Bug#1027897: python3-vtk9: Not installable with Python 3.11
Package: python3-vtk9 Version: 9.1.0+really9.1.0+dfsg2-5 Severity: important X-Debbugs-Cc: moel...@debian.org Dear Anton, dear Gert, dear Nico, $ sudo apt install python3-vtk9 ... python3-vtk9 : Depends on: python3 (< 3.11) but 3.11.1-1 shall be installed I apparently fixed this locally with a mere rebuild. Many thanks! Steffen -- System Information: Debian Release: bookworm/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.0.0-6-rt-amd64 (SMP w/4 CPU threads; PREEMPT) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-vtk9 depends on: ii libc6 2.36-7 ii libgcc-s1 12.2.0-12 ii libopenmpi3 4.1.4-3 ii libpython3.11 3.11.1-2 ii libstdc++6 12.2.0-12 ii libtbb122021.8.0-1 ii libvtk9.1 9.1.0+really9.1.0+dfsg2-5 ii libvtk9.1-qt9.1.0+really9.1.0+dfsg2-5 ii python3 3.11.1-1 pn python3-mpi4py python3-vtk9 recommends no packages. Versions of packages python3-vtk9 suggests: pn mayavi2 pn vtk9-doc pn vtk9-examples -- no debconf information
Bug#1027457: ITP: mesact -- Mesa Configuration Tools for LinuxCNC
Package: wnpp Severity: wishlist X-Debbugs-Cc: moel...@debian.org Subject: ITP: mesact -- Mesa Configuration Tools for LinuxCNC Package: wnpp Owner: Severity: wishlist * Package name: mesact Version : 1.2.0 Upstream Author : , J. E. Thornton * URL : * License : Expat Programming Lang: Python Description : Mesa Configuration Tools for LinuxCNC Between the program controling the execution of a CNC mill, CNC lathe or a robot, and the powerful drivers that know how to turn a motor, is some glue-hardware required that can trigger the drivers to step or spin. . It is not uncommon to see the parallel printer port being that trigger. For higher frequencies, and with the confidence of a perfect clock without the involvement of the computer's CPU, a small card may come to the assistance. This may be microcontroller, or as it is for the Mesa cards, an FPGA. . This software knows how to configure LinuxCNC for using one of the 5i25/6i25, 7i76e, 7i80, 7i92, 7i95, 7i96, 7i97 Mesa LinuxCNC motion control boards and daughter cards. Remark: This package is maintained by John Thornton at https://github.com/jethornton/mesact/
Bug#1027055: ITP: python-hiyapyco -- A simple python lib allowing hierarchical overlay of config files
Package: wnpp Severity: wishlist Owner: Steffen Moeller X-Debbugs-Cc: debian-de...@lists.debian.org, moel...@debian.org * Package name: python-hiyapyco Version : 0.5.1 * URL : https://github.com/zerwes/hiyapyco * License : GPL Programming Lang: Python Description : Hierarchical YAML Python Config A simple python lib allowing hierarchical overlay of config files. The package is a reverse dependency for the periphery of LinuxCNC, basically handling with the overloading of default configurations in more specialized setups.
Bug#1025167: ITP: python-oyaml -- YAML parser but wit preserved dict ordering
Package: wnpp Severity: wishlist Subject: ITP: python-oyaml -- YAML parser but wit preserved dict ordering Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-oyaml Version : 1.0 Upstream Author : Wim Glenn * URL : https://github.com/wimglenn/oyaml * License : Expat Programming Lang: Python Description : YAML parser but wit preserved dict ordering YAML is yet another meta language for the exchange of structured data, think of it as an easier, mostly human-readable XML. In fact, the descriptions of Debian packages are mostly compatible with YAML. . oyaml is a drop-in replacement for the well-established PyYAML module, but preserves dict ordering. Remark: This package is maintained by Debian Python Team at https://salsa.debian.org/python-team/packages/python-oyaml
Bug#1021041: ITP: parallel-hashmap --
Package: wnpp Severity: wishlist Subject: ITP: parallel-hashmap -- Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: parallel-hashmap Version : 1.37 Upstream Author : Copyright: * URL : https://github.com/greg7mdp/parallel-hashmap * License : Apache-2.0 Programming Lang: C Description : This repository aims to provide a set of excellent hash map implementations, as well as a btree alternative to std::map and std::set, with the following characteristics: . * Header only: nothing to build, just copy the parallel_hashmap directory to your project and you are good to go. * drop-in replacement for std::unordered_map, std::unordered_set, std::map and std::set * Compiler with C++11 support required, C++14 and C++17 APIs are provided (such as try_emplace) * Very efficient, significantly faster than your compiler's unordered map/set or Boost's, or than sparsepp * Memory friendly: low memory usage, although a little higher than sparsepp * Supports heterogeneous lookup * Easy to forward declare: just include phmap_fwd_decl.h in your header files to forward declare Parallel Hashmap containers [note: this does not work currently for hash maps with pointer keys] * Dump/load feature: when a flat hash map stores data that is std::trivially_copyable, the table can be dumped to disk and restored as a single array, very efficiently, and without requiring any hash computation. This is typically about 10 times faster than doing element-wise serialization to disk, but it will use 10% to 60% extra disk space. See examples/serialize.cc. (flat hash map/set only) * Tested on Windows (vs2015 & vs2017, vs2019, Intel compiler 18 and 19), linux (g++ 4.8.4, 5, 6, 7, 8, clang++ 3.9, 4.0, 5.0) and MacOS (g++ and clang++) - click on travis and appveyor icons above for detailed test status. * Automatic support for boost's hash_value() method for providing the hash function (see examples/hash_value.h). Also default hash support for std::pair and std::tuple. Remark: This package is maintained by Debian Science Maintainers at https://salsa.debian.org/science-team/parallel-hashmap
Bug#1014274: reverse dependencies
Am 06.09.2022 um 10:12 schrieb Petter Reinholdtsen: [Steffen Moeller] I have seen it. I just do not understand what should be done about the reverse dependencies. @petter, if you could operationalize what needs to be done, this would be great. I believe someone need to contact the maintainers of all the reverse dependencies and ask them to request removal of their package from the architecture in question and adjust their package to drop the architecture from its Architecture: field. You just mean the RM request for those architectures to be issued, right? IMHO we should not change anything concerning the Debian packaging since those reverse dependencies per se are not platform dependent. PS: bugs.debian.org only send email to @bugs.debian.org to the package maintainer, not the others involved in the bug report. I did not get a copy and only discovered this message by luck Feeling Lucky :) Steffen
Bug#1014274: reverse dependencies
Am 05.09.2022 um 23:24 schrieb Petter Reinholdtsen: [Thorsten Alteholz] there are reverse dependencies that needs to be taken care of: Checking reverse dependencies... # Broken Depends: arachne-pnr: arachne-pnr qflow: qflow # Broken Build-Depends: qflow: yosys This needs to be addressed first. Please remove the moreinfo tag once that is done. It is not clear from the To: field of the above quoted email that it reached those involved with yosys maintenance, so I try a reply with the set of earlier contributor to this thread in Cc. I have seen it. I just do not understand what should be done about the reverse dependencies. @petter, if you could operationalize what needs to be done, this would be great. Cheers, Steffen
Bug#1019212: linuxcnc: QTvcp error - dev snapshot not ready to transition to testing
Package: linuxcnc-uspace Version: 2.9.0~pre0+git20220903.c8c4c539b1-1 Severity: important Tags: upstream Upstream discussed this at https://github.com/LinuxCNC/linuxcnc/issues/2000
Bug#1018681: ITP: spnavcfg -- GUI to configure 3Dconnexion devices
Package: wnpp Severity: wishlist Owner: Steffen Moeller X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: spnavcfg Version : 1.0 * URL : https://github.com/FreeSpacenav/spnavcfg * License : GPL Description : GUI to configure 3Dconnexion devices To arrive team-maintained at https://salsa.debian.org/science-team/spnavcfg
Bug#1018294: ITP: openfpgaloader -- Universal utility for programming FPGAs
Package: wnpp Severity: wishlist Owner: Steffen Moeller X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: openfpgaloader Version : 0.9 * URL : https://github.com/trabucayre/openFPGALoader * License : Apache-2.0 Programming Lang: C/C++ Description : Universal utility for programming FPGAs To appear on https://salsa.debian.org/electronics-team/openfpgaloader.
Bug#1014734: RM: yosys [s390x] -- ROM; Not in maintainer's arch list
Package: ftp.debian.org Severity: normal X-Debbugs-Cc: moel...@debian.org Not in arch list and can hence not be tested, which blocks the transition of that package as seen on https://tracker.debian.org/pkg/yosys
Bug#1014692: RM: qiime [armel armhf i386] -- ROM; FTBFS, no longer builds on 32bit platforms
Package: ftp.debian.org Severity: normal X-Debbugs-Cc: moel...@debian.org There is no point (scientifically) and not resources on Debian's side to substitute upstream's lack of interest in maintaining the 32bit platform.
Bug#1008740: ITP: megadepth -- computes coverage from BigWig and BAM sequencing files
Package: wnpp Severity: wishlist Subject: ITP: megadepth -- computes coverage from BigWig and BAM sequencing files Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: megadepth Version : 1.2.0 Upstream Author : Copyright: * URL : https://github.com/ChristopherWilks/megadepth * License : Expat Programming Lang: C Description : computes coverage from BigWig and BAM sequencing files A major concern for the interpretation of DNA and RNA (!) sequencing is the number of reads that cover a particular area. This package has interesting statistics for the distinction of coding and non-coding parts of the genome and knows how to interpret transcripts that span multiple exons. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/megadepth
Bug#1008737: ITP: r-bioc-megadepth -- megadepth: BigWig and BAM related utilities
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-megadepth -- megadepth: BigWig and BAM related utilities Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-megadepth Version : 1.4.0 Upstream Author : Leonardo Collado-Torres, * URL : https://bioconductor.org/packages/megadepth/ * License : Artistic-2.0 Programming Lang: GNU R Description : megadepth: BigWig and BAM related utilities This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-megadepth
Bug#1008732: ITP: r-cran-cmdfun -- Framework for Building Interfaces to Shell Commands
Package: wnpp Severity: wishlist Subject: ITP: r-cran-cmdfun -- Framework for Building Interfaces to Shell Commands Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-cmdfun Version : 1.0.2 Upstream Author : Spencer Nystrom * URL : https://cran.r-project.org/package=cmdfun * License : MIT Programming Lang: GNU R Description : Framework for Building Interfaces to Shell Commands Writing interfaces to command line software is cumbersome. 'cmdfun' provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line arguments. 'cmdfun' also provides methods for handling user-specific paths to tool installs or secrets like API keys. Its focus is to equally serve package builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non- R software. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-cmdfun
Bug#1008568: ITP: r-bioc-annotationforge -- Tools for building SQLite-based annotation data packages
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-annotationforge -- Tools for building SQLite-based annotation data packages Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-annotationforge Version : 1.36.0 Upstream Author : Marc Carlson, Hervé Pagès * URL : https://bioconductor.org/packages/AnnotationForge/ * License : Artistic-2.0 Programming Lang: GNU R Description : Tools for building SQLite-based annotation data packages Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-annotationforge
Bug#1008565: ITP: r-bioc-kegg.db -- A set of annotation maps for KEGG
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-kegg.db -- A set of annotation maps for KEGG Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-kegg.db Version : 3.2.3 Upstream Author : Marc Carlson * URL : https://bioconductor.org/packages/KEGG.db/ * License : academic-use-only Programming Lang: (C, C++, C#, Perl, Python, etc.) Description : A set of annotation maps for KEGG A set of annotation maps for KEGG assembled using data from KEGG . This package is deprecated in BioConductor and should not be used in new projects. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-kegg.db
Bug#1008256: ITP: r-bioc-mfuzz -- Soft clustering of time series gene expression data
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-mfuzz -- Soft clustering of time series gene expression data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-mfuzz Version : 2.54.0 Upstream Author : Matthias Futschik * URL : https://bioconductor.org/packages/Mfuzz/ * License : GPL-2 Programming Lang: GNU R Description : Soft clustering of time series gene expression data Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-mfuzz
Bug#1008255: ITP: r-bioc-tkwidgets -- R based tk widgets
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-tkwidgets -- R based tk widgets Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-tkwidgets Version : 1.72.0 Upstream Author : J. Zhang * URL : https://bioconductor.org/packages/tkWidgets/ * License : Artistic-2.0 Programming Lang: GNU R Description : R based tk widgets Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-tkwidgets
Bug#1008251: ITP: r-bioc-dyndoc -- Dynamic document tools
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-dyndoc -- Dynamic document tools Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-dyndoc Version : 1.72.0 Upstream Author : R. Gentleman, Jeff Gentry * URL : https://bioconductor.org/packages/DynDoc/ * License : Artistic-2.0 Programming Lang: GNU R Description : Dynamic document tools A set of functions to create and interact with dynamic documents and vignettes. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-dyndoc
Bug#1008250: ITP: r-bioc-widgettools -- Creates an interactive tcltk widget
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-widgettools -- Creates an interactive tcltk widget Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-widgettools Version : 1.72.0 Upstream Author : Jianhua Zhang * URL : https://bioconductor.org/packages/widgetTools/ * License : LGPL-2 Programming Lang: GNU R Description : Creates an interactive tcltk widget This packages contains tools to support the construction of tcltk widgets Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-widgettools
Bug#1008221: ITP: r-bioc-tmixclust -- mixed-effects gene-expression time-series analysis
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-tmixclust -- mixed-effects gene-expression time-series analysis Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-tmixclust Version : 1.16.0 Upstream Author : Monica Golumbeanu * URL : https://bioconductor.org/packages/TMixClust/ * License : GPL-2+ Programming Lang: GNU R Description : mixed-effects gene-expression time-series analysis To investigate how a drug effects a tissue sample over time, one commonly determines the transcriptomes at different time points to distinguish genes that react early from those that react late, which are steadily going up or down, which are oscillating, and what molecular process are those subsets of genes contributing to. . Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-tmixclust
Bug#1008218: ITP: r-bioc-spem -- S-system parameter estimation method
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-spem -- S-system parameter estimation method Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-spem Version : 1.34.0 Upstream Author : Xinyi YANG (Developer) * URL : https://bioconductor.org/packages/SPEM/ * License : GPL-2 Programming Lang: GNU R Description : S-system parameter estimation method This package can optimize the parameter in S-system models given time series data Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-spem
Bug#1008217: ITP: r-cran-flexclust -- Flexible Cluster Algorithms
Package: wnpp Severity: wishlist Subject: ITP: r-cran-flexclust -- Flexible Cluster Algorithms Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-flexclust Version : 1.4 Upstream Author : Friedrich Leisch * URL : https://cran.r-project.org/package=flexclust * License : GPL-2 Programming Lang: GNU R Description : Flexible Cluster Algorithms The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-flexclust
Bug#1005952: RFP: libjs-vega -- programmed web graphics with JSON
Package: wnpp Severity: wishlist * Package name: libjs-vega Version : 5.21.0 * URL : https://github.com/vega/vega * License : BSD Programming Lang: JavaScript Description : programmed web graphics with JSON Vega is a visualization grammar, a declarative format for creating, saving, and sharing interactive visualization designs. With Vega you can describe data visualizations in a JSON format, and generate interactive views using either HTML5 Canvas or SVG.
Bug#1004908: ITP: faber -- software build system
Package: wnpp Severity: wishlist X-Debbugs-Cc: moel...@debian.org Subject: ITP: faber -- software build system Package: wnpp Owner: Severity: wishlist * Package name: faber Version : 0.6.0.dev1 Upstream Author : Stefan Seefeld * URL : http://stefan.seefeld.name/faber/ * License : Boost-1.0 Programming Lang: Python Description : software build system Software developers prepare a bunch of files with their source code that may be taken as they are or somehow processed to constitute the final software package. This can be tricky when the processing itself is tricky, and because the processing of one file may depend on the processing of other files, e.g. to link against a library. And when linking against external libraries, this need to be in the right version. And then there are tests performed to check that all is fine on that particular platoform that the build is performed on. And finally, the developer wants an easy way to be pointed to where the problem occurred. . Traditionally, the building of software is done with Make, but many new tools have evolved ever since, often adapted to a new programming language. This package provides the executable of the faber software build system that was adopted by the Python Boost interface but is not specific for Python. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/python-team/packages/faber
Bug#1002080: ITP: r-other-ibi-disgenet2r -- an R package to query, visualize, and expand DisGeNET data
Package: wnpp Severity: wishlist Subject: ITP: r-other-ibi-disgenet2r -- an R package to query, visualize, and expand DisGeNET data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-other-ibi-disgenet2r Version : 0.99.2+git20210805+8d8ce37da738+ds Upstream Author : IBI group * URL : https://www.disgenet.org/disgenet2r * License : MIT Programming Lang: GNU R Description : an R package to query, visualize, and expand DisGeNET data R package to query and expand DisGeNET data (www.disgenet.org), and to visualize the results within R framework. The disgenet2r package is designed to retrieve data from DisGeNET v6.0 (Jan, 2019). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-other-disgenet2r
Bug#1002075: ITP: r-cran-sparql -- SPARQL client
Package: wnpp Severity: wishlist Subject: ITP: r-cran-sparql -- SPARQL client Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-sparql Version : 1.16 Upstream Author : Willem Robert van Hage , * URL : https://cran.r-project.org/package=SPARQL * License : GPL-3 Programming Lang: GNU R Description : SPARQL client Use SPARQL to pose SELECT or UPDATE queries to an end-point. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-sparql
Bug#1001436: ITP: r-bioc-txdb.hsapiens.ucsc.hg19.knowngene -- Annotation package for TxDb object(s)
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-txdb.hsapiens.ucsc.hg19.knowngene -- Annotation package for TxDb object(s) Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-txdb.hsapiens.ucsc.hg19.knowngene Version : 3.2.2 Upstream Author : Marc Carlson, Bioconductor Package Maintainer * URL : https://bioconductor.org/packages/data/experiment/TxDb.Hsapiens.UCSC.hg19.knownGene/ * License : Artistic-2.0 Programming Lang: GNU R Description : Annotation package for TxDb object(s) Exposes an annotation databases generated from UCSC by exposing these as TxDb objects Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene
Bug#1001397: ITP: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-fishpond Version : 2.0.1+ds Upstream Author : Anzi Zhu, * URL : https://bioconductor.org/packages/fishpond/ * License : GPL-2 Programming Lang: GNU R Description : Fishpond: differential transcript and gene expression with inferential replicates Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains utilities for working with Salmon and Alevin quantification files. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-fishpond
Bug#998085: ITP: python-rdata -- parses R dataset (.rda) files
Package: wnpp Severity: wishlist Subject: ITP: python-rdata -- parses R dataset (.rda) files Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-rdata Version : 0.5 Upstream Author : Carlos Ramos Carreño * URL : https://github.com/vnmabus/rdata * License : Expat Programming Lang: Python Description : parses R dataset (.rda) files The common way of reading an R dataset consists on two steps: . * First, the file is parsed using the function parse_file. This provides a literal description of the file contents as a hierarchy of Python objects representing the basic R objects. This step is unambiguous and always the same. * Then, each object must be converted to an appropriate Python object. In this step there are several choices on which Python type is the most appropriate as the conversion for a given R object. Thus, we provide a default convert routine, which tries to select Python objects that preserve most information of the original R object. For custom R classes, it is also possible to specify conversion routines to Python objects. . The basic convert routine only constructs a SimpleConverter objects and calls its convert method. All arguments of convert are directly passed to the SimpleConverter initialization method. . It is possible, although not trivial, to make a custom Converter object to change the way in which the basic R objects are transformed to Python objects. However, a more common situation is that one does not want to change how basic R objects are converted, but instead wants to provide conversions for specific R classes. This can be done by passing a dictionary to the SimpleConverter initialization method, containing as keys the names of R classes and as values, callables that convert a R object of that class to a Python object. By default, the dictionary used is DEFAULT_CLASS_MAP, which can convert commonly used R classes such as data.frame and factor. Remark: This package is maintained by Debian Python Team at https://salsa.debian.org/python-team/packages/python-rdata
Bug#998044: ITP: python-pyreadr -- read/write R data files via Python pandas
Package: wnpp Severity: wishlist Subject: ITP: python-pyreadr -- read/write R data files via Python pandas Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-pyreadr Version : 0.4.2 Upstream Author : Copyright: Otto Fajardo * URL : https://github.com/ofajardo/pyreadr * License : GNU-Affero-3.0 Programming Lang: Python Description : read/write R data files via Python pandas A python package to read and write R RData and Rds files into/from pandas dataframes. It does not need to have R or other external dependencies installed. . It can read mainly R data frames and tibbles. Also supports vectors, matrices, arrays and tables. R lists and R S4 objects (such as those from Bioconductor) are not supported. Please read the Known limitations section and the section on what objects can be read for more information. . This package is based on the librdata C library by Evan Miller and a modified version of the cython wrapper around librdata jamovi-readstat by the Jamovi team. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/python-team/packages/python-pyreadr
Bug#998030: r-cran-dt: Add xdg-open app open attempts as recommended
Package: r-cran-dt Version: 0.17+dfsg-3 Severity: minor Tags: a11y The command DT::datatable(data = inputSettings, extensions = 'FixedColumns', options = list(fixedColumns = TRUE, scrollX = TRUE, pageLength = 9, dom = 't')) stimulates Set the BROWSER environment variable to your desired browser. Warning: program returned non-zero exit code #256 /usr/bin/xdg-open: 882: www-browser: not found /usr/bin/xdg-open: 882: links2: not found /usr/bin/xdg-open: 882: elinks: not found /usr/bin/xdg-open: 882: links: not found /usr/bin/xdg-open: 882: lynx: not found /usr/bin/xdg-open: 882: w3m: not found xdg-open: no method available for opening '/tmp/RtmpGZs59M/viewhtmlba7f058dcace0/index.html' which likely should affect the recommended packages.
Bug#996981: multiqc: Link to jquery missing
Package: multiqc Version: 1.11+dfsg-1 Severity: normal Reminder to self: distutils.errors.DistutilsFileError: can't copy '/usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js': doesn't exist or not a regular file -- System Information: Debian Release: bookworm/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 5.10.0-8-amd64 (SMP w/24 CPU threads) Kernel taint flags: TAINT_FIRMWARE_WORKAROUND Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages multiqc depends on: ii fonts-glyphicons-halflings 1.009~3.4.1+dfsg-2 ii libjs-bootstrap 3.4.1+dfsg-2 ii libjs-jquery3.5.1+dfsg+~3.5.5-7 ii libjs-jquery-tablesorter1:2.31.3+dfsg1-1 ii libjs-jquery-ui 1.12.1+dfsg-8 ii python3 3.9.2-3 ii python3-click 8.0.2-1 ii python3-coloredlogs 7.3-2 ii python3-distutils 3.9.7-1 ii python3-future 0.18.2-5 ii python3-humanfriendly 10.0-1 ii python3-jinja2 3.0.1-2 ii python3-lzstring1.0.4-1.1 ii python3-markdown3.3.4-1 ii python3-matplotlib 3.3.4-2 ii python3-networkx2.5+ds-2 ii python3-numpy 1:1.19.5-1 ii python3-requests2.25.1+dfsg-2 ii python3-rich9.11.0-1 ii python3-simplejson 3.17.5-2 ii python3-spectra 0.0.11-2 ii python3-yaml5.4.1-1 Versions of packages multiqc recommends: ii libjs-filesaver 2.0.2+dfsg-3 ii node-clipboard 2.0.6+ds+~cs7.6.4-1 ii pandoc 2.9.2.1-1+b2 ii texlive-xetex2021.20210921-1 multiqc suggests no packages. -- no debconf information
Bug#996965: ITP: r-cran-bslib -- Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Package: wnpp Severity: wishlist Subject: ITP: r-cran-bslib -- Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown' Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-bslib Version : 0.3.1 Upstream Author : Carson Sievert, * URL : https://cran.r-project.org/package=bslib * License : MIT Programming Lang: GNU R Description : Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown' Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports both 'Bootstrap' 3 and 4 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-bslib
Bug#996868: ITP: python-connection-pool -- thread-safe connection pool for python
Package: wnpp Severity: wishlist Subject: ITP: python-connection-pool -- thread-safe connection pool for python Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-connection-pool Version : 0.0.3 Upstream Author : ZhouYL <81438...@qq.com> * URL : https://github.com/zhouyl/ConnectionPool * License : Expat Programming Lang: Python Description : thread-safe connection pool for python This package provides a thread-safe connection pool for Python 3. These are sets database connections that are readily available for anticipated repeated requests to the same database. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/python-team/packages/python-connection-pool
Bug#996605: ITP: r-cran-susier -- Sum of Single Effects Linear Regression
Package: wnpp Severity: wishlist Subject: ITP: r-cran-susier -- Sum of Single Effects Linear Regression Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-susier Version : 0.11.42 Upstream Author : Gao Wang * URL : https://cran.r-project.org/package=susieR * License : MIT Programming Lang: GNU R Description : Sum of Single Effects Linear Regression Implements methods for variable selection in linear regression based on the "Sum of Single Effects" (SuSiE) model, as described in Wang et al (2020) . These methods provide simple summaries, called "Credible Sets", for accurately quantifying uncertainty in which variables should be selected. The methods are motivated by genetic fine-mapping applications, and are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse. The fitting algorithm, a Bayesian analogue of stepwise selection methods called "Iterative Bayesian Stepwise Selection" (IBSS), is simple and fast, allowing the SuSiE model be fit to large data sets (thousands of samples and hundreds of thousands of variables). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-susier
Bug#996585: ITP: r-cran-mixsqp -- Quadratic Programming for Estimation of Mixture Proportions
Package: wnpp Severity: wishlist Subject: ITP: r-cran-mixsqp -- Quadratic Programming for Estimation of Mixture Proportions Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-mixsqp Version : 0.3 Upstream Author : Youngseok Kim * URL : https://cran.r-project.org/package=mixsqp * License : MIT Programming Lang: GNU R Description : Quadratic Programming for Estimation of Mixture Proportions Provides an optimization method based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithm is expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly when the number of samples is large and the number of mixture components is not too large. This implements the "mix-SQP" algorithm, with some improvements, described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2020) . Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-mixsqp
Bug#996582: ITP: r-cran-coloc -- Colocalisation Tests of Two Genetic Traits
Package: wnpp Severity: wishlist Subject: ITP: r-cran-coloc -- Colocalisation Tests of Two Genetic Traits Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-coloc Version : 5.1.0 Upstream Author : Chris Wallace * URL : https://cran.r-project.org/package=coloc * License : GPL-2 Programming Lang: GNU R Description : Colocalisation Tests of Two Genetic Traits Performs the colocalisation tests described in Giambartolomei et al (2013) , Wallace (2020) , Wallace (2021) . Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-coloc
Bug#995943: ITP: r-cran-osqp -- Quadratic Programming Solver using the 'OSQP' Library
Package: wnpp Severity: wishlist Subject: ITP: r-cran-osqp -- Quadratic Programming Solver using the 'OSQP' Library Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-osqp Version : 0.6.0.3 Upstream Author : Bartolomeo Stellato * URL : https://cran.r-project.org/package=osqp * License : Apache-2.0 Programming Lang: GNU R Description : Quadratic Programming Solver using the 'OSQP' Library Provides bindings to the 'OSQP' solver. The 'OSQP' solver is a numerical optimization package or solving convex quadratic programs written in 'C' and based on the alternating direction method of multipliers. See for details. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-osqp
Bug#995938: ITP: r-cran-scs -- Splitting Conic Solver
Package: wnpp
Severity: wishlist
Subject: ITP: r-cran-scs -- Splitting Conic Solver
Package: wnpp
Owner: Steffen Moeller
Severity: wishlist
* Package name: r-cran-scs
Version : 1.3
Upstream Author : Florian Schwendinger
* URL : https://cran.r-project.org/package=scs
* License : GPL-3
Programming Lang: GNU R
Description : Splitting Conic Solver
Solves convex cone programs via operator splitting. Can solve: linear
programs ('LPs'), second-order cone programs ('SOCPs'), semidefinite
programs ('SDPs'), exponential cone programs ('ECPs'), and power cone
programs ('PCPs'), or problems with any combination of those cones.
'SCS' uses 'AMD' (a set of routines for permuting sparse matrices prior
to factorization) and 'LDL' (a sparse 'LDL' factorization and solve
package) from 'SuiteSparse' (<http://www.suitesparse.com>).
Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-cran-scs
Bug#995902: ITP: r-cran-rmpfr -- R MPFR - Multiple Precision Floating-Point Reliable
Package: wnpp
Severity: wishlist
Subject: ITP: r-cran-rmpfr -- R MPFR - Multiple Precision Floating-Point
Reliable
Package: wnpp
Owner: Steffen Moeller
Severity: wishlist
* Package name: r-cran-rmpfr
Version : 0.8
Upstream Author : Martin Maechler,
* URL : https://cran.r-project.org/package=Rmpfr
* License : GPL-2+
Programming Lang: GNU R
Description : R MPFR - Multiple Precision Floating-Point Reliable
Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-cran-rmpfr
Bug#995901: ITP: r-cran-cvxr -- Disciplined Convex Optimization
Package: wnpp Severity: wishlist Subject: ITP: r-cran-cvxr -- Disciplined Convex Optimization Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-cvxr Version : 1.0 Upstream Author : Anqi Fu * URL : https://cran.r-project.org/package=CVXR * License : Apache-2.0 Programming Lang: GNU R Description : Disciplined Convex Optimization An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, ). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-cvxr
Bug#995834: ITP: r-other-kcha-psiplot -- plots relative abundance alterantively spliced transcripts
Package: wnpp Severity: wishlist Subject: ITP: r-other-kcha-psiplot -- plots relative abundance alterantively spliced transcripts Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-other-kcha-psiplot Version : 2.3.0 Upstream Author : Kevin Ha * URL : https://github.com/kcha/psiplot * License : MIT Programming Lang: GNU R Description : plots relative abundance alterantively spliced transcripts Provides functions to create plots of PSI values of alternatively-spliced exons or cRPKMs. Requires PSI cRPKM data generated by the program vast-tools (https://github.com/vastgroup/vast-tools). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-other-psiplot
Bug#995816: ITP: r-cran-mclustcomp -- Measures for Comparing Clusters
Package: wnpp Severity: wishlist Subject: ITP: r-cran-mclustcomp -- Measures for Comparing Clusters Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-mclustcomp Version : 0.3.3 Upstream Author : Kisung You * URL : https://cran.r-project.org/package=mclustcomp * License : GPL-3+ Programming Lang: GNU R Description : Measures for Comparing Clusters Given a set of data points, a clustering is defined as a disjoint partition where each pair of sets in a partition has no overlapping elements. This package provides 25 methods that play a role somewhat similar to distance or metric that measures similarity of two clusterings - or partitions. For a more detailed description, see Meila, M. (2005) . Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-mclustcomp
Bug#995727: ITP: r-cran-labdsv -- Ordination and Multivariate Analysis for Ecology
Package: wnpp Severity: wishlist Subject: ITP: r-cran-labdsv -- Ordination and Multivariate Analysis for Ecology Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-labdsv Version : 2.0 Upstream Author : David W. Roberts * URL : https://cran.r-project.org/package=labdsv * License : GPL-2+ Programming Lang: GNU R Description : Ordination and Multivariate Analysis for Ecology A variety of ordination and community analyses useful in analysis of data sets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-labdsv
Bug#995726: ITP: r-cran-shapes -- Statistical Shape Analysis
Package: wnpp Severity: wishlist Subject: ITP: r-cran-shapes -- Statistical Shape Analysis Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-shapes Version : 1.2.6 Upstream Author : Copyright: FIXME-2021 Ian L. Dryden * URL : https://cran.r-project.org/package=shapes * License : GPL-2 Programming Lang: GNU R Description : Statistical Shape Analysis Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-shapes
Bug#995723: ITP: r-cran-dbscan -- Density Based Clustering of Applications with Noise (DBSCAN)
Package: wnpp Severity: wishlist Subject: ITP: r-cran-dbscan -- Density Based Clustering of Applications with Noise (DBSCAN) Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-dbscan Version : 1.1 Upstream Author : Michael Hahsler, * URL : https://cran.r-project.org/package=dbscan * License : GPL-2+ Programming Lang: GNU R Description : Density Based Clustering of Applications with Noise (DBSCAN) Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms provides a fast reimplementation of several density- based algorithms of the DBSCAN family for spatial data. Includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering points to identify the clustering structure), and the outlier detection algorithm LOF (local outlier factor). The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided. Hahsler, Piekenbrock and Doran (2019) . Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-dbscan
Bug#995713: ITP: r-cran-rcppdist -- 'Rcpp' Integration of Additional Probability Distributions
Package: wnpp Severity: wishlist Subject: ITP: r-cran-rcppdist -- 'Rcpp' Integration of Additional Probability Distributions Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-rcppdist Version : 0.1.1 Upstream Author : JB Duck-Mayr * URL : https://cran.r-project.org/package=RcppDist * License : GPL-2+ Programming Lang: GNU R Description : 'Rcpp' Integration of Additional Probability Distributions The 'Rcpp' package provides a C++ library to make it easier to use C++ with R. R and 'Rcpp' provide functions for a variety of statistical distributions. Several R packages make functions available to R for additional statistical distributions. However, to access these functions from C++ code, a costly call to the R functions must be made. 'RcppDist' provides a header-only C++ library with functions for additional statistical distributions that can be called from C++ when writing code using 'Rcpp' or 'RcppArmadillo'. Functions are available that return a 'NumericVector' as well as doubles, and for multivariate or matrix distributions, 'Armadillo' vectors and matrices. 'RcppDist' provides functions for the following distributions: the four parameter beta distribution; the location- scale t distribution; the truncated normal distribution; the truncated t distribution; a truncated location-scale t distribution; the triangle distribution; the multivariate normal distribution*; the multivariate t distribution*; the Wishart distribution*; and the inverse Wishart distribution*. Distributions marked with an asterisk rely on 'RcppArmadillo'. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-rcppdist
Bug#995711: ITP: r-cran-maotai -- Tools for Matrix Algebra, Optimization and Inference
Package: wnpp Severity: wishlist Subject: ITP: r-cran-maotai -- Tools for Matrix Algebra, Optimization and Inference Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-maotai Version : 0.2.1 Upstream Author : Kisung You * URL : https://cran.r-project.org/package=maotai * License : MIT Programming Lang: GNU R Description : Tools for Matrix Algebra, Optimization and Inference Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-maotai
Bug#995707: ITP: r-cran-rcsdp -- R Interface to the CSDP Semidefinite Programming Library
Package: wnpp Severity: wishlist Subject: ITP: r-cran-rcsdp -- R Interface to the CSDP Semidefinite Programming Library Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-rcsdp Version : 0.1.57.1 Upstream Author : Hector Corrada Bravo * URL : https://cran.r-project.org/package=Rcsdp * License : CPL-1.0 Programming Lang: GNU R Description : R Interface to the CSDP Semidefinite Programming Library R interface to the CSDP semidefinite programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if required. An existing installation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-rcsdp
Bug#995489: ITP: r-bioc-eir -- Accelerated similarity searching of small molecules
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-eir -- Accelerated similarity searching of small molecules Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-eir Version : 1.32.0+ds Upstream Author : Kevin Horan, Yiqun Cao and Tyler Backman * URL : https://bioconductor.org/packages/eiR/ * License : Artistic-2.0 Programming Lang: GNU R Description : Accelerated similarity searching of small molecules The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-eir
Bug#995422: ITP: long-read-assembler -- assembly from long reads against reference genome
Package: wnpp Severity: wishlist Subject: ITP: long-read-assembler -- assembly from long reads against reference genome Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: long-read-assembler Version : 1.3.2 Upstream Author : Copyright: Bonnie Phan Wolfe * URL : https://github.com/ChaissonLab/LRA * License : USC-RL-1.0 Programming Lang: C Description : assembly from long reads against reference genome Machines that determine the DNA sequence do not provide answers en block, but as many comparatively short reads that by chance also overlap. From these, the complete genome is puzzled together assembled. This is less easy than one may think because of redundancies of the genome, so you do not know where a read comes from if that read is too short. A reference genome helps, but people differ, e.g. with local duplications, and you may be interested in diseases that have chromosomal rearrangements. . lra is a sequence alignment program that aligns long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies. These technologies provide reads that are 1000 or 10k times longer than what can be achieved with the Sanger Sequencing technology and help the assembly. . lra implements seed chaining sparse dynamic programming with a concave gap function to read and assembly alignment, which is also extended to allow for inversion cases. lra alignment approach increases sensitivity and specificity for SV discovery, particularly for variants above 1kb and when discovering variation from ONT reads, while having runtime that arecomparable (1.05-3.76×) to current methods. When applied to calling variation from *de novo* assembly contigs, there is a 3.2% increase in Truvari F1 score compared to minimap2+htsbox. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/med-team/long-read-assembler
Bug#995255: ITP: r-bioc-isoformswitchanalyzer -- Identify, Annotate and Visualize Alternative Splicing and
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-isoformswitchanalyzer -- Identify, Annotate and Visualize Alternative Splicing and Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-isoformswitchanalyzer Version : 1.14.0 Upstream Author : Kristoffer Vitting-Seerup * URL : https://bioconductor.org/packages/IsoformSwitchAnalyzeR/ * License : GPL-2+ Programming Lang: GNU R Description : Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-isoformswitchanalyzer
Bug#995252: ITP: r-bioc-drimseq -- Differential transcript usage and tuQTL analyses with
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-drimseq -- Differential transcript usage and tuQTL analyses with Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-drimseq Version : 1.20.0 Upstream Author : Malgorzata Nowicka * URL : https://bioconductor.org/packages/DRIMSeq/ * License : GPL-3+ Programming Lang: GNU R Description : Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-drimseq
Bug#995247: ITP: r-bioc-mofa2 -- Multi-Omics Factor Analysis v2
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-mofa2 -- Multi-Omics Factor Analysis v2 Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-mofa2 Version : 1.2.2+ds Upstream Author : Ricard Argelaguet * URL : https://bioconductor.org/packages/MOFA2/ * License : GPL-2+ Programming Lang: GNU R Description : Multi-Omics Factor Analysis v2 The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-mofa2
Bug#994541: ITP: r-cran-svunit -- SciViews - Unit, Integration and System Testing
Package: wnpp Severity: wishlist Subject: ITP: r-cran-svunit -- SciViews - Unit, Integration and System Testing Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-svunit Version : 1.0.6 Upstream Author : Philippe Grosjean * URL : https://cran.r-project.org/package=svUnit * License : GPL-2 Programming Lang: GNU R Description : SciViews - Unit, Integration and System Testing A complete unit test system and functions to implement its GUI part. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-svunit
Bug#994398: ITP: r-cran-sqldf -- Manipulate R Data Frames Using SQL
Package: wnpp Severity: wishlist Subject: ITP: r-cran-sqldf -- Manipulate R Data Frames Using SQL Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-sqldf Version : 0.4 Upstream Author : Copyright: FIXME-2017 G. Grothendieck * URL : https://cran.r-project.org/package=sqldf * License : GPL-2 Programming Lang: GNU R Description : Manipulate R Data Frames Using SQL The sqldf() function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. sqldf() transparently sets up a database, imports the data frames into that database, performs the SQL select or other statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The sqldf() or read.csv.sql() functions can also be used to read filtered files into R even if the original files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-sqldf
Bug#994397: ITP: r-cran-gsubfn -- Utilities for Strings and Function Arguments
Package: wnpp Severity: wishlist Subject: ITP: r-cran-gsubfn -- Utilities for Strings and Function Arguments Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-gsubfn Version : 0.7 Upstream Author : G. Grothendieck * URL : https://cran.r-project.org/package=gsubfn * License : GPL-2+ Programming Lang: GNU R Description : Utilities for Strings and Function Arguments The gsubfn function is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable. There is also a facility for returning multiple objects from functions and a version of transform that allows the RHS to refer to LHS used in the same transform. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-gsubfn
Bug#994394: ITP: r-bioc-stringdb -- Search Tool for the Retrieval of Interacting proteins database
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-stringdb -- Search Tool for the Retrieval of Interacting proteins database Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-stringdb Version : 2.4.1 Upstream Author : Andrea Franceschini * URL : https://bioconductor.org/packages/STRINGdb/ * License : GPL-2 Programming Lang: GNU R Description : Search Tool for the Retrieval of Interacting proteins database The STRINGdb package provides a R interface to the STRING protein-protein interactions database. . The original database is accessible on https://www.string-db.org. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-stringdb
Bug#994004: ITP: r-bioc-bcellviper -- Human B-cell transcriptional interactome and expression data
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-bcellviper -- Human B-cell transcriptional interactome and expression data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-bcellviper Version : 1.28.0 Upstream Author : Mariano Javier Alvarez * URL : https://bioconductor.org/packages/data/experiment/bcellViper/ * License : GPL-2+ Programming Lang: GNU R Description : Human B-cell transcriptional interactome and expression data This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-bcellviper
Bug#993977: ITP: r-bioc-dorothea -- Collection Of Human And Mouse TF Regulons
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-dorothea -- Collection Of Human And Mouse TF Regulons Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-dorothea Version : 1.4.1 Upstream Author : Christian H. Holland * URL : https://bioconductor.org/packages/data/experiment/dorothea/ * License : GPL-3 Programming Lang: GNU R Description : Collection Of Human And Mouse TF Regulons This package contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-dorothea
Bug#993976: ITP: r-bioc-progeny -- activity inference from gene expression
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-progeny -- activity inference from gene expression Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-progeny Version : 1.14.0+ds Upstream Author : Michael Schubert * URL : https://bioconductor.org/packages/progeny/ * License : Apache-2.0 Programming Lang: GNU R Description : activity inference from gene expression This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression". Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-progeny
Bug#993321: ITP: seqwish -- alignment to variation graph inducer
Package: wnpp Severity: wishlist Subject: ITP: seqwish -- alignment to variation graph inducer Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: seqwish Version : 0.7.1 Upstream Author : Erik Garrison * URL : https://github.com/ekg/seqwish * License : MIT Programming Lang: C++ Description : alignment to variation graph inducer Seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when working with large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/seqwish
Bug#993310: ITP: r-cran-shades -- Simple Colour Manipulation
Package: wnpp Severity: wishlist Subject: ITP: r-cran-shades -- Simple Colour Manipulation Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-shades Version : 1.4.0 Upstream Author : Jon Clayden * URL : https://cran.r-project.org/package=shades * License : BSD-3-clause Programming Lang: GNU R Description : Simple Colour Manipulation Functions for easily manipulating colours, creating colour scales and calculating colour distances. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-shades
Bug#993306: ITP: r-cran-ggfittext -- Fit Text Inside a Box in 'ggplot2'
Package: wnpp Severity: wishlist Subject: ITP: r-cran-ggfittext -- Fit Text Inside a Box in 'ggplot2' Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-ggfittext Version : 0.9.1+ds Upstream Author : David Wilkins * URL : https://cran.r-project.org/package=ggfittext * License : GPL-2 Programming Lang: GNU R Description : Fit Text Inside a Box in 'ggplot2' Provides 'ggplot2' geoms to fit text into a box by growing, shrinking or wrapping the text. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-ggfittext
Bug#993305: ITP: r-cran-gggenes -- Draw Gene Arrow Maps in 'ggplot2'
Package: wnpp Severity: wishlist Subject: ITP: r-cran-gggenes -- Draw Gene Arrow Maps in 'ggplot2' Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-gggenes Version : 0.4.1 Upstream Author : David Wilkins * URL : https://cran.r-project.org/package=gggenes * License : GPL-2 Programming Lang: GNU R Description : Draw Gene Arrow Maps in 'ggplot2' Provides a 'ggplot2' geom and helper functions for drawing gene arrow maps. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-gggenes
Bug#993273: ITP: virify -- finds viruses in metagenomic and metatranscriptomic data
Package: wnpp Severity: wishlist Subject: ITP: virify -- finds viruses in metagenomic and metatranscriptomic data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: virify Version : 0.3.0 Upstream Author : Martín Beracochea * URL : https://github.com/EBI-Metagenomics/emg-viral-pipeline * License : Apache-2.0 Programming Lang: Python Description : finds viruses in metagenomic and metatranscriptomic data This pipeline is run when there is an interest in finding viruses in a sample but one does not really know what to look for. The sequences provides all RNA sequences or all DNA sequences that it could find, likely somehow helped biochemically to increase chances to find the viral DNA/RNA, not the host's DNA/RNA, but any such enrichment is not ultimately required. Just sequence more, aka "deeper". Once this analysis is run, one will likely define PCR tests for the virus(es) identified. . VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by the European Bioinformatics Institute. . VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs. , The pipeline is implemented and available in CWL and Nextflow. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/med-team/virify
Bug#993268: ITP: mashmap -- mapping whole genomes or long reads (PacBio/ONT) to reference
Package: wnpp Severity: wishlist Subject: ITP: mashmap -- mapping whole genomes or long reads (PacBio/ONT) to reference Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: mashmap Version : 2.0 Upstream Author : Copyright: * URL : https://github.com/marbl/MashMap * License : PD Programming Lang: C Description : mapping whole genomes or long reads (PacBio/ONT) to reference MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using k-mers. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Minimizers and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined using the given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mashmap
Bug#993267: ITP: virsorter2 -- classifier to detect DNA and RNA virus genomes
Package: wnpp Severity: wishlist Subject: ITP: virsorter2 -- classifier to detect DNA and RNA virus genomes Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: virsorter2 Version : 2.2.3 Upstream Author : Jiarong Guo * URL : https://github.com/jiarong/VirSorter2 * License : GPL-2.0 Programming Lang: Python Description : classifier to detect DNA and RNA virus genomes VirSorter is a customizable pipeline to identify viral sequences from (meta)genomic data. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/med-team/virsorter2
Bug#993226: ITP: r-other-virfinder -- identifying viral sequences from metagenomic data
Package: wnpp Severity: wishlist Subject: ITP: r-other-virfinder -- identifying viral sequences from metagenomic data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-other-virfinder Version : 1.1 Upstream Author : Jie Ren, Nathan Ahlgren, Jed Fuhrman, Fengzhu Sun * URL : https://github.com/jessieren/VirFinder * License : GPL-2+ Programming Lang: GNU R Description : identifying viral sequences from metagenomic data The package provides functions to predict viral sequences in a fasta file. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-other-virfinder
Bug#992720: ITP: r-bioc-apeglm -- Approximate posterior estimation for GLM coefficients
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-apeglm -- Approximate posterior estimation for GLM coefficients Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-apeglm Version : 1.14.0+ds Upstream Author : Anqi Zhu * URL : https://bioconductor.org/packages/apeglm/ * License : GPL-2 Programming Lang: GNU R Description : Approximate posterior estimation for GLM coefficients apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-apeglm
Bug#992717: ITP: r-cran-emdbook -- Support Functions and Data for "Ecological Models and Data"
Package: wnpp Severity: wishlist Subject: ITP: r-cran-emdbook -- Support Functions and Data for "Ecological Models and Data" Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-emdbook Version : 1.3.12 Upstream Author : Copyright: FIXME-2020 Ben Bolker, * URL : https://cran.r-project.org/package=emdbook * License : GPL-2 Programming Lang: GNU R Description : Support Functions and Data for "Ecological Models and Data" Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-emdbook
Bug#992714: ITP: r-cran-rcppnumerical -- 'Rcpp' Integration for Numerical Computing Libraries
Package: wnpp Severity: wishlist Subject: ITP: r-cran-rcppnumerical -- 'Rcpp' Integration for Numerical Computing Libraries Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-rcppnumerical Version : 0.4 Upstream Author : Yixuan Qiu, * URL : https://cran.r-project.org/package=RcppNumerical * License : GPL-2+ Programming Lang: GNU R Description : 'Rcpp' Integration for Numerical Computing Libraries A collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with 'Rcpp'. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-rcppnumerical
Bug#992713: ITP: r-cran-rcppnumerical -- 'Rcpp' Integration for Numerical Computing Libraries
Package: wnpp Severity: wishlist Subject: ITP: r-cran-rcppnumerical -- 'Rcpp' Integration for Numerical Computing Libraries Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-rcppnumerical Version : 0.4 Upstream Author : Yixuan Qiu, * URL : https://cran.r-project.org/package=RcppNumerical * License : GPL-2+ Programming Lang: GNU R Description : 'Rcpp' Integration for Numerical Computing Libraries A collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with 'Rcpp'. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-rcppnumerical
Bug#992709: ITP: r-bioc-ggbio -- Visualization tools for genomic data
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-ggbio -- Visualization tools for genomic data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-ggbio Version : 1.40.0 Upstream Author : Tengfei Yin, * URL : https://bioconductor.org/packages/ggbio/ * License : Artistic-2.0 Programming Lang: GNU R Description : Visualization tools for genomic data The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-ggbio
Bug#992632: ITP: r-bioc-degnorm -- DegNorm: degradation normalization for RNA-seq data
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-degnorm -- DegNorm: degradation normalization for RNA-seq data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-degnorm Version : 1.2.0+ds Upstream Author : Bin Xiong and Ji-Ping Wang * URL : https://bioconductor.org/packages/DegNorm/ * License : LGPL-3.0+ Programming Lang: GNU R Description : DegNorm: degradation normalization for RNA-seq data This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-degnorm
Bug#992630: ITP: r-bioc-degnorm -- DegNorm: degradation normalization for RNA-seq data
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-degnorm -- DegNorm: degradation normalization for RNA-seq data Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-degnorm Version : 1.2.0+ds Upstream Author : Bin Xiong and Ji-Ping Wang * URL : https://bioconductor.org/packages/DegNorm/ * License : LGPL-3.0+ Programming Lang: GNU R Description : DegNorm: degradation normalization for RNA-seq data This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-degnorm
Bug#992494: ITP: pytest-ordering -- order execution of build-tests with pytest
Package: wnpp Severity: wishlist Subject: ITP: pytest-ordering -- order execution of build-tests with pytest Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: pytest-ordering Version : 0.6 Upstream Author : Copyright: Frank Tobia * URL : https://github.com/ftobia/pytest-ordering/ * License : MIT Programming Lang: Python Description : order execution of build-tests with pytest When a test can only be successful if another test was already succeeding, then it is of interest to run the more specialised tests later. Another motivation may be to order tests by some workflow so, the human following the outputs does not need to mentally switch between them too much. Whatever it may be, this package allows you to specify the execution order of your build tests. Remark: This package is maintained by Debian Python Team at https://salsa.debian.org/python-team/pacakges/pytest-ordering
Bug#992104: ITP: q2-diversity-lib -- QIIME2 plugin to expose diversity metrics/measures as actions
Package: wnpp Severity: wishlist Subject: ITP: q2-diversity-lib -- QIIME2 plugin to expose diversity metrics/measures as actions Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: q2-diversity-lib Version : 2020.11.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2 plugin to expose diversity metrics/measures as actions QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) . QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline. . QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/q2-diversity-lib
Bug#992037: ITP: python-pillow -- successor of Python Image Library (PIL)
Package: wnpp Severity: wishlist Subject: ITP: python-pillow -- successor of Python Image Library (PIL) Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-pillow Version : 8.3.1 Upstream Author : by Secret Labs AB * URL : https://github.com/python-pillow/Pillow * License : HPND Programming Lang: Python Description : successor of Python Image Library (PIL) The PIL was _the_ library to use to craft images with Python. But last updates happened in 2010. All developments since then went into this "friendly fork". Remark: This package is maintained by Debian Python Team at https://salsa.debian.org/python-team/packages/python-pillow
Bug#992007: ITP: q2-longitudinal -- QIIME2 plugin for longitudinal studies and paired comparisons
Package: wnpp Severity: wishlist Subject: ITP: q2-longitudinal -- QIIME2 plugin for longitudinal studies and paired comparisons Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: q2-longitudinal Version : 2020.11.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2 plugin for longitudinal studies and paired comparisons QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) . QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline. . QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/q2-longitudinal
Bug#992005: ITP: q2-composition -- QIIME2 plugin for Compositional statistics
Package: wnpp Severity: wishlist Subject: ITP: q2-composition -- QIIME2 plugin for Compositional statistics Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: q2-composition Version : 2020.11.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2 plugin for Compositional statistics QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) . QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline. . QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/q2-composition
Bug#991992: ITP: q2-diversity -- QIIME2 plugin for core diversity analysis
Package: wnpp Severity: wishlist Subject: ITP: q2-diversity -- QIIME2 plugin for core diversity analysis Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: q2-diversity Version : 2020.11.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2 plugin for core diversity analysis QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) . QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline. . QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/q2-diversity
Bug#991990: ITP: q2-emperor -- QIIME2 plugin for display of ordination plots
Package: wnpp Severity: wishlist Subject: ITP: q2-emperor -- QIIME2 plugin for display of ordination plots Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: q2-emperor Version : 2020.11.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2 plugin for display of ordination plots QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) . QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline. . QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/q2-emperor
Bug#991983: ITP: q2-gneiss -- QIIME2 plugin for Compositional Data Analysis and Visualization
Package: wnpp Severity: wishlist Subject: ITP: q2-gneiss -- QIIME2 plugin for Compositional Data Analysis and Visualization Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: q2-gneiss Version : 2020.11.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2 plugin for Compositional Data Analysis and Visualization QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) . QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline. . QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/q2-quality-filter
Bug#991981: python3-skbio: package installs .../dist-packages/benchmarks/..
Package: python3-skbio Version: 0.5.6-4 Severity: normal Dear Maintainer, Unpacking python3-skbio (0.5.6-4) ... dpkg: error processing archive /var/cache/apt/archives/python3-skbio_0.5.6-4_amd64.deb (--unpack): trying to overwrite '/usr/lib/python3/dist-packages/benchmarks/__init__.py', which is also in package cutesv 1.0.11-1 dpkg-deb: error: paste subprocess was killed by signal (Broken pipe) Errors were encountered while processing: /var/cache/apt/archives/python3-skbio_0.5.6-4_amd64.deb I just fixed cutesv, leaving this as a reminder to also fix skbio. Cheers, Steffen
Bug#991862: ITP: shark -- Mapping-free filtering of useless RNA-Seq reads
Package: wnpp Severity: wishlist Subject: ITP: shark -- Mapping-free filtering of useless RNA-Seq reads Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: shark Version : 1.2.0 Upstream Author : Copyright:2019 Tamara Ceccato, Luca Denti, Yuri Pirola, Marco Previtali * URL : https://algolab.github.io/shark/ * License : GPL-3.0+ Programming Lang: C Description : Mapping-free filtering of useless RNA-Seq reads For RNA-seq, to determine the identity of a gene that is described by a read, one maps it against a reference genome. Now, such may not be available, or one has an special variant that would make it too lossy to perform the mapping. This tool allows to filter for those reads that have a redundancy between themselves, i.e. that occur more frequently and are hence likely to be meaningful for subsequent comparisons. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/debian/shark
Bug#991859: ITP: r-bioc-basilisk -- Freezing Python Dependencies Inside Bioconductor Packages
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-basilisk -- Freezing Python Dependencies Inside Bioconductor Packages Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-basilisk Version : 1.4.0 Upstream Author : Aaron Lun, * URL : https://bioconductor.org/packages/basilisk/ * License : GPL-3 Programming Lang: GNU R Description : Freezing Python Dependencies Inside Bioconductor Packages Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-basilisk
Bug#991858: ITP: r-bioc-basilisk.utils -- Basilisk Installation Utilities
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-basilisk.utils -- Basilisk Installation Utilities Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-basilisk.utils Version : 1.4.0+ds Upstream Author : Aaron Lun * URL : https://bioconductor.org/packages/basilisk.utils/ * License : GPL-3 Programming Lang: GNU R Description : Basilisk Installation Utilities Implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. This allows us to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed package binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-basilisk.utils
Bug#991825: ITP: r-bioc-organismdbi -- smooth interfacing of different database packages
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-organismdbi -- smooth interfacing of different database packages Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-organismdbi Version : 1.34.0 Upstream Author : Marc Carlson, Hervé Pagès, Martin Morgan, Valerie Obenchain * URL : https://bioconductor.org/packages/OrganismDbi/ * License : Artistic-2.0 Programming Lang: GNU R Description : smooth interfacing of different database packages The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-organismdbi
Bug#991824: ITP: r-bioc-dir.expiry -- Managing Expiration for Cache Directories
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-dir.expiry -- Managing Expiration for Cache Directories Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-bioc-dir.expiry Version : 1.0.0 Upstream Author : Aaron Lun * URL : https://bioconductor.org/packages/dir.expiry/ * License : GPL-3 Programming Lang: GNU R Description : Managing Expiration for Cache Directories Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-bioc-dir.expiry
Bug#991814: ITP: ragtag -- library for scaffolding and improving modern genome assemblies
Package: wnpp Severity: wishlist Subject: ITP: ragtag -- library for scaffolding and improving modern genome assemblies Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: ragtag Version : 2.0.1 Upstream Author : Copyright: Michael Alonge * URL : https://github.com/malonge/RagTag * License : MIT Programming Lang: Python Description : library for scaffolding and improving modern genome assemblies RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: . * Homology-based misassembly correction * Homology-based assembly scaffolding and patching * Scaffold merging . The package provides the Python3 module. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/med-team/ragtag
Bug#991805: ITP: dask-jobqueue -- deploy Dask on Job Qeueing systems
Package: wnpp Severity: wishlist Subject: ITP: dask-jobqueue -- deploy Dask on Job Qeueing systems Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: dask-jobqueue Version : 0.7.3 Upstream Author : , Anaconda, Inc. and contributors * URL : https://github.com/dask/dask-jobqueue * License : custom Programming Lang: Python Description : deploy Dask on Job Qeueing systems Dask is an environment/library to compute on files that may be larger than the computer reading them and to optionally accelerate that challenge by distributing the computational workfload across many machines on the network. This package knows how different queueing systems (like slurm, pbs, sun grid engine) allow their jobs to communicate, also between hosts. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/python-team/packages/dask-jobqueue
Bug#991786: ITP: python-billard -- fork of the Python 2.7 multiprocessing package
Package: wnpp Severity: wishlist Subject: ITP: python-billard -- fork of the Python 2.7 multiprocessing package Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-billard Version : 3.6.4.0 Upstream Author : , R Oudkerk and Contributors * URL : https://github.com/celery/billiard * License : License: Programming Lang: Python Description : fork of the Python 2.7 multiprocessing package The multiprocessing package billard is a renamed and updated version of R Oudkerk's pyprocessing package. This standalone variant draws its fixes/improvements from python-trunk and provides additional bug fixes and improvements. . Also, it is a fork of the multiprocessing backport package by Christian Heims. It includes the no-execv patch contributed by R. Oudkerk. And the Pool improvements previously located in Celery. Billiard is used in and is a dependency for Celery and is maintained by the Celery team. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/python-team/packages/python-billard
Bug#991769: ITP: python-ml-collections -- collections designed for ML usecases
Package: wnpp Severity: wishlist Subject: ITP: python-ml-collections -- collections designed for ML usecases Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-ml-collections Version : 0.1.0 Upstream Author : xx-20yy ML Collections Authors * URL : https://github.com/google/ml_collections * License : Apache-2.0 Programming Lang: Python Description : collections designed for ML usecases The package provices two classes called ConfigDict and FrozenConfigDict that are "dict-like" data structures with dot access to nested elements. Together, they are supposed to be used as a main way of expressing configurations of experiments and models. . Features: * Dot-based access to fields. * Locking mechanism to prevent spelling mistakes. * Lazy computation. * FrozenConfigDict() class which is immutable and hashable. * Type safety. * "Did you mean" functionality. * Human readable printing (with valid references and cycles), using valid YAML format. * Fields can be passed as keyword arguments using the ** operator. . There are two exceptions to the strong type-safety of the ConfigDict. int values can be passed in to fields of type float. In such a case, the value is type-converted to a float before being stored. Similarly, all string types (including Unicode strings) can be stored in fields of type str or unicode. Remark: This package is maintained by Debian Python Team at https://salsa.debian.org/python-team/packages/python-ml-collections
Bug#991557: ITP: broad-catch -- design sets of primers to identify genomes
Package: wnpp Severity: wishlist Subject: ITP: broad-catch -- design sets of primers to identify genomes Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: broad-catch Version : 1.4.0 Upstream Author : Hayden Metsky * URL : https://github.com/broadinstitute/catch * License : MIT Programming Lang: Python Description : design sets of primers to identify genomes CATCH (Compact Aggregation of Targets for Comprehensive Hybridization) is a Python package for designing probe sets to use for nucleic acid capture of diverse sequence. . * Comprehensive coverage: CATCH accepts any collection of unaligned sequences — typically whole genomes of all known genetic diversity of one or more microbial species. It designs oligo sequences that guarantee coverage of this diversity, enabling rapid design of exhaustive probe sets for customizable targets. * Compact designs: CATCH can design with a specified constraint on the number of oligos (e.g., array size). It searches a space of probe sets, which may pool many species, to find an optimal design. This allows its designs to scale well with known genetic diversity, and also supports cost-effective applications. * Flexibility: CATCH supports applications beyond whole genome enrichment, such as differential identification of species. It allows blacklisting sequence from the design (e.g., background in microbial enrichment), supports customized models of hybridization, enables weighting the sensitivity for different species, and more. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/catch
Bug#991490: ITP: r-cran-r2html -- HTML Exportation for R Objects
Package: wnpp Severity: wishlist Subject: ITP: r-cran-r2html -- HTML Exportation for R Objects Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: r-cran-r2html Version : 2.3.2 Upstream Author : Eric Lecoutre, * URL : https://cran.r-project.org/package=R2HTML * License : GPL-2+ Programming Lang: GNU R Description : HTML Exportation for R Objects Includes HTML function and methods to write in an HTML file. Thus, making HTML reports is easy. Includes a function that allows redirection on the fly, which appears to be very useful for teaching purpose, as the student can keep a copy of the produced output to keep all that he did during the course. Package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for 'Sweave' allows to parse HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-r2html
Bug#991315: ITP: python-immutabledict -- immutable wrapper around dictionaries (fork of frozendict)
Package: wnpp Severity: wishlist Subject: ITP: python-immutabledict -- immutable wrapper around dictionaries (fork of frozendict) Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: python-immutabledict Version : 2.1.0 Upstream Author : Copyright: Corentin Garcia * URL : https://github.com/corenting/immutabledict/ * License : MIT Programming Lang: Python Description : immutable wrapper around dictionaries (fork of frozendict) Immutabledict implements the complete mapping interface and can be used as a drop-in replacement for dictionaries where immutability is desired. The immutabledict constructor mimics dict, and all of the expected interfaces (iter, len, repr, hash, getitem) are provided. Note that an immutabledict does not guarantee the immutability of its values, so the utility of hash method is restricted by usage. . The only difference is that the copy() method of immutable takes variable keyword arguments, which will be present as key/value pairs in the new, immutable copy. Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/debian/python-immutabledict
Bug#991277: ITP: cutesv -- comprehensive discovery of structural variations of genomic sequences
Package: wnpp Severity: wishlist Subject: ITP: cutesv -- comprehensive discovery of structural variations of genomic sequences Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: cutesv Version : 1.0.11 Upstream Author : JiangTao * URL : https://github.com/tjiangHIT/cuteSV * License : MIT Programming Lang: Python Description : comprehensive discovery of structural variations of genomic sequences Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. . cuteSV is a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/cutesv
