bioconductor packages (r-bioc-genomeinfodbdata and r-bioc-go.db)
FTBFS because of missing 'git_branch' field in the DESCRIPTION file.
This need to be clarified with upstream. But, at the same time, we can
relax the requirement of this field for these packages. i.e. switch
the 'die' at line 249 by a 'say'.

https://salsa.debian.org/r-pkg-team/dh-r/blob/master/dh/R.pm#L249

Bug#914445: ITP: fastp -- Ultra-fast all-in-one FASTQ preprocessor

[Dylan Aïssi]

Package: wnpp
Owner: Debian Med Packaging Team 
Severity: wishlist

Package name: fastp
Version: 0.19.5
Upstream Author : Shifu Chen
URL: https://github.com/OpenGene/fastp
License: MIT
Description: Ultra-fast all-in-one FASTQ preprocessor
 All-in-one FASTQ preprocessor, fastp provides functions including quality
 profiling, adapter trimming, read filtering and base correction. It supports
 both single-end and paired-end short read data and also provides basic support
 for long-read data.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/fastp

Bug#913305: [R-pkg-team] Bug#913305: r-bioc-s4vectors breaks multiple autopkgtests

[Dylan Aïssi]

Hi,

Le lun. 12 nov. 2018 à 13:25, Andreas Tille  a écrit :
>
> On Mon, Nov 12, 2018 at 11:07:36AM +0100, Dylan Aďssi wrote:
> >
> > As it's not recommended mixing BioC packages from different BioC
> > releases, maybe we can introduce (for next BioC release?) a mechanism
> > similar to the virtual r-api-3.5 package i.e. r-api-bioc-3.8 (provided
> > by r-bioc-biocgenerics).
>
> I think that's a pretty sensible solution and if you don't mind we could
> add this even to this BioC release.  It might involve dh-r hacking
> thought.

I have implemented it into dh-r [1]. As I am not very confident with
my perl skills, it would be nice if someone could check if there is no
big mistake.
I have tested those changes to build some packages and it works. So, I
will start to deploy this in the next days.

Best,
Dylan

[1] https://salsa.debian.org/r-pkg-team/dh-r/merge_requests/1/diffs

Bug#914834: xfce4-settings: Keyboard layout switching keys make default actions not work

[Dylan Thurston]

Package: xfce4-settings
Version: 4.12.4-1
Severity: normal

Dear Maintainer,

In the Keyboard Settings dialog, if the "Change layout option" is set
to (say) "Both Alt together", then the right Alt key stops working in
applications.

To reproduce:

* Set "Change layout option" to "Both Alt together"
* Open xev
* Press left Alt; result is "Alt_L"
* Press right Alt; result is "ISO_Level3_Shift"
* Set "Change layout option" to "-" (disabled)
* Press right Alt in xev window; result is "Alt_R"

My other keyboard layout options are:

Keyboard model: "Generic 105-key PC (intl.)"
Compose key: "Menu"
Keyboard layout: English (US) -> English (Dvorak) [selected]
 Hebrew -> Hebrew (Biblical, Tiro) [alternate]

I also use 'setxkbmap -option ctrl:nocaps', which there is no current
setting for.

-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.18.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) (ignored: LC_ALL 
set to en_US.UTF-8), LANGUAGE=en_US.utf8 (charmap=UTF-8) (ignored: LC_ALL set 
to en_US.UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages xfce4-settings depends on:
ii  libc62.27-8
ii  libcairo21.16.0-1
ii  libdbus-1-3  1.12.10-1
ii  libdbus-glib-1-2 0.110-3
ii  libexo-1-0   0.12.2-2
ii  libfontconfig1   2.13.1-2
ii  libgarcon-1-00.6.1-2
ii  libgarcon-common 0.6.1-2
ii  libgdk-pixbuf2.0-0   2.38.0+dfsg-6
ii  libglib2.0-0 2.58.1-2
ii  libgtk2.0-0  2.24.32-3
ii  libnotify4   0.7.7-3
ii  libpango-1.0-0   1.42.4-4
ii  libpangocairo-1.0-0  1.42.4-4
ii  libupower-glib3  0.99.9-1
ii  libx11-6 2:1.6.7-1
ii  libxcursor1  1:1.1.15-2
ii  libxfce4ui-1-0   4.12.1-3
ii  libxfce4util74.12.1-3
ii  libxfconf-0-24.12.1-1
ii  libxi6   2:1.7.9-1
ii  libxklavier165.4-3
ii  libxrandr2   2:1.5.1-1
ii  xfconf   4.12.1-1

Versions of packages xfce4-settings recommends:
ii  x11-utils  7.7+4

xfce4-settings suggests no packages.

-- no debconf information

Bug#926259: ITP: optimir -- Integrating genetic variations in miRNA alignment

[Dylan Aïssi]

Package: wnpp
Owner: Debian Med Packaging Team 
Severity: wishlist

Package name: optimir
Upstream Author : Florian Thibord
URL: https://github.com/FlorianThibord/OptimiR
License: GPL-3
Description: Integrating genetic variations in miRNA alignment
 OptimiR is a miRSeq data alignment workflow. It integrates genetic information
 to assess the impact of variants on miRNA expression.
 .
 OptimiR: A bioinformatics pipeline designed to detect and quantify miRNAs,
 isomiRs and polymiRs from miRSeq data, & study the impact of genetic
 variations on polymiRs' expression.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/optimir

Bug#921559:

[Dylan Aïssi]

Control: severity -1 important

Hi,

I tried to reproduce this problem with an up-to-date (2019-04-01) live Buster.
And I was not able to reproduce this problem with all my Android
devices (Nexus 5, Nexus 7, Galaxy S3, Galaxy J5 2018 and Galaxy Tab A
2018). So, I reduce the severity of this bug for the moment.

Best,
Dylan

Bug#925348: Backport r-cran-sys >= 3.1 to Buster

[Dylan Aïssi]

Package: r-cran-sys
Severity: wishlist

To not forget the Jeroen's request (upstream dev) to backport a new
version of r-cran-sys (>= 3.1) in Buster.

Bug#925347: Backport r-cran-openssl >= 1.3.0 to Buster

[Dylan Aïssi]

Package: r-cran-openssl
Severity: wishlist

To not forget the Jeroen's request (upstream dev) to backport a new
version of r-cran-openssl (>= 1.3.0) in Buster.

> The main reason I want to upgrade r-cran-openssl is
> that I found out that `ssh-keygen` on Buster now defaults to storing
> ssh keys in a new format. And many R users use their default ssh key
> for crypto operations with the openssl package. So in order to read an
> ssh key that was generated with the latest ssh-keygen, they need the
> latest version of the openssl pkg.

Bug#926506: stretch-pu: package bwa/0.7.15-2+deb9u1

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian@packages.debian.org
Usertags: pu

Dear release team,
Upstream has fixed CVE-2019-10269 which is non-dsa.
I have already backported a patch to unstable/testing and now I would
like to fix the Stretch version.
Please find attached a corresponding debdiff.

Best,
Dylan


bwa_0.7.15-2+deb9u1.debdiff
Description: Binary data

Bug#926041: unblock: bwa/0.7.17-3

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock

Please unblock package bwa.

   [ Dylan Aïssi ]
   * Add patch from upstream to fix CVE-2019-10269.
   (Closes: #926014)

   [ Jelmer Vernooij ]
   * Trim trailing whitespace.


Thanks.
Dylan

Bug#925500: ITP: shapeit4 -- fast and accurate method for estimation of haplotypes

[Dylan Aïssi]

Package: wnpp
Owner: Debian Med Packaging Team 
Severity: wishlist

Package name: shapeit4
Upstream Author : Olivier Delaneau
URL: https://odelaneau.github.io/shapeit4/
License: Expat
Description: fast and accurate method for estimation of haplotypes (phasing)
 Segmented HAPlotype Estimation and Imputation Tools version 4 (SHAPEIT4).
 SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka
 phasing) for SNP array and sequencing data.

This package will be maintained by the Debian Med Packaging Team at:
https://salsa.debian.org/med-team/shapeit4

Bug#923556: stretch-pu: package r-cran-igraph/1.0.1-1+deb9u1

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian@packages.debian.org
Usertags: pu

Dear release team,
Upstream has fixed CVE-2018-20349 which is non-dsa.
I already backported a patch to unstable/testing and now I would like
to fix the Stretch version.
Please find attached a corresponding debdiff.

Best,
Dylan


r-cran-igraph_1.0.1-1+deb9u1.debdiff
Description: Binary data

Bug#922736: texlive-pictures: TikZ libraries spath3, knots, and calligraphy produce errors

[Dylan Thurston]

On Wed, Feb 20, 2019 at 02:37:48PM +0900, Norbert Preining wrote:
> On Wed, 20 Feb 2019, Dylan Thurston wrote:
> > I opened this bug because I thought this might be a candidate for
> > "small targeted fixes", per the soft freeze policy. It would be an
> > update to one TeXlive package, that is currently broken.
> 
> Updates to texlive packages cannot (easily) be done only for one single
> package like the one you mentioned. One would need to either patch the
> sources, or include the changed files in the .debian.tar.gz
> I usually do full updates of all of TL from the current tlnet.

Fair enough, thanks for the explanation.

--Dylan

Bug#923556: stretch-pu: package r-cran-igraph/1.0.1-1+deb9u1

[Dylan Aïssi]

Le sam. 9 mars 2019 à 15:17, Adam D. Barratt
 a écrit :
>
> Please go ahead.

Thanks, uploaded!

Best,
Dylan

Bug#919569: r-cran-rnexml: autopkgtest depends on r-cran-rdflib which is not in testing

[Dylan Aïssi]

Hi Andreas,

Le mer. 6 févr. 2019 à 12:05, Andreas Tille  a écrit :
> to experimental.  Since r-cran-v8 is needed for several other packages
> we will loose if it is not in testing I wonder whether you have a plan
> for the experimental -> unstable (and thus testing) migration.

Upstream will release a new version of r-cran-v8 this week, so yes I
will upload this one in unstable asap ;-)
https://github.com/jeroen/V8/issues/49#issuecomment-460897217

Best,
Dylan

Bug#921709: RM: r-cran-v8 [armel hurd-i386 kfreebsd-amd64 kfreebsd-i386] -- ROM; no longer builds

[Dylan Aïssi]

Package: ftp.debian.org
Severity: normal

Hi,

The old r-cran-v8 version (1.5) was built against libv8-3.14-dev which
is too buggy for Buster. Since the new version 2.0, upstream made it
compatible to libnode-dev. So, there was a change in the build-deps of
r-cran-v8 which lead to missing builds due to differential
architectures supported by libv8 and libnode. At least the missing
build for armel will block the transition to buster. According to

$ rmadison r-cran-v8 | grep "unstable "
r-cran-v8  | 1.5-3| unstable  | source, armel,
hurd-i386, kfreebsd-amd64, kfreebsd-i386
r-cran-v8  | 2.0+dfsg-1| buildd-unstable | source, amd64, arm64,
armhf, i386, mips, mipsel, ppc64el, s390x
r-cran-v8  | 2.0+dfsg-1| unstable  | source, amd64, arm64,
armhf, i386, mips, mipsel, ppc64el, s390x

version 1.5-3 should be removed from Debian.

Thanks a lot.

Best,
Dylan

Bug#922736: texlive-pictures: TikZ libraries spath3, knots, and calligraphy produce errors

[Dylan Thurston]

On Wed, Feb 20, 2019 at 01:32:54PM +0900, Norbert Preining wrote:
> Hi
> 
> > The spath3 library has recently (2019-02-12) been updated to fix this.
> 
> Thanks, unfortunately I cannot upload new packages to Debian, and Buster
> is already in freeze. If it is important for you, please see
> intermediate packages as described here:
>   https://www.preining.info/blog/2019/01/debian-updates/
> The latest build is from 2019-02-19

I opened this bug because I thought this might be a candidate for
"small targeted fixes", per the soft freeze policy. It would be an
update to one TeXlive package, that is currently broken.

Bug#922736: texlive-pictures: TikZ libraries spath3, knots, and calligraphy produce errors

[Dylan Thurston]

Package: texlive-pictures
Version: 2018.20190131-1
Severity: normal

Dear Maintainer,

The TikZ library 'spath3' uses illicit variant forms, and stops with a
warning. As a result, the 'knots' and 'calligraphy' libraries are also
broken, and should not be released as-is. Details here:
https://tex.stackexchange.com/questions/408378/warning-with-tikzlibrary-calligraphy

The spath3 library has recently (2019-02-12) been updated to fix this.

##
minimal input file

\documentclass{article}

\usepackage{tikz}
\usetikzlibrary{knots}

\begin{document}
Testing.
\end{document}

##
 List of ls-R files

-rw-r--r-- 1 root root 1289 Feb  2 19:29 /var/lib/texmf/ls-R
lrwxrwxrwx 1 root root 29 Sep  2 08:32 /usr/share/texmf/ls-R -> 
/var/lib/texmf/ls-R-TEXMFMAIN
lrwxrwxrwx 1 root root 31 Jan 30 22:53 /usr/share/texlive/texmf-dist/ls-R -> 
/var/lib/texmf/ls-R-TEXLIVEDIST
lrwxrwxrwx 1 root root 31 Jan 30 22:53 /usr/share/texlive/texmf-dist/ls-R -> 
/var/lib/texmf/ls-R-TEXLIVEDIST
##
 Config files
-rw-r--r-- 1 root root 475 Sep  4 14:08 /etc/texmf/web2c/texmf.cnf
lrwxrwxrwx 1 root root 33 Jan 30 22:53 /usr/share/texmf/web2c/fmtutil.cnf -> 
/var/lib/texmf/fmtutil.cnf-DEBIAN
lrwxrwxrwx 1 root root 32 Jan 30 22:53 /usr/share/texmf/web2c/updmap.cfg -> 
/var/lib/texmf/updmap.cfg-DEBIAN
-rw-r--r-- 1 root root 3032 Feb  2 19:29 
/var/lib/texmf/tex/generic/config/language.dat
##
 Files in /etc/texmf/web2c/
total 8
-rw-r--r-- 1 root root 283 Jan 16  2017 mktex.cnf
-rw-r--r-- 1 root root 475 Sep  4 14:08 texmf.cnf
##
 md5sums of texmf.d
ca40c66f144b4bafc3e59a2dd32ecb9c  /etc/texmf/texmf.d/00debian.cnf

-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) (ignored: LC_ALL 
set to en_US.UTF-8), LANGUAGE=en_US.utf8 (charmap=UTF-8) (ignored: LC_ALL set 
to en_US.UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages texlive-pictures depends on:
ii  python 2.7.15-4
ii  tex-common 6.10
ii  texlive-base   2018.20190131-1
ii  texlive-binaries   2018.20181218.49446-1
ii  texlive-latex-recommended  2018.20190131-1

Versions of packages texlive-pictures recommends:
ii  ruby  1:2.5.1
ii  tk8.6.0+9

Versions of packages texlive-pictures suggests:
pn  dot2tex 
pn  prerex  
pn  ruby-tcltk | libtcltk-ruby  
ii  texlive-latex-extra 2018.20190131-1
ii  texlive-pictures-doc2018.20190131-1
pn  vprerex 

Versions of packages tex-common depends on:
ii  dpkg  1.19.4
ii  ucf   3.0038+nmu1

Versions of packages tex-common suggests:
ii  debhelper  12.1

Versions of packages texlive-pictures is related to:
ii  tex-common6.10
ii  texlive-binaries  2018.20181218.49446-1

-- no debconf information

Bug#927068: stretch-pu: package vcftools/0.1.14+dfsg-4+deb9u1

[Dylan Aïssi]

Le dim. 14 avr. 2019 à 20:56, Adam D. Barratt
 a écrit :
>
> Please go ahead.
>

Thanks, uploaded!

Best,
Dylan

Bug#926894: stretch-pu: package igraph/0.7.1-2.1+deb9u1

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian@packages.debian.org
Usertags: pu

Dear release team,
Upstream has fixed CVE-2018-20349 which is non-dsa.
The patch is already backported to unstable/testing and now I would
like to fix the Stretch version.
Please find attached a corresponding debdiff.

Best,
Dylan


igraph_0.7.1-2.1+deb9u1.debdiff
Description: Binary data

Bug#926894: stretch-pu: package igraph/0.7.1-2.1+deb9u1

[Dylan Aïssi]

Le sam. 13 avr. 2019 à 22:52, Adam D. Barratt
 a écrit :
>
> Please go ahead.
>

Thanks, uploaded!

Best,
Dylan

Bug#926506: stretch-pu: package bwa/0.7.15-2+deb9u1

[Dylan Aïssi]

Le sam. 13 avr. 2019 à 22:54, Adam D. Barratt
 a écrit :
>
> Please go ahead.
>

Thanks, uploaded!

Best,
Dylan

Bug#927068: stretch-pu: package vcftools/0.1.14+dfsg-4+deb9u1

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian@packages.debian.org
Usertags: pu

Dear release team,
Upstream has fixed CVE-2018-11099, CVE-2018-11129 and CVE-2018-11130
which are non-dsa.
The fix is already applied in unstable/testing and now I would like to
fix the Stretch version.
Please find attached a corresponding debdiff.

Best,
Dylan


vcftools_0.1.14+dfsg-4+deb9u1.debdiff
Description: Binary data

Bug#929008: unblock: cohomcalg/0.32+ds-2

[Dylan Aïssi]

Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock

Dear release team,
Please unblock package cohomcalg.

cohomcalg (0.32+ds-2) unstable; urgency=medium

  * Team upload.

  [ Helmut Grohne ]
  * Fix FTCBFS: Pass C++ compiler as LD. (Closes: #928881)
  * Fix arch-only FTBFS: don't run pdflatex. (Closes: #928881)

 -- Dylan Aïssi   Tue, 14 May 2019 22:29:08 +0200

Thanks.
Best,
Dylan


cohomcalg_0.32+ds-2.debdiff
Description: Binary data