Bug#1002142: shasta: FTBFS: PythonModule.cpp:40:29: error: expected primary-expression before ‘(’ token
Hello, Thank you for the report. I will have a look at whether or not I can reproduce this, and will fix accordingly. Kind regards, Shayan -- Shayan Doust - 201427418 Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395 Note: all emails sent by me are signed with my PGP key. signature.asc Description: PGP signature
Bug#901973: ITP: node-destroy -- Node.js stream destruction utility, with quirk handling
Control: owner -1 Shayan Doust -- Shayan Doust - 201427418 Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395 Note: all emails sent by me are signed with my PGP key. signature.asc Description: PGP signature
Bug#901973: ITP: node-destroy -- Node.js stream destruction utility, with quirk handling
Hello, I will be packaging send-transform soon and this is a dependency. Any progress with this? If not, I'll package node-destroy. Kind regards, Shayan Doust On Wed, 20 Jun 2018 16:33:13 -0400 Zebulon McCorkle wrote: > Package: wnpp > Severity: wishlist > Owner: Zebulon McCorkle > > * Package name: node-destroy > Version : 1.0.4 > Upstream Author : Jonathan Ong > * URL : https://github.com/stream-utils/destroy > * License : MIT > Programming Lang: Node.js > Description : Node.js stream destruction utility, with quirk handling > > Maintained in pkg-javascript-devel > > -- Shayan Doust - 201427418 Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395 Note: all emails sent by me are signed with my PGP key. signature.asc Description: PGP signature
Bug#990011: ITP: r-cran-xmlr -- Read, Write and Work with 'XML' Data
Package: wnpp Severity: wishlist X-Debbugs-Cc: he...@shayandoust.me Subject: ITP: r-cran-xmlr -- Read, Write and Work with 'XML' Data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-xmlr Version : 0.1.2 Upstream Author : Per Nyfelt, * URL : https://cran.r-project.org/package=xmlr * License : MIT Programming Lang: GNU R Description : Read, Write and Work with 'XML' Data 'XML' package for creating and reading and manipulating 'XML', with an object model based on 'Reference Classes'. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-xmlr
Bug#989850: ITP: python-flask-talisman -- HTTP security headers for Flask
Package: wnpp Severity: wishlist X-Debbugs-Cc: he...@shayandoust.me Subject: ITP: python-flask-talisman -- HTTP security headers for Flask Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: python-flask-talisman Version : 0.7.0 Upstream Author : Google Inc. * URL : https://github.com/GoogleCloudPlatform/flask-talisman * License : Apache-2.0 Programming Lang: Python Description : HTTP security headers for Flask Talisman is a small Flask extension that handles setting HTTP headers that can help protect against a few common web application security measures. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/flask-talisman
Bug#986386: ITP: r-cran-performanceanalytics -- GNU R Econometric Tools for Performance and Risk Analysis
Package: wnpp Severity: wishlist X-Debbugs-Cc: he...@shayandoust.me Subject: ITP: r-cran-performanceanalytics -- GNU R Econometric Tools for Performance and Risk Analysis Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-performanceanalytics Version : 2.0.4 Upstream Author : Brian G. Peterson, * URL : https://cran.r-project.org/package=PerformanceAnalytics * License : GPL-2 Programming Lang: GNU R Description : GNU R Econometric Tools for Performance and Risk Analysis Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-performanceanalytics
Bug#986042: texlive-base: Post-installation script fails with exit status 1
Hello Norbert,
Thanks for your prompt reply.
In fact, running dpkg-reconfigure libpaper1, I get the "system defaults paper
size" selection menu, to which I select a4.
I do not get the extra tl-paper output after this. Perhaps this is a
side-effect to my unconfigured texlive-base installation.
Running the script you gave me, I get:
=== xdvi ===
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
=== pdftex ===
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
=== dvips ===
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
=== dvipdfmx ===
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
=== context ===
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
There is currently no urgency with getting this figured out quickly -
texlive-base and all the needed components
work perfectly fine in my chroot environment. It's just very odd, and I'm not
sure what is broken on my system.
Kind regards.
On Mon, Mar 29, 2021 at 09:28:32AM +0900, Norbert Preining wrote:
> On Sun, 28 Mar 2021, Shayan Doust wrote:
> > Running "dpkg-reconfigure libpaper1" again, and then trying again for
> > texlive-base, spits out the
> > same issue I've reported.
>
> Interesting, I don't see that in my case ...
>
> $ pkg-reconfigure libpaper1
> Replacing config file /etc/papersize with new version
> tl-paper: setting paper size for context to letter:
> /var/lib/texmf/tex/context/user/cont-sys-paper.tex
> tl-paper: setting paper size for dvipdfmx to letter:
> /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
> tl-paper: setting paper size for dvips to letter:
> /var/lib/texmf/dvips/config/config-paper.ps
> tl-paper: setting paper size for pdftex to letter:
> /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
> tl-paper: setting paper size for xdvi to letter:
> /var/lib/texmf/xdvi/XDvi-paper
> Running mktexlsr. This may take some time... done.
> Building format(s) --refresh.
> This may take some time...
> ...
> $
>
> Can you please do
> for i in xdvi|pdftex|dvips|dvipdfmx|context ; do
> echo "=== $i ==="
> tl-paper get $i
> done
> and send the output? And then we continue debugging. It fails in
> tl-paper get $prg
> calls and thus it seems something in your configurations files for one
> of these programs (or all) seem to be broken.
>
> Best
>
> Norbert
>
> --
> PREINING Norbert https://www.preining.info
> Fujitsu Research Labs + IFMGA Guide + TU Wien + TeX Live + Debian Dev
> GPG: 0x860CDC13 fp: F7D8 A928 26E3 16A1 9FA0 ACF0 6CAC A448 860C DC13
--
Shayan Doust - 201427418
Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395
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Bug#986042: texlive-base: Post-installation script fails with exit status 1
Hello Hilmar,
The content of /etc/papersize is a4.
Running "dpkg-reconfigure libpaper1" again, and then trying again for
texlive-base, spits out the
same issue I've reported.
Kind regards
On Sun, Mar 28, 2021 at 04:53:56PM +0200, Hilmar Preuße wrote:
> Am 28.03.2021 um 15:58 teilte Shayan Doust mit:
>
> Hi,
>
> > Setting up texlive-binaries (2020.20200327.54578-7) ...
> > update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin
> > (xdvi.bin) in auto mode
> > update-alternatives: using /usr/bin/bibtex.original to provide
> > /usr/bin/bibtex (bibtex) in auto mode
> > Setting up lmodern (2.004.5-6.1) ...
> > Setting up texlive-base (2020.20210202-3) ...
> > mktexlsr: Updating /var/lib/texmf/ls-R-TEXLIVEDIST...
> > mktexlsr: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
> > mktexlsr: Updating /var/lib/texmf/ls-R...
> > mktexlsr: Done.
> > Can't use string ("2") as an ARRAY ref while "strict refs" in use at
> > /usr/bin/tl-paper line 112.
> > Can't use string ("2") as an ARRAY ref while "strict refs" in use at
> > /usr/bin/tl-paper line 112.
> > Can't use string ("2") as an ARRAY ref while "strict refs" in use at
> > /usr/bin/tl-paper line 112.
> > Can't use string ("2") as an ARRAY ref while "strict refs" in use at
> > /usr/bin/tl-paper line 112.
> > Can't use string ("2") as an ARRAY ref while "strict refs" in use at
> > /usr/bin/tl-paper line 112.
> > dpkg: error processing package texlive-base (--configure):
> > installed texlive-base package post-installation script subprocess
> > returned error exit status 1
> > Processing triggers for desktop-file-utils (0.26-1) ...
> > Processing triggers for gnome-menus (3.36.0-1) ...
> > Processing triggers for libc-bin (2.31-10) ...
> > Processing triggers for man-db (2.9.4-2) ...
> > Processing triggers for install-info (6.7.0.dfsg.2-6) ...
> > Processing triggers for mailcap (3.69) ...
> > Processing triggers for fontconfig (2.13.1-4.2) ...
> > Processing triggers for tex-common (6.16) ...
> > texlive-base is not ready, delaying updmap-sys call
> > update-language: texlive-base not installed and configured, doing nothing!
> > texlive-base is not ready, skipping fmtutil --all call
> > Errors were encountered while processing:
> > texlive-base
> > E: Sub-process /usr/bin/dpkg returned an error code (1)
> >
> What is the content of /etc/papersize? Does running "dpkg-reconfigure
> libpaper1" and then try again solve your issue?
>
> Hilmar
> --
> sigfault
>
>
--
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Bug#986042: texlive-base: Post-installation script fails with exit status 1
Package: texlive-base
Version: 2020.20210202-3
Severity: normal
X-Debbugs-Cc: he...@shayandoust.me
Dear Maintainer,
All tex packages were working fine for me until a couple of days ago,
when I did an apt update. I realised that texlive-base could not
configure itself. Unfortunately, no logs on that.
I did however purge and remove any stray files/directories belonging to
anything tex on my machine. I then proceeded to apt install texlive-base
to see if I can rectify the issue with a reinstall. I get the following
output:
[TRUNCATED]
Setting up texlive-binaries (2020.20200327.54578-7) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin
(xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex
(bibtex) in auto mode
Setting up lmodern (2.004.5-6.1) ...
Setting up texlive-base (2020.20210202-3) ...
mktexlsr: Updating /var/lib/texmf/ls-R-TEXLIVEDIST...
mktexlsr: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
mktexlsr: Updating /var/lib/texmf/ls-R...
mktexlsr: Done.
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
Can't use string ("2") as an ARRAY ref while "strict refs" in use at
/usr/bin/tl-paper line 112.
dpkg: error processing package texlive-base (--configure):
installed texlive-base package post-installation script subprocess returned
error exit status 1
Processing triggers for desktop-file-utils (0.26-1) ...
Processing triggers for gnome-menus (3.36.0-1) ...
Processing triggers for libc-bin (2.31-10) ...
Processing triggers for man-db (2.9.4-2) ...
Processing triggers for install-info (6.7.0.dfsg.2-6) ...
Processing triggers for mailcap (3.69) ...
Processing triggers for fontconfig (2.13.1-4.2) ...
Processing triggers for tex-common (6.16) ...
texlive-base is not ready, delaying updmap-sys call
update-language: texlive-base not installed and configured, doing nothing!
texlive-base is not ready, skipping fmtutil --all call
Errors were encountered while processing:
texlive-base
E: Sub-process /usr/bin/dpkg returned an error code (1)
I am not quite sure what is going on here. I also attempted to remove
this package and install the texlive-full metapackage, however that
fails due to the cascading issue relating to texlive-base not being
configured & failing.
Any help and suggestions is much appreciated. I am not sure if this is
related to the package or not - it seems to be with the postinst script.
I am currently running on a system where sources.list is set to
bullseye.
Please feel free to write back if you require any further information,
or if there is something trivial and non-package related, to which I
understand this bug report being closed.
##
minimal input file
##
other files
##
List of ls-R files
lrwxrwxrwx 31 root 17 Feb 20:30 /usr/share/texlive/texmf-dist/ls-R ->
/var/lib/texmf/ls-R-TEXLIVEDIST
##
Config files
.rw-r--r-- 475 root 28 Mar 14:47 /etc/texmf/web2c/texmf.cnf
Warning: fmtutil.cnf cannot be found with kpsewhich!
Warning: updmap.cfg cannot be found with kpsewhich!
Warning: language.dat cannot be found with kpsewhich!
##
Files in /etc/texmf/web2c/
.rw-r--r-- 283 root 12 Feb 22:13 mktex.cnf
.rw-r--r-- 475 root 28 Mar 14:47 texmf.cnf
##
md5sums of texmf.d
ca40c66f144b4bafc3e59a2dd32ecb9c /etc/texmf/texmf.d/00debian.cnf
-- System Information:
Debian Release: bullseye/sid
APT prefers testing-security
APT policy: (500, 'testing-security'), (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.10.0-4-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8),
LANGUAGE=en_GB:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages texlive-base depends on:
ii debconf [debconf-2.0] 1.5.75
ii libpaper-utils 1.1.28+b1
ii sensible-utils 0.0.14
ii tex-common 6.16
ii texlive-binaries 2020.20200327.54578-7
ii ucf3.0043
ii xdg-utils 1.1.3-4
Versions of packages texlive-base recommends:
ii lmodern 2.004.5-6.1
Versions of packages texlive-base suggests:
ii evince [postscript-viewer] 3.38.2-1
ii ghostscript [postscript-viewer] 9.53.3~dfsg-7
ii perl-tk 1:804.035-0.1+b1
pn xpdf | pdf-viewer
pn xzdec
Bug#980671: bmtk: FTBFS: Signal: Aborted (6)
Hello, I've finally had the chance to look at this, and I have also not been able to reproduce this issue using sbuild. Kind regards, Shayan Doust On Fri, 22 Jan 2021 08:29:25 +0100 Andreas Tille wrote: > Control: severity -1 important > > On Thu, Jan 21, 2021 at 10:49:20PM +0100, Étienne Mollier wrote: > > Control: tag -1 moreinfo > > Control: tag -1 unreproducible > > ... > > Anyone else is able to reproduce the problem ? > > The package builds nicely in my pbuilder chroot as well. So I'm > setting severity from serious to important. > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > OpenPGP_0x6D7D441919D02395.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital signature
Bug#977391: ITP: r-cran-bma -- Bayesian Model Averaging
Package: wnpp Severity: wishlist Subject: ITP: r-cran-bma -- Bayesian Model Averaging Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-bma Version : 3.18.14 Upstream Author : Adrian Raftery , * URL : https://cran.r-project.org/package=BMA * License : GPL-2+ Programming Lang: GNU R Description : Bayesian Model Averaging Package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-bma
Bug#960906: shiny-server -- put Shiny web apps online
Hello Andreas, As of now, there still stands a single dependency called [node-http-proxy]. Unfortunately, it looks like it relies on socket.io, which has not been packaged yet. Kind regards, Shayan Doust [node-http-proxy]: https://salsa.debian.org/js-team/node-http-proxy/ OpenPGP_0x6D7D441919D02395.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital signature
Bug#972392: ITP: r-cran-bios2cor -- GNU R from Biological Sequences and Simulations to Correlation
Package: wnpp Severity: wishlist Subject: ITP: r-cran-bios2cor -- GNU R from Biological Sequences and Simulations to Correlation Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-bios2cor Version : 2.2 Upstream Author : Bruck Taddese, * URL : https://cran.r-project.org/package=Bios2cor * License : GPL-2+ Programming Lang: GNU R Description : GNU R from Biological Sequences and Simulations to Correlation Analysis Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) . An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) . This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-bios2cor
Bug#971177: intake: FTBFS: TypeError: 'NoneType' object is not iterable
Control: tags -1 help This seems to be a tricky one that I never spotted and just managed to reproduce (although, I do not understand why during my packaging efforts, this error did not occur whereas now it does). It seems like intake, specifically its gui component, relies on [panel], which is not yet packaged. However, panel relies on Bokeh, where if I remember correctly is currently a mess[2] and doesn't seem like any progress has been made. So, I am not too sure what to do here. Kind regards, Shayan Doust [panel]: https://pypi.org/project/panel/ [2]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=756017 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#971699: ITP: r-cran-circular -- GNU R Circular Statistics
Package: wnpp Severity: wishlist Subject: ITP: r-cran-circular -- GNU R Circular Statistics Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-circular Version : 0.4 Upstream Author : Ulric Lund , * URL : https://cran.r-project.org/package=circular * License : GPL-2 Programming Lang: GNU R Description : GNU R Circular Statistics Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-circular
Bug#970829: covtobed FTCBFS: uses the build architecture compiler
Hello Helmut, Acknowledged. Thank you for this. Kind regards, Shayan Doust On Thu, 24 Sep 2020 06:15:21 +0200 Helmut Grohne wrote: > Source: covtobed > Version: 1.1.2+dfsg-2 > Tags: patch > User: debian-cr...@lists.debian.org > Usertags: ftcbfs > > covtobed fails to cross build from source, because debian/rules uses the > build architecture compiler as a make default. Please consider letting > dpkg's buildtools.mk set up the CXX variable to make covtobed cross > buildable. I'm attaching a patch for your convenience. > > Helmut 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello again Andreas, This [commit] now rectifies the build issue for r-cran-prophet. I can build r-cran-prophet successfully after re-building r-cran-rstan with the new patch. Within r-cran-prophet: $ autopkgtest . -- null [TRUNCATED] /usr/bin/ld: cannot find -lStanHeaders collect2: error: ld returned 1 exit status make: *** [/usr/share/R/share/make/shlib.mk:6: sourceCpp_2.so] Error 1 -- 2. Error: (unknown) (@test_stan_functions.R#9) - $ operator is invalid for atomic vectors Backtrace: 1. base::tryCatch(...) 2. base:::tryCatchList(expr, classes, parentenv, handlers) 3. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. value[[3L]](cond) 5. rstan::expose_stan_functions(...) == testthat results === [ OK: 160 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 2 ] 1. Error: (unknown) (@test_prophet.R#9) 2. Error: (unknown) (@test_stan_functions.R#9) There exists some failed tests, however 160 pass! Kind regards, Shayan Doust [commit]: https://salsa.debian.org/r-pkg-team/r-cran-rstan/-/commit/7351289242ba080c112b1c15784e57f154a79076 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello Andreas,
I see the error within r-cran-prophet's build.
It seems like this issue stems from r-cran-rstan (as the call stack shows).
Specifically:
$ grep -r "system.file(\"lib\""
R/plugin.R:RcppParallel_pkg_libs <- system.file("lib", .Platform$r_arch,
R/plugin.R:rstan_StanServices <- system.file("lib", .Platform$r_arch,
"libStanServices.a",
I believe the first line (regarding RcppParallel_pkg_libs) is of concern and the
cause as again, the library location assumption is wrong.
I will write a patch for this too, and I'll test anymore findings.
Kind regards,
Shayan Doust
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Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello Andreas, The [commit] is now pushed for r-cran-rcppparallel, which fixes the "TBB library not found" error thrown for r-cran-rstanarm. Just a note that I did not make it through the entire build process. I gave the build 40 mins before giving up. Compiling r-cran-stanarm used almost all of my 4 GB of RAM on my test server and it resorted to using most of my swap space, so I am unable to test for any other issues. I've left this bug open. Kind regards, Shayan Doust [commit]: https://salsa.debian.org/r-pkg-team/r-cran-rcppparallel/-/commit/e8fcee92d68a420ca1441479661d74add27f519e 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#963392: [Help] Re: r-cran-rstanarm: FTBFS: error: (converted from warning) TBB library not found.
Hello Andreas, Yes, this does seem like a local issue to r-cran-rcppparallel. tbb and variants are loaded when r-cran-rcppparallel is imported, as seen in [hooks.R]. The function of interest is 'tbbLibPath()', which seems to depict tbb library path. With some more investigation, you can see this function within [build.R]. You can see for all supported platforms apart from Windows and Sparc systems, it seems like it expects the library to be situated under lib/ (due to the first argument used within system.file()). I'll try to write a simple patch for this hook file. For a Debian package, this assumption for library location is plain wrong. Kind regards, Shayan Doust [hooks.R]: https://github.com/RcppCore/RcppParallel/blob/b216ba27dcbd3c523932bd918b6dd0b1b08d3566/R/hooks.R#L8 [build.R]: https://github.com/RcppCore/RcppParallel/blob/b216ba27dcbd3c523932bd918b6dd0b1b08d3566/R/build.R#L66 On Tue, 8 Sep 2020 20:32:53 +0200 Andreas Tille wrote: > Control: tags -1 help > > Hi, > > any help why TBB is not found? I think this issue is actually causes by > r-cran-rcppparallel since the code copy of libtbb was removed there - > but it seems to not provide the Debian packaged lib properly. > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#970452: ITP: argh -- C++ header-only command line processing library
Package: wnpp Severity: wishlist Subject: ITP: argh -- C++ header-only command line processing library Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: argh Version : 1.3.1+ds Upstream Author : Adi Shavit * URL : https://github.com/adishavit/argh * License : BSD-3-Clause Programming Lang: C Description : C++ header-only command line processing library So many different command line processing libraries out there and none of them just work! Some bring their whole extended family of related and unrelated external dependencies (yes, I'm looking at you Boost). Some require quirky syntax and/or very verbose setups that sacrifice simplicity for the generation of a cute usage message and validation. Many come to dominate your main() file and yet others do not build on multiple plaforms - for some even their own tests and trivial usage cause crashes on some systems. Argh! . If you're writing a highly-sophisticated command line tool, then Boost.Program_options and its kind might give you many advanced options. However, if you need to get up and running quickly, effectively and with minimal fuss, give the single header-file argh a try. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/argh
Bug#970389: ITP: r-cran-textdata -- GNU R Download and Load Various Text Datasets
Package: wnpp Severity: wishlist Subject: ITP: r-cran-textdata -- GNU R Download and Load Various Text Datasets Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-textdata Version : 0.4.1 Upstream Author : Emil Hvitfeldt , * URL : https://cran.r-project.org/package=textdata * License : MIT Programming Lang: GNU R Description : GNU R Download and Load Various Text Datasets Provides a framework to download, parse, and store text datasets on the disk and load them when needed. Includes various sentiment lexicons and labeled text data sets for classification and analysis. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-textdata
Bug#969639: ITP: r-cran-poissonbinomial -- GNU R Efficient Computation of Ordinary and Generalized Poisson
Package: wnpp Severity: wishlist Subject: ITP: r-cran-poissonbinomial -- GNU R Efficient Computation of Ordinary and Generalized Poisson Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-poissonbinomial Version : 1.1.2 Upstream Author : Copyright: Florian Junge * URL : https://cran.r-project.org/package=PoissonBinomial * License : GPL-2+ Programming Lang: GNU R Description : GNU R Efficient Computation of Ordinary and Generalized Poisson Binomial Distributions Efficient implementations of multiple exact and approximate methods as described in Hong (2013) , Biscarri, Zhao & Brunner (2018) and Zhang, Hong & Balakrishnan (2018) for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-poissonbinomial
Bug#968716: ITP: shasta -- nanopore whole genome assembly (binaries and scripts)
Package: wnpp Severity: wishlist Subject: ITP: shasta -- nanopore whole genome assembly (binaries and scripts) Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: shasta Version : 0.5.1 Upstream Author : Chan Zuckerberg Initiative * URL : https://github.com/chanzuckerberg/shasta * License : Expat Programming Lang: C++ Description : nanopore whole genome assembly (binaries and scripts) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the executable binaries (tools) and accommodating scripts. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/shasta
Bug#968565: ITP: r-cran-cmstatr -- GNU R Statistical Methods for Composite Material Data
Package: wnpp Severity: wishlist Subject: ITP: r-cran-cmstatr -- GNU R Statistical Methods for Composite Material Data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-cmstatr Version : 0.7.0 Upstream Author : Stefan Kloppenborg , * URL : https://cran.r-project.org/package=cmstatr * License : AGPL-3 Programming Lang: GNU R Description : GNU R Statistical Methods for Composite Material Data An implementation of the statistical methods commonly used for advanced composite materials in aerospace applications. This package focuses on calculating basis values (lower tolerance bounds) for material strength properties, as well as performing the associated diagnostic tests. This package provides functions for calculating basis values assuming several different distributions, as well as providing functions for non-parametric methods of computing basis values. Functions are also provided for testing the hypothesis that there is no difference between strength and modulus data from an alternate sample and that from a "qualification" or "baseline" sample. For a discussion of these statistical methods and their use, see the Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4). Additional details about this package are available in the paper by Kloppenborg (2020, ). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-cmstatr
Bug#968191: ITP: damapper -- long read to reference genome mapping tool
Package: wnpp Severity: wishlist Subject: ITP: damapper -- long read to reference genome mapping tool Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: damapper Version : 0.0+git20200322.b2c9d7f Upstream Author : Dr. Eugene W. Myers * URL : https://github.com/thegenemyers/DAMAPPER * License : BSD-3-Clause Programming Lang: C Description : long read to reference genome mapping tool Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/damapper
Bug#966611: pelican: New upstream version available
Package: pelican Version: 4.0.1+dfsg-1 Severity: wishlist The version packaged that is within unstable, testing and stable is 4.0.1, however upstream has, at this time, generated a tarball for 4.2.0. As a regular user of Pelican, would you kindly consider packaging the latest upstream tarball (4.2.0)? Some new features, such as live browser reload and inline SVGs would come really handy. Kind regards, Shayan Doust
Bug#966559: ITP: r-cran-ksamples -- GNU R K-Sample Rank Tests and their Combinations
Package: wnpp Severity: wishlist Subject: ITP: r-cran-ksamples -- GNU R K-Sample Rank Tests and their Combinations Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-ksamples Version : 1.2 Upstream Author : Fritz Scholz * URL : https://cran.r-project.org/package=kSamples * License : GPL-2+ Programming Lang: GNU R Description : GNU R K-Sample Rank Tests and their Combinations Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples. Also analyzed are 2 x t contingency tables and their blocked combinations using the Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous confidence bounds for shift parameters. A plotting function compares tail probabilities obtained under asymptotic approximation with those obtained via simulation or exact calculations. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-ksamples
Bug#966558: ITP: fast5-research -- command line executable tools for python3-fast5-research
Package: wnpp Severity: wishlist Subject: ITP: fast5-research -- command line executable tools for python3-fast5-research Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: fast5-research Version : 1.2.21 Upstream Author : Oxford Nanopore Technologies Ltd. * URL : https://github.com/nanoporetech/fast5_research * License : MPL-2.0 Programming Lang: Python Description : command line executable tools for python3-fast5-research Python fast5 reading and writing functionality provided by ONT Research. This package comprises an API to HDF containers used by the research groups within Oxford Nanopore Technologies. It complements the official API. Reading and writing of read files can be accomplished as well as reading of bulk .fast5 files. It reads interface bulk .fast5 files for extracting reads, channel states, voltage, etcetera. . This package contains the executables and command line tools for python3-fast5-research. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/fast5-research
Bug#958010: yubikey-personalization: ftbfs with GCC-10
Hello, Any rough timeframe as to when this FTBFS is fixed? Kind regards, Shayan Doust 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#966267: ITP: google-auth-oauthlib -- oauthlib integration with google-auth
Package: wnpp Severity: wishlist Subject: ITP: google-auth-oauthlib -- oauthlib integration with google-auth Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: google-auth-oauthlib Version : 0.4.1 Upstream Author : , 2016, 2017, 2019 Google Inc. * URL : https://pypi.org/project/google-auth-oauthlib/ * License : Apache-2.0 Programming Lang: Python Description : oauthlib integration with google-auth This library provides oauthlib integration for use with google-auth. Remark: This package is maintained by Debian Python Modules Team at https://salsa.debian.org/python-team/modules/google-auth-oauthlib
Bug#966266: ITP: r-cran-suppdists -- GNU R Supplementary Distributions
Package: wnpp Severity: wishlist Subject: ITP: r-cran-suppdists -- GNU R Supplementary Distributions Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-suppdists Version : 1.1 Upstream Author : Bob Wheeler, * URL : https://cran.r-project.org/package=SuppDists * License : GPL-2+ Programming Lang: GNU R Description : GNU R Supplementary Distributions Ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-suppdists
Bug#966204: ITP: relacy -- meticulous synchronization algorithm verifier for relaxed memory models
Package: wnpp Severity: wishlist Subject: ITP: relacy -- meticulous synchronization algorithm verifier for relaxed memory models Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: relacy Version : 0.0+git20191025.acc09bb Upstream Author : Dmitry S. Vyukov * URL : https://github.com/dvyukov/relacy * License : BSD-3-Clause Programming Lang: C Description : meticulous synchronization algorithm verifier for relaxed memory models Relacy Race Detector is a tool for efficient execution of unit tests for synchronization algorithms written in C++0x. Every user thread is represented as a fiber (ucontext). Every time only one fiber is running, and special scheduler controls interleaving between fibers. With random scheduler it just executes numerous amount of various interleavings between threads. With full search scheduler or context-bound scheduler it systematically executes all possible interleavings between threads. While executing particular interleaving it makes exhaustive verification of various aspects of execution (races, accesses to freed memory etc). . If no errors found then verification terminates when particular number of interleavings are verified (for random scheduler), or when all possible interleavings are verified (for full search scheduler). If error is found then tool outputs execution history which leads to error and terminates. Physically Relacy Race Detector is a header-only library for C++98. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/relacy
Bug#965226: ITP: r-cran-dslabs -- Data Science Labs
Package: wnpp Severity: wishlist Subject: ITP: r-cran-dslabs -- Data Science Labs Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-dslabs Version : 0.7.3 Upstream Author : Rafael A. Irizarry * URL : https://cran.r-project.org/package=dslabs * License : Artistic-2.0 Programming Lang: GNU R Description : Data Science Labs Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-dslabs
Bug#965079: ITP: graphbin -- refined binning of metagenomic contigs using assembly graphs
Package: wnpp Severity: wishlist Subject: ITP: graphbin -- refined binning of metagenomic contigs using assembly graphs Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: graphbin Version : 1.1 Upstream Author : Graphbin Project * URL : https://github.com/Vini2/GraphBin * License : GPL-2.0+ Programming Lang: Python Description : refined binning of metagenomic contigs using assembly graphs GraphBin is a NGS data-based metagenomic contig bin refinment tool that makes use of the contig connectivity information from the assembly graph to bin contigs. It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis-binned contigs and predict the labels of contigs which are discarded due to short length. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/graphbin
Bug#964976: ITP: tao-config -- C++ header-only library that reads config files and produces a JSON value
Package: wnpp Severity: wishlist Subject: ITP: tao-config -- C++ header-only library that reads config files and produces a JSON value Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: tao-config Version : 0.0+git20200604.84a7383 Upstream Author : Dr. Colin Hirsch * URL : https://github.com/taocpp/config * License : Expat Programming Lang: C Description : C++ header-only library that reads config files and produces a JSON value C++ header-only library that reads config files based on JSON and JAXN formats and in turn, produces a single JSON valur as a result. . Its features are as follows: 1. JAXN syntax with extensions (backwards compatible with JSON). 2. JAXN data model (JSON extended with binary data and non-finites). 3. Meta data, all sub-values are annotated with filename and position. 4. Copy, reference, replace and delete anything in the JSON structure. 5. Multiple ways to read and parse other config and data files. 6. Uses environmental variables and the output of arbitrary shell commands. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/tao-config
Bug#964801: ITP: gneiss -- data analysis and visualisation toolbox for high dimensional proportions
Package: wnpp Severity: wishlist Subject: ITP: gneiss -- data analysis and visualisation toolbox for high dimensional proportions Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: gneiss Version : 0.4.6 Upstream Author : gneiss development team * URL : https://github.com/biocore/gneiss * License : BSD-3-Clause Programming Lang: Python Description : data analysis and visualisation toolbox for high dimensional proportions Canonically pronounced as 'nice', gneiss is a compositional data analysis and visualisation toolbox designed for analysing high dimensional proportions. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/gneiss
Bug#756017: Partial packaging
Hello Diane et. al., I am packaging gneiss[1], where one of its dependency is Bokeh. What is the progress of Bokeh at this time? Additionally, is this a WIP? Kind regards, Shayan Doust [1]: https://salsa.debian.org/med-team/gneiss On Sat, 14 Sep 2019 00:22:04 +0200 Pierre-Elliott =?utf-8?B?QsOpY3Vl?= wrote: > Le mardi 08 septembre 2015 à 22:25:11-0700, Diane Trout a écrit : > > I have a packaging tree that I'm using at: > > https://github.com/detrout/python-bokeh > > > > It can't be released to Debian until we find a solution for building > > BokehJS. > > (And that it also needs a jquery 2.1.1). > > > > But at least its a start. > > Dear Diane, > > It seems that bokeh 1.3.4 ships a version of BokehJS that is > non-minified and ready-to-use. Wouldn't that be a correct solution for > an initial packaging, even though one could wish to finish the proper > javascript package in a second time? > > With best regards, > > -- > Pierre-Elliott Bécue > GPG: 9AE0 4D98 6400 E3B6 7528 F493 0D44 2664 1949 74E2 > It's far easier to fight for one's principles than to live up to them. 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#964392: ITP: tao-json -- multifunctional and zero-dependency C++ header-only JSON library
Package: wnpp Severity: wishlist Subject: ITP: tao-json -- multifunctional and zero-dependency C++ header-only JSON library Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: tao-json Version : 1.0.0~beta.11 Upstream Author : Dr. Colin Hirsch * URL : https://github.com/taocpp/json * License : Expat Programming Lang: C++ Description : multifunctional and zero-dependency C++ header-only JSON library taoJSON is a zero-dependency C++ header-only JSON library that provides a generic Value Class, uses Type Traits to interoperate with C++ types, uses an Events Interface to convert to and from JSON, JAXN, CBOR, MsgPack and UBJSON, and much, much more. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/tao-json
Bug#964202: ITP: mecat2 -- ultra-fast and accurate de novo assembly tools for SMRT reads
Package: wnpp Severity: wishlist Subject: ITP: mecat2 -- ultra-fast and accurate de novo assembly tools for SMRT reads Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: mecat2 Version : 0.0+git20200428.f54c542 Upstream Author : Chuan-Le Xiao * URL : https://github.com/xiaochuanle/MECAT2 * License : GPL-3 Programming Lang: C Description : ultra-fast and accurate de novo assembly tools for SMRT reads An improved version of MECAT. It is an ultra-fast and accurate mapping and error correcting de novo assembly tools for single molecula sequencing (SMRT) reads. MECAT2 consists of the following three modules: 1. mecat2map: a fast and accurate alignment tool for SMRT reads. 2. mecat2cns: correct noisy reads based on their pairwise overlaps. 3. fsa: a string graph based assembly tool. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mecat2
Bug#963981: ITP: dextractor -- (d)extractor and compression command library
Package: wnpp Severity: wishlist Subject: ITP: dextractor -- (d)extractor and compression command library Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: dextractor Version : 1.0 Upstream Author : Dr. Eugene W. Myers (EWM) * URL : https://github.com/thegenemyers/DEXTRACTOR * License : BSD-3-Clause Programming Lang: C Description : (d)extractor and compression command library Dextractor commands allow one to pull exactly and only the information needed for assembly and reconstruction from the source HDF5 files produced by the PacBio RS II sequencer, or from the source BAM files produced by the PacBio Sequel sequencer. . For each of the three extracted file types -- fasta, quiva, and arrow -- the library contains commands to compress the given file type, and to decompress it, which is a reversible process delivering the original uncompressed file. The compressed .fasta files, with the extension .dexta, consume 1/4 byte per base. The compressed .quiva files, with the extension .dexqv, consume 1.5 bytes per base on average, and the compressed .arrow files, with the extension .dexar, consume 1/4 byte per base . For more information, please view the available documentation at https://github.com/thegenemyers/DEXTRACTOR Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/dextractor
Bug#963565: ITP: marginphase -- simultaneous haplotyping and genotyping
Package: wnpp Severity: wishlist Subject: ITP: marginphase -- simultaneous haplotyping and genotyping Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: marginphase Version : 0.0+git20181109.cdf139e Upstream Author : Benedict Paten * URL : https://github.com/benedictpaten/marginPhase * License : Expat Programming Lang: C Description : simultaneous haplotyping and genotyping MarginPhase is a program for simultaneous haplotyping and genotyping. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/marginphase
Bug#963218: ITP: libpll-2 -- Phylogenetic Likelihood Library 2
Package: wnpp Severity: wishlist Subject: ITP: libpll-2 -- Phylogenetic Likelihood Library 2 Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: libpll-2 Version : 0.3.2 Upstream Author : Tomas Flouri * URL : https://github.com/xflouris/libpll-2 * License : AGPL-3+ Programming Lang: C Description : Phylogenetic Likelihood Library 2 PLL is a highly optimised, parallelised software library to ease the development of new software tools dealing with phylogenetic inference. . Among the function included in PLL are parsing multiple sequence alignments (MSA) from PHYLIP and FASTA files, reading Newick trees, performing topological moves such as SPR and NNI, model optimisation, likelihood evaluation and partitioned analysis by assigning different substitution models to each partition of the MSA. PLL fully implements the GTR nucleotide substitution model for DNA data and a number of models for aminoacid data. . libpll-2 is the new official fork of libpll. It implements site repeats to speed up computations. . This package contains the dynamic library. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/libpll-2
Bug#963160: ITP: intake -- lightweight package for finding and investigating data
Package: wnpp Severity: wishlist Subject: ITP: intake -- lightweight package for finding and investigating data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: intake Version : 0.6.0 Upstream Author : Anaconda Inc., Intake contributors * URL : https://github.com/intake/intake * License : BSD-2-clause Programming Lang: Python Description : lightweight package for finding and investigating data Intake is a leightweight set of tools for loading and sharing data in data science projects. Intake helps you: 1. Load data from a variety of formats into containers you already know, like Pandas dataframes, Python lists, NumPy arrays and more. 2. Convert boilerplate data loading code into reusable intake plugins. 3. Describe data sets in catalog files for easy reuse and sharing between projects and with others. 4. Share catalog information (and data sets) over the network with the Intake server. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/intake
Bug#962977: ITP: nanofilt -- filtering and trimming of long read sequencing data
Package: wnpp Severity: wishlist Subject: ITP: nanofilt -- filtering and trimming of long read sequencing data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: nanofilt Version : 2.6.0 Upstream Author : Wouter De Coster * URL : https://github.com/wdecoster/nanofilt * License : GPL-3 Programming Lang: Python Description : filtering and trimming of long read sequencing data Filtering and trimming of long read sequencing data. Filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. . Intended to be used: 1. directly after fastq extraction. 2. prior to mapping. 3. in a stream between extraction and mapping. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/nanofilt
Bug#962850: haskell-platform: New upstream version
Package: haskell-platform Version: 2014.2.0.0.debian8 Severity: wishlist Hello, I am not too informed on Haskell but I'm not sure if haskell-platform[1] still (or if it did) follow Stackage LTS, however the latest version is now available labelled as Haskell 16.0 featuring the newer ghc-8.8.3[2]. Kind regards, Shayan Doust [1]: https://downloads.haskell.org/~platform/ [2]: https://www.stackage.org/lts-16.0 -- System Information: Debian Release: 10.4 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.19.0-8-amd64 (SMP w/8 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages haskell-platform depends on: ii alex 3.2.4-4 ii cabal-install2.2.0.0-2 ii ghc [libghc-xhtml-dev] 8.4.4+dfsg1-3 pn ghc-haddock ii happy1.19.9-6 ii hscolour 1.24.4-2+b2 ii libghc-async-dev 2.2.1-2+b2 ii libghc-attoparsec-dev0.13.2.2-6+b1 ii libghc-case-insensitive-dev 1.2.0.11-3+b2 ii libghc-fgl-dev 5.6.0.0-4+b1 ii libghc-gluraw-dev2.0.0.4-2+b2 ii libghc-glut-dev 2.7.0.14-2+b2 ii libghc-hashable-dev 1.2.7.0-5+b1 ii libghc-haskell-src-dev 1.0.3.0-2+b2 ii libghc-html-dev 1.0.1.2-15+b2 ii libghc-http-dev 1:4000.3.12-4+b2 ii libghc-hunit-dev 1.6.0.0-2+b2 ii libghc-network-dev 2.6.3.6-1+b2 ii libghc-opengl-dev3.0.2.2-2+b2 ii libghc-openglraw-dev 3.3.1.0-2+b2 ii libghc-parallel-dev 3.2.2.0-1+b2 ii libghc-primitive-dev 0.6.4.0-2+b2 ii libghc-quickcheck2-dev 2.11.3-1+b2 ii libghc-random-dev1.1-7+b2 ii libghc-regex-base-dev0.93.2-13+b2 ii libghc-regex-compat-dev 0.95.1-12+b2 ii libghc-regex-posix-dev 0.95.2-11+b2 ii libghc-split-dev 0.2.3.3-2+b2 ii libghc-syb-dev 0.7-3+b2 pn libghc-transformers-dev ii libghc-unordered-containers-dev 0.2.9.0-2+b2 ii libghc-vector-dev0.12.0.1-8+b2 ii libghc-zlib-dev 0.6.2-2+b2 haskell-platform recommends no packages. Versions of packages haskell-platform suggests: pn haskell-platform-doc pn haskell-platform-prof -- debconf-show failed
Bug#962822: ITP: bmtk -- development package for building, simulating and analysing large-scale networks
Package: wnpp Severity: wishlist Subject: ITP: bmtk -- development package for building, simulating and analysing large-scale networks Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: bmtk Version : 0.0.7 Upstream Author : Allen Institute * URL : https://github.com/AllenInstitute/bmtk * License : BSD-3-Clause Programming Lang: Python Description : development package for building, simulating and analysing large-scale networks The brain modelling toolkit is a software development package for building, simulating and analysing large-scale networks of different levels of resolution. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/bmtk
Bug#962544: ITP: enlighten -- a console progress bar module for Python3
Package: wnpp Severity: wishlist Subject: ITP: enlighten -- a console progress bar module for Python3 Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: enlighten Version : 1.5.2 Upstream Author : , Avram Lubkin * URL : https://github.com/Rockhopper-Technologies/enlighten * License : MPL-2.0 Programming Lang: Python Description : a console progress bar module for Python3 Enlighten progress bar is a console progress bar module for Python3 which allows writing for stdout and stderr without any redirection. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/enlighten
Bug#962417: ITP: pll-modules -- high level modules for the low level phylogenetic likelihood library (devel)
Package: wnpp Severity: wishlist Subject: ITP: pll-modules -- high level modules for the low level phylogenetic likelihood library (devel) Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: pll-modules Version : 0.0+git20170809.d6cc565 Upstream Author : , 2016, Diego Darriba * URL : https://github.com/ddarriba/pll-modules * License : AGPL-3+ Programming Lang: C Description : high level modules for the low level phylogenetic likelihood library (devel) This package provides high level modules for the low level phylogenetic likelihood library. . This package contains the static library and header files. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/pll-modules
Bug#962057: ITP: covtobed -- convert the coverage track from a BAM file into a BED file
Package: wnpp Severity: wishlist Subject: ITP: covtobed -- convert the coverage track from a BAM file into a BED file Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: covtobed Version : 1.1.2 Upstream Author : Giovanni Birolo and Andrea Telatin * URL : https://github.com/telatin/covtobed * License : Expat Programming Lang: C Description : convert the coverage track from a BAM file into a BED file Reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/covtobed
Bug#944029: ITP: megahit -- ultra-fast and memory-efficient meta-genome assembler
Package: wnpp Severity: wishlist Subject: ITP: megahit -- ultra-fast and memory-efficient meta-genome assembler Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: megahit Version : 1.2.9 Upstream Author : The University of Hong Kong & L3 Bioinformatics Limited * URL : https://github.com/voutcn/megahit * License : GPL-3 Programming Lang: C Description : ultra-fast and memory-efficient meta-genome assembler Megahit is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/megahit
Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)
Hello Andreas, Thanks for the reminder. I have not had the chance to look at this again yet but eager enough to have made it the thing I will look at again now. Kind regards, Shayan Doust
Bug#936681: gwyddion: Python2 removal in sid/bullseye
Hello, Just a notice to those who read this: it seems like with the python2 -> python3 migration, python-gtk2-dev becomes redundant and should be avoided. I will try contact upstream to see if this is a possible change to incorporate into their workflow as any future releases will probably be big and therefore more time has to be spent re-doing any patchwork. Kind regards, Shayan Doust signature.asc Description: OpenPGP digital signature
Bug#941280: ITP: bcalm -- de Bruijn compaction in low memory
Package: wnpp Severity: wishlist Subject: ITP: bcalm -- de Bruijn compaction in low memory Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: bcalm Version : 2.2.1 Upstream Author : INRIA <https://inria.fr/> * URL : https://github.com/GATB/bcalm * License : Expat Programming Lang: C Description : de Bruijn compaction in low memory A bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. . This is the parallel version of the BCALM software using gatb-core library. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/bcalm
Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)
Hello Andreas, This is new territory - I have spent some time looking at this and so far I could only reproduce all of what was already mentioned above. I will later go more in-depth and try using mem profiling / debugging and some trial and error to try figure out why this gets a segmentation fault because this issue is really annoying and needs rectifying. Kind regards, Shayan Doust
Bug#940559: ITP: simka -- comparative metagenomics method dedicated to NGS datasets
Package: wnpp Severity: wishlist Subject: ITP: simka -- comparative metagenomics method dedicated to NGS datasets Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: simka Version : 1.5.1 Upstream Author : Inria * URL : https://github.com/GATB/simka * License : AGPL-3 Programming Lang: C Description : comparative metagenomics method dedicated to NGS datasets Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/simka
Bug#806214: Status of build time test suites of tree-puzzle
Hello Andreas, > Would you mind pinging upstream about this? I have no idea about their > release schedule. Version 5.3~rc16 is out for quite some while but may > be its the right moment to approach them. I'll notify them. I agree, even this particular release candidate has been out for a while. Anything useful or any replies I will also CC or forward to this mailing list. Kind regards, Shayan Doust On 05/09/2019 06:27, Andreas Tille wrote: > Hi Shayan, > > On Thu, Sep 05, 2019 at 01:45:36AM +0100, Shayan Doust wrote: >> Some investigative work. I also compiled a clean copy directly from the >> upstream website to prevent any sort of contamination and to rule out >> possible upstream fault and then a packaging build attempt (debhelper 11). > > Thanks a lot for diving into this. > >>> I have some gut feeling that the test files for comparison do not >>> really fit the proper result. >> >> This may be the case, but I am having a hard time getting the same >> output as >> https://buildd.debian.org/status/fetch.php?pkg=tree-puzzle&arch=all&ver=5.2-11&stamp=1539685923&raw=0 >> >> I have just ran qp-pure-prot.test as an example: >> >> 113,114c86,87 >> < WARNING: Result of chi-square test may not be valid because of >> < small maximum likelihood frequencies and short sequence length! >> --- >>> WARNING: Result of chi-square test may not be valid because of small >>> maximum likelihood frequencies and short sequence length! >> >> * Diffs like this indicate formatting faults which are easy to rectify, >> or remove as a whole. >> >> * The first line of the test output file contains TEST-PUZZLE and the >> version number. This version number (5.3.rc16) is not visible in the >> upstream expected output file, so diff will of course display this as a >> delta. >> >> * There is a higher verbosity of paragraphed description / output in the >> test's newly-generated results file compared to what upstream has. Maybe >> upstream is running an older / more obselete version of the program? >> >> * From what I can see, the numbers seem to match for the most part, but >> upstream has introduced chi2-value column which is not present in the >> expected results file. >> >> For instance, running qp-pure-bin.test. Here is a small slice of my output: >> >> 194c169 >> < (bipartition with sequences in input order : number of times seen (and >> ratio)) >> --- >>> (bipartition with sequences in input order : number of times seen) >> 196,197c171,172 >> < *..** : 1000 (1.000) >> < *...* : 1000 (1.000) >> --- >>> *..** : 1000 >>> *...* : 1000 >> 201c176 >> < (bipartition with sequences in input order : number of times seen (and >> ratio)) >> --- >>> (bipartition with sequences in input order : number of times seen) >> >> Ratios seem to have been added to the test. Scanning through all the >> other test binaries and their outputs, my values seem to match up to >> what is expected regardless of the issues above. >> >> So next I decided to see when the tests directory was added. This >> happened to be version 5.2. Quickly testing a couple of test binaries, >> they run successfully. It seems like to me that the expected test >> results file introduced in 5.2 were just never updated to 5.3~rc16. > > This matches perfectly my suspicion after a way less deep inspection. > Thanks for confirming. > >> I am >> not sure why your build log is different in terms of value. Maybe >> upstream modified the current release candidate and version (some do >> this). I will keep this updated with anything else that I spot or comes >> to mind. > > Would you mind pinging upstream about this? I have no idea about their > release schedule. Version 5.3~rc16 is out for quite some while but may > be its the right moment to approach them. > >> Kind regards, > > Thanks again for your very valuable contribution > > Andreas. > >> On Mon, 8 Jul 2019 21:26:02 +0200 Andreas Tille wrote: >>> Hi, >>> >>> after switching tree-puzzle debhelper level to 9 I was cheating around >>> the build time test suite via >>> >>> override_dh_auto_test: >>> # unfortunately most tests are failing for the moment >>> # the issue is documented in >>> # debian/patches/patch_test_results.patch >>> # and needs to be discussed with upstream >>> dh_auto_test || true >>> >>> The rat
Bug#806214: Status of build time test suites of tree-puzzle
Hello Andreas, Some investigative work. I also compiled a clean copy directly from the upstream website to prevent any sort of contamination and to rule out possible upstream fault and then a packaging build attempt (debhelper 11). > I have some gut feeling that the test files for comparison do not > really fit the proper result. This may be the case, but I am having a hard time getting the same output as https://buildd.debian.org/status/fetch.php?pkg=tree-puzzle&arch=all&ver=5.2-11&stamp=1539685923&raw=0 I have just ran qp-pure-prot.test as an example: 113,114c86,87 < WARNING: Result of chi-square test may not be valid because of < small maximum likelihood frequencies and short sequence length! --- > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! * Diffs like this indicate formatting faults which are easy to rectify, or remove as a whole. * The first line of the test output file contains TEST-PUZZLE and the version number. This version number (5.3.rc16) is not visible in the upstream expected output file, so diff will of course display this as a delta. * There is a higher verbosity of paragraphed description / output in the test's newly-generated results file compared to what upstream has. Maybe upstream is running an older / more obselete version of the program? * From what I can see, the numbers seem to match for the most part, but upstream has introduced chi2-value column which is not present in the expected results file. For instance, running qp-pure-bin.test. Here is a small slice of my output: 194c169 < (bipartition with sequences in input order : number of times seen (and ratio)) --- > (bipartition with sequences in input order : number of times seen) 196,197c171,172 < *..** : 1000 (1.000) < *...* : 1000 (1.000) --- > *..** : 1000 > *...* : 1000 201c176 < (bipartition with sequences in input order : number of times seen (and ratio)) --- > (bipartition with sequences in input order : number of times seen) Ratios seem to have been added to the test. Scanning through all the other test binaries and their outputs, my values seem to match up to what is expected regardless of the issues above. So next I decided to see when the tests directory was added. This happened to be version 5.2. Quickly testing a couple of test binaries, they run successfully. It seems like to me that the expected test results file introduced in 5.2 were just never updated to 5.3~rc16. I am not sure why your build log is different in terms of value. Maybe upstream modified the current release candidate and version (some do this). I will keep this updated with anything else that I spot or comes to mind. Kind regards, Shayan Doust On Mon, 8 Jul 2019 21:26:02 +0200 Andreas Tille wrote: > Hi, > > after switching tree-puzzle debhelper level to 9 I was cheating around > the build time test suite via > > override_dh_auto_test: > # unfortunately most tests are failing for the moment > # the issue is documented in > # debian/patches/patch_test_results.patch > # and needs to be discussed with upstream > dh_auto_test || true > > The rationale was that just by switching the debhelper level the build > time test suite was run at all. Most probably it was failing all the > time before and simply nobody realised this. To sort this out we need > to talk to upstream. The issue is documented in bug #806214 (bug in > CC). > > I now bumped the upstream source in Git to the latest upstream release > candidate. Since this had not changed quite some time I assume upstream > is not very rapidly pushing a final release. However, this might be the > right point in time to sort things out. > > If you check the build log of 5.2-11 at > > > https://buildd.debian.org/status/fetch.php?pkg=tree-puzzle&arch=all&ver=5.2-11&stamp=1539685923&raw=0 > > you can find > > ... > dh_auto_test || true > make -j1 check VERBOSE=1 > make[2]: Entering directory '/<>' > Making check in src > make[3]: Entering directory '/<>/src' > make[3]: Leaving directory '/<>/src' > Making check in doc > make[3]: Entering directory '/<>/doc' > make[4]: Entering directory '/<>/doc' > make[4]: Nothing to be done for 'check-am'. > make[4]: Leaving directory '/<>/doc' > make[3]: Leaving directory '/<>/doc' > Making check in data > make[3]: Entering directory '/<>/data' > make[3]: Nothing to be done for 'check'. > make[3]: Leaving directory '/<>/data' > Making check in tests > make[3]: Entering directory '/<>/tests' > make check-TESTS > make[4]: Entering directory '/<>/tests' > make[5]: Entering directory '/<>/tests' > SKIP: build-puzzle > FAIL: qp-pure-bin.test > FAIL: qp-pure-nucl.test > FAIL: qp-tn-nucl.test > FAIL: qp-hky-clock-nucl.test > FAIL: qp-hky-rhet-nucl.test > FAIL: qp-hky-rhet-clock-nucl.test > FAIL: qp-pure-prot.test > FAIL: qp-mtrev-prot.test signature.asc Description: OpenPGP digital signature
Bug#933235: ITP: fast -- framework for Heterogeneous Medical Image Computing
Package: wnpp Severity: wishlist Subject: ITP: fast -- framework for Heterogeneous Medical Image Computing Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: fast Version : 3.0.0 Upstream Author : Norwegian University of Science and Technology * URL : https://github.com/smistad/FAST * License : BSD-2-Clause Programming Lang: C Description : framework for Heterogeneous Medical Image Computing An open-source cross-platform framework with the main goal of making it easier to do processing and visualization of medical images on heterogeneous systems (CPU+GPU). Has data streaming, deep learning, high- level data management, high-performance algorithms, interoperability with Insight Toolkit & integration with existing VTK / Qt applications as well as a fast concurrent visualization. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/fast
Bug#927166: libbiod0: not installable in sid
Hello Andreas, Honestly never even heard of Dlang so I thought I'd give this a try. I decided to disect and manually experiment with the Makefile to understand this. The compilation stage works well, and this is failing at the linker stage with symbolic handling of the object files. This also tends to happen with poor linker parameters or just some plain misconfig. I am not sure what the main flag in DFLAGS does, but utilising the main flag on the compiler line in Makefile and not the linker line links the software successfully. I am not sure why a linker would need an extensive set of flags that is the same as the compiler. The only fault I now see with this is that it fails at the dh_install stage, as the debian/tmp file for me is empty. I am not sure why and I am not sure what weighing that main flag had on the linker. I decided to manually run dub and dub test and the library unit test does run successfully. The generated binary in the bin file also seems to invoke without a complaint. Those are my discoveries so far with something I've never touched before. First bug reply so I do apologise if I did violate some reply policy. Best Regards, Shayan Doust On 16/04/2019 10:55, Andreas Tille wrote: > On Mon, Apr 15, 2019 at 09:39:17PM +0200, Ralf Treinen wrote: >> Package: libbiod0 >> Version: 0.2.1-1 >> Severity: serious >> User: trei...@debia.org > ^ > @Ralf: Are you sure there is no typo in one of your scripts? > >> libbiod0 is not installable on amd64 or i386 (the only architectures >> for which this binary package exists) in sid, at least since >> 2018-10-30 : it depends on libphobos2-ldc-shared81 which does >> not exist in sid. > > My guess is that this can be simply solved by a rebuild which > is fixed by a new changelog entry in Git. > > @Matthias: > > When I try to build the current state in Git I get: > > ... > ldc2 -wi -g -relocation-model=pic -unittest -main -Icontrib/undead -L-lz -O0 > -d-debug -link-debuglib contrib/undead/cstream.o contrib/undead/stream.o > contrib/undead/doformat.o contrib/ undead/utf.o contrib/undead/*/*.o > bio/core/sequence.o bio/core/kmer.o bio/core/genotype.o bio/core/tinymap.o > bio/core/base.o bio/core/decompress.o bio/core/call.o bio/core/region.o bio/ > core/bgzf/inputstream.o bio/core/bgzf/constants.o bio/core/bgzf/block.o > bio/core/bgzf/virtualoffset.o bio/core/bgzf/compress.o bio/core/bgzf/chunk.o > bio/core/bgzf/outputstream.o bio/core/ utils/format.o > bio/core/utils/exception.o bio/core/utils/outbuffer.o bio/core/utils/stream.o > bio/core/utils/algo.o bio/core/utils/tmpfile.o bio/core/utils/memoize.o > bio/core/utils/ switchendianness.o bio/core/utils/roundbuf.o > bio/core/utils/zlib.o bio/core/utils/bylinefast.o bio/core/utils/range.o > bio/std/file/fastq.o bio/std/file/fasta.o bio/std/file/fai.o bio/std/ > genotype/maf.o bio/std/genotype/snp.o bio/std/range/splitter.o > bio/std/sff/writer.o bio/std/sff/readrange.o bio/std/sff/index.o > bio/std/sff/reader.o bio/std/sff/read.o bio/std/sff/ constants.o > bio/std/maf/reader.o bio/std/maf/block.o bio/std/maf/parser.o > bio/std/experimental/hts/logger.o bio/std/experimental/hts/pileup.o > bio/std/experimental/hts/bgzf_writer.o bio/std/experimental/hts/reads.o > bio/std/experimental/hts/bgzf.o bio/std/experimental/hts/unpack.o > bio/std/experimental/hts/constants.o bio/std/experimental/hts/hashing.o > bio/std/sff/utils/roundup.o bio/std/hts/iontorrent/flowcall.o > bio/std/hts/iontorrent/flowindex.o bio/std/hts/sam/reader.o > bio/std/hts/sam/header.o bio/std/hts/snpcallers/maq.o > bio/std/hts/snpcallers/simple.o bio/ std/hts/bam/abstractreader.o > bio/std/hts/bam/randomaccessmanager.o bio/std/hts/bam/baifile.o > bio/std/hts/bam/writer.o bio/std/hts/bam/pileup.o bio/std/hts/bam/splitter.o > bio/std/hts/bam/ tagvalue.o bio/std/hts/bam/constants.o > bio/std/hts/bam/reference.o bio/std/hts/bam/baseinfo.o > bio/std/hts/bam/readrange.o bio/std/hts/bam/referenceinfo.o > bio/std/hts/bam/multireader.o bio/ std/hts/bam/reader.o > bio/std/hts/bam/read.o bio/std/hts/bam/cigar.o bio/std/hts/bam/region.o > bio/std/hts/thirdparty/msgpack.o bio/std/hts/utils/array.o > bio/std/hts/utils/value.o bio/std/ hts/utils/samheadermerger.o > bio/std/hts/utils/graph.o bio/std/experimental/hts/bam/reader.o > bio/std/experimental/hts/bam/writer.o bio/std/experimental/hts/bam/header.o > bio/std/hts/sam/ utils/recordparser.o > bio/std/hts/sam/utils/fastrecordparser.o bio/std/hts/bam/md/core.o > bio/std/hts/bam/md/operation.o bio/std/hts/bam/md/reconstruct.o > bio/std/hts/bam/md/parse.o bio/std/ hts/bam/bai/bin.o > bio/std/hts/bam/bai/indexing.o bio/std/hts/bam/validation/alignment.o > bio/std/hts/bam/validat
Bug#932369: ITP: mmseqs2 -- ultra fast and sensitive protein search and clustering.
Package: wnpp Severity: wishlist Subject: ITP: mmseqs2 -- ultra fast and sensitive protein search and clustering. Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: mmseqs2 Version : 9 Upstream Author : Söding Lab <https://mpibpc.mpg.de/soeding> * URL : https://github.com/soedinglab/MMseqs2 * License : GPLv3 Programming Lang: C Description : ultra fast and sensitive protein search and clustering. MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 1 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mmseqs2
Bug#931826: ITP: mindthegap -- Performs detection and assembly of DNA insertion variants in NGS read datasets.
Package: wnpp Severity: wishlist Subject: ITP: mindthegap -- Performs detection and assembly of DNA insertion variants in NGS read datasets. Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: mindthegap Version : 2.2.0 Upstream Author : GATB * URL : http://github.com/GATB/MindTheGap * License : AGPL-3 Programming Lang: C Description : Performs detection and assembly of DNA insertion variants in NGS read datasets. Designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detection insertion sites, the other is the set of assembled insertions for each breakpoint. MindTheGap can also be used as a genome assembly finishing tool. It can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mindthegap
