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ExecutablesPythonR StatsJuliaOctaveSageMath
Ubuntu22.04
20.04
18.04
CoCalc Logo Icon
ExecutablesPythonR StatsJuliaOctaveSageMath
Ubuntu22.04
20.04
18.04

Executables in CoCalc (Ubuntu 22.04)

Terminal showing listing executables in CoCalc
This is a non-comprehensive list of executables available on CoCalc.
To run anything listed below, you need to either open a "Terminal" or run the command indirectly via a Jupyter notebook.
On CoCalc, you can also install or compile your own executable binaries. You have a lot of control about your own project, which is a containerized environment based on x86_64 Ubuntu Linux 22.04.

Showing 311 executables

PathInformation
/usr/bin/4ti2-zsolve
-------------------------------------------------
4ti2 version 1.6.9
Copyright 1998, 2002, 2006, 2015 4ti2 team.
4ti2 comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.
For details, see the file COPYING.
-------------------------------------------------
/usr/bin/7z

7-Zip [64] 16.02 : Copyright (c) 1999-2016 Igor Pavlov : 2016-05-21
p7zip Version 16.02 (locale=C.UTF-8,Utf16=on,HugeFiles=on,64 bits,8 CPUs Intel(R) Xeon(R) CPU @ 2.80GHz (50657),ASM,AES-NI)

Usage: 7z <command> [<switches>...] <archive_name> [<file_names>...]
       [<@listfiles...>]

<Commands>
  a : Add files to archive
  b : Benchmark
  d : Delete files from archive
  e : Extract files from archive (without using directory names)
  h : Calculate hash values for files
  i : Show information about supported formats
  l : List contents of archive
  rn : Rename files in archive
  t : Test integrity of archive
  u : Update files to archive
  x : eXtract files with full paths

<Switches>
  -- : Stop switches parsing
  -ai[r[-|0]]{@listfile|!wildcard} : Include archives
  -ax[r[-|0]]{@listfile|!wildcard} : eXclude archives
  -ao{a|s|t|u} : set Overwrite mode
  -an : disable archive_name field
  -bb[0-3] : set output log level
  -bd : disable progress indicator
  -bs{o|e|p}{0|1|2} : set output stream for output/error/progress line
  -bt : show execution time statistics
  -i[r[-|0]]{@listfile|!wildcard} : Include filenames
  -m{Parameters} : set compression Method
    -mmt[N] : set number of CPU threads
  -o{Directory} : set Output directory
  -p{Password} : set Password
  -r[-|0] : Recurse subdirectories
  -sa{a|e|s} : set Archive name mode
  -scc{UTF-8|WIN|DOS} : set charset for for console input/output
  -scs{UTF-8|UTF-16LE|UTF-16BE|WIN|DOS|{id}} : set charset for list files
  -scrc[CRC32|CRC64|SHA1|SHA256|*] : set hash function for x, e, h commands
  -sdel : delete files after compression
  -seml[.] : send archive by email
  -sfx[{name}] : Create SFX archive
  -si[{name}] : read data from stdin
  -slp : set Large Pages mode
  -slt : show technical information for l (List) command
  -snh : store hard links as links
  -snl : store symbolic links as links
  -sni : store NT security information
  -sns[-] : store NTFS alternate streams
  -so : write data to stdout
  -spd : disable wildcard matching for file names
  -spe : eliminate duplication of root folder for extract command
  -spf : use fully qualified file paths
  -ssc[-] : set sensitive case mode
  -ssw : compress shared files
  -stl : set archive timestamp from the most recently modified file
  -stm{HexMask} : set CPU thread affinity mask (hexadecimal number)
  -stx{Type} : exclude archive type
  -t{Type} : Set type of archive
  -u[-][p#][q#][r#][x#][y#][z#][!newArchiveName] : Update options
  -v{Size}[b|k|m|g] : Create volumes
  -w[{path}] : assign Work directory. Empty path means a temporary directory
  -x[r[-|0]]{@listfile|!wildcard} : eXclude filenames
  -y : assume Yes on all queries
/usr/bin/advpng
advancecomp vnone by Andrea Mazzoleni, http://www.advancemame.it
/usr/bin/ag
ag version 2.2.0

Features:
  +jit +lzma +zlib
/usr/bin/ant
Picked up _JAVA_OPTIONS: -Xms64m
Apache Ant(TM) version 1.10.12 compiled on January 17 1970
/ext/bin/nosudo/apt
                                                               
╔═════════════════════════════════════════════════════════════╗
║  ⚠  SYSTEM UTILITY NOT AVAILABLE -> USE COMPUTE SERVERS  ⚠  ║
╠═════════════════════════════════════════════════════════════╣
║ It is not possible to run this utility in a CoCalc project. ║
╟─────────────────────────────────────────────────────────────╢
║ However, you can become an admin in a 𝗖𝗢𝗠𝗣𝗨𝗧𝗘 𝗦𝗘𝗥𝗩𝗘𝗥!       ║
║ Learn more here: https://doc.cocalc.com/compute_server.html ║
╚═════════════════════════════════════════════════════════════╝
                                                               
apt 2.4.11 (amd64)
Usage: apt [options] command

apt is a commandline package manager and provides commands for
searching and managing as well as querying information about packages.
It provides the same functionality as the specialized APT tools,
like apt-get and apt-cache, but enables options more suitable for
interactive use by default.

Most used commands:
  list - list packages based on package names
  search - search in package descriptions
  show - show package details
  install - install packages
  reinstall - reinstall packages
  remove - remove packages
  autoremove - Remove automatically all unused packages
  update - update list of available packages
  upgrade - upgrade the system by installing/upgrading packages
  full-upgrade - upgrade the system by removing/installing/upgrading packages
  edit-sources - edit the source information file
  satisfy - satisfy dependency strings

See apt(8) for more information about the available commands.
Configuration options and syntax is detailed in apt.conf(5).
Information about how to configure sources can be found in sources.list(5).
Package and version choices can be expressed via apt_preferences(5).
Security details are available in apt-secure(8).
                                        This APT has Super Cow Powers.
/ext/bin/nosudo/apt-get
                                                               
╔═════════════════════════════════════════════════════════════╗
║  ⚠  SYSTEM UTILITY NOT AVAILABLE -> USE COMPUTE SERVERS  ⚠  ║
╠═════════════════════════════════════════════════════════════╣
║ It is not possible to run this utility in a CoCalc project. ║
╟─────────────────────────────────────────────────────────────╢
║ However, you can become an admin in a 𝗖𝗢𝗠𝗣𝗨𝗧𝗘 𝗦𝗘𝗥𝗩𝗘𝗥!       ║
║ Learn more here: https://doc.cocalc.com/compute_server.html ║
╚═════════════════════════════════════════════════════════════╝
                                                               
apt 2.4.11 (amd64)
Usage: apt-get [options] command
       apt-get [options] install|remove pkg1 [pkg2 ...]
       apt-get [options] source pkg1 [pkg2 ...]

apt-get is a command line interface for retrieval of packages
and information about them from authenticated sources and
for installation, upgrade and removal of packages together
with their dependencies.

Most used commands:
  update - Retrieve new lists of packages
  upgrade - Perform an upgrade
  install - Install new packages (pkg is libc6 not libc6.deb)
  reinstall - Reinstall packages (pkg is libc6 not libc6.deb)
  remove - Remove packages
  purge - Remove packages and config files
  autoremove - Remove automatically all unused packages
  dist-upgrade - Distribution upgrade, see apt-get(8)
  dselect-upgrade - Follow dselect selections
  build-dep - Configure build-dependencies for source packages
  satisfy - Satisfy dependency strings
  clean - Erase downloaded archive files
  autoclean - Erase old downloaded archive files
  check - Verify that there are no broken dependencies
  source - Download source archives
  download - Download the binary package into the current directory
  changelog - Download and display the changelog for the given package

See apt-get(8) for more information about the available commands.
Configuration options and syntax is detailed in apt.conf(5).
Information about how to configure sources can be found in sources.list(5).
Package and version choices can be expressed via apt_preferences(5).
Security details are available in apt-secure(8).
                                        This APT has Super Cow Powers.
/usr/bin/asciidoc
asciidoc 10.1.2
/usr/bin/aspell
@(#) International Ispell Version 3.1.20 (but really Aspell 0.60.8)
/usr/bin/asy
Asymptote version 2.78 [(C) 2004 Andy Hammerlindl, John C. Bowman, Tom Prince]

ENABLED OPTIONS:
V3D      3D vector graphics output
WebGL    3D HTML rendering
OpenGL   3D OpenGL rendering
SSBO     GLSL shader storage buffer objects
GSL      GNU Scientific Library (special functions)
FFTW3    Fast Fourier transforms
XDR      External Data Representation (portable binary file format for V3D)
CURL     URL support
LSP      Language Server Protocol
Readline Interactive history and editing
Sigsegv  Distinguish stack overflows from segmentation faults
GC       Boehm garbage collector
threads  Render OpenGL in separate thread

DISABLED OPTIONS:
/usr/bin/autoconf
autoconf (GNU Autoconf) 2.71
Copyright (C) 2021 Free Software Foundation, Inc.
License GPLv3+/Autoconf: GNU GPL version 3 or later
<https://gnu.org/licenses/gpl.html>, <https://gnu.org/licenses/exceptions.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by David J. MacKenzie and Akim Demaille.
/usr/bin/automake
automake (GNU automake) 1.16.5
Copyright (C) 2021 Free Software Foundation, Inc.
License GPLv2+: GNU GPL version 2 or later <https://gnu.org/licenses/gpl-2.0.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Tom Tromey <[email protected]>
       and Alexandre Duret-Lutz <[email protected]>.
/usr/local/bin/autopep8
autopep8 2.0.4 (pycodestyle: 2.10.0)
/usr/bin/bash
GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
/usr/bin/bazel
bazel 7.0.2
/ext/bin/bedtools
bedtools v2.31.1
/usr/bin/biber
biber version: 2.17
/usr/bin/bibtex
BibTeX 0.99d (TeX Live 2022/dev/Debian)
kpathsea version 6.3.4/dev
Copyright 2021 Oren Patashnik.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the BibTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the BibTeX source.
Primary author of BibTeX: Oren Patashnik.
/usr/local/bin/black
black, 23.12.1 (compiled: yes)
Python (CPython) 3.10.12
/ext/bin/bliss
bliss version 0.77
/usr/bin/bun
1.0.26
/usr/bin/bup
0.32
/usr/bin/cabal
cabal-install version 3.0.0.0
compiled using version 3.0.1.0 of the Cabal library 
/usr/local/bin/cadabra2
Info at https://cadabra.science/
Available under the terms of the GNU General Public License v3

Cadabra 2.3.9 (build 1.be7ecac dated 2022-06-26)
Copyright (C) 2001-2022  Kasper Peeters <[email protected]>
Using SymPy version 1.9
> > 
now exiting Shell...
/usr/bin/cal
   February 2024      
Su Mo Tu We Th Fr Sa  
             1  2  3  
 4  5  6  7  8  9 10  
11 12 13 14 15 16 17  
18 19 20 21 22 23 24  
25 26 27 28 29        
                      
/usr/bin/calc
C-style arbitrary precision calculator w/custom functions (version 2.12.7.2)
/ext/bin/cargo
cargo 1.71.1 (7f1d04c00 2023-07-29)
/usr/bin/cbc
Welcome to the CBC MILP Solver 
Version: 2.10.7 
Build Date: Feb 14 2022 

command line - cbc -help (default strategy 1)
Cbc version 2.10.7, build Feb 14 2022
Non default values:-
Perturbation 50 (default 100)
Presolve being done with 5 passes
Dual steepest edge steep/partial on matrix shape and factorization
density
Clpnnnn taken out of messages
If Factorization frequency default then done on size of matrix

(-)unitTest, (-)netlib or (-)netlibp will do standard tests

You can switch to interactive mode at any time so
clp watson.mps -scaling off -primalsimplex
is the same as
clp watson.mps -
scaling off
primalsimplex
Total time (CPU seconds):       0.02   (Wallclock seconds):       0.01
/usr/bin/ccache
ccache version 4.5.1
Features: file-storage http-storage redis-storage

Copyright (C) 2002-2007 Andrew Tridgell
Copyright (C) 2009-2021 Joel Rosdahl and other contributors

See <https://ccache.dev/credits.html> for a complete list of contributors.

This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 3 of the License, or (at your option) any later
version.
/usr/bin/ccmake
ccmake version 3.28.1

CMake suite maintained and supported by Kitware (kitware.com/cmake).
/ext/bin/cdo
Climate Data Operators version 2.3.0 (https://mpimet.mpg.de/cdo)
System: x86_64-conda-linux-gnu
CXX Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1697853988338/_build_env/bin/x86_64-conda-linux-gnu-c++ -fPIC -DPIC -g -O2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2023/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1697853988338/work=/usr/local/src/conda/cdo-2.3.0 -fdebug-prefix-map=/ext/miniforge2023=/usr/local/src/conda-prefix -fopenmp -pthread
CXX version : unknown
C Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1697853988338/_build_env/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2023/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1697853988338/work=/usr/local/src/conda/cdo-2.3.0 -fdebug-prefix-map=/ext/miniforge2023=/usr/local/src/conda-prefix -fopenmp -pthread -pthread
C version : unknown
F77 Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1697853988338/_build_env/bin/x86_64-conda-linux-gnu-gfortran -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2023/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1697853988338/work=/usr/local/src/conda/cdo-2.3.0 -fdebug-prefix-map=/ext/miniforge2023=/usr/local/src/conda-prefix
F77 version : GNU Fortran (conda-forge gcc 12.3.0-2) 12.3.0
Features: 62GB 8threads c++17 OpenMP45 Fortran pthreads HDF5 NC4/HDF5/threadsafe OPeNDAP udunits2 proj xml2 magics curl fftw3 sse3
Libraries: yac/3.0.1 NetCDF/4.9.2 HDF5/1.14.3(h1.14.2) proj/9.3.0 xml2/2.11.5 curl/8.5.0(h8.4.0) magics/4.14.2
CDI data types: SizeType=size_t
CDI file types: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5 nczarr 
     CDI library version : 2.3.0
 cgribex library version : 2.1.1
 ecCodes library version : 2.33.0
  NetCDF library version : 4.9.2 of Sep  1 2023 15:19:07 $
    exse library version : 1.5.0
    FILE library version : 1.9.1
/usr/bin/chafa
Chafa version 1.8.0

Features: mmx sse4.1 popcnt
Applying: mmx sse4.1 popcnt

Copyright (C) 2018-2021 Hans Petter Jansson et al.
Incl. libnsgif copyright (C) 2004 Richard Wilson, copyright (C) 2008 Sean Fox

This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/cheetah3
3.2.6
/usr/bin/chromedriver
ChromeDriver 120.0.6099.109 (3419140ab665596f21b385ce136419fde0924272-refs/branch-heads/6099@{#1483})
/usr/bin/clang
Ubuntu clang version 14.0.0-1ubuntu1.1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
/usr/bin/clang-format
Ubuntu clang-format version 14.0.0-1ubuntu1.1
/usr/bin/clasp
clasp version 3.3.5
Address model: 64-bit
libclasp version 3.3.5 (libpotassco version 1.1.0)
Configuration: WITH_THREADS=1
Copyright (C) Benjamin Kaufmann
License: The MIT License <https://opensource.org/licenses/MIT>
/usr/bin/clojure
Picked up _JAVA_OPTIONS: -Xms64m
"1.10.2"
/usr/bin/clp
Coin LP version 1.17.5, build Feb 17 2020
command line - clp -help 
No match for help - ? for list of commands
Clp takes input from arguments ( - switches to stdin)
Enter ? for list of commands or help
Clp:
/usr/local/bin/cmake
cmake version 3.26.0

CMake suite maintained and supported by Kitware (kitware.com/cmake).
/usr/bin/code
Visual Studio Code 1.85.2

Usage: code [options][paths...]

To read from stdin, append '-' (e.g. 'ps aux | grep code | code -')

Options
  -d --diff <file> <file>                    Compare two files with each
                                             other.
  -m --merge <path1> <path2> <base> <result> Perform a three-way merge by
                                             providing paths for two modified
                                             versions of a file, the common
                                             origin of both modified versions
                                             and the output file to save merge
                                             results.
  -a --add <folder>                          Add folder(s) to the last active
                                             window.
  -g --goto <file:line[:character]>          Open a file at the path on the
                                             specified line and character
                                             position.
  -n --new-window                            Force to open a new window.
  -r --reuse-window                          Force to open a file or folder in
                                             an already opened window.
  -w --wait                                  Wait for the files to be closed
                                             before returning.
  --locale <locale>                          The locale to use (e.g. en-US or
                                             zh-TW).
  --user-data-dir <dir>                      Specifies the directory that user
                                             data is kept in. Can be used to
                                             open multiple distinct instances
                                             of Code.
  --profile <profileName>                    Opens the provided folder or
                                             workspace with the given profile
                                             and associates the profile with
                                             the workspace. If the profile
                                             does not exist, a new empty one
                                             is created.
  -h --help                                  Print usage.

Extensions Management
  --extensions-dir <dir>              Set the root path for extensions.
  --list-extensions                   List the installed extensions.
  --show-versions                     Show versions of installed extensions,
                                      when using --list-extensions.
  --category <category>               Filters installed extensions by provided
                                      category, when using --list-extensions.
  --install-extension <ext-id | path> Installs or updates an extension. The
                                      argument is either an extension id or a
                                      path to a VSIX. The identifier of an
                                      extension is '${publisher}.${name}'. Use
                                      '--force' argument to update to latest
                                      version. To install a specific version
                                      provide '@${version}'. For example:
                                      '[email protected]'.
  --pre-release                       Installs the pre-release version of the
                                      extension, when using
                                      --install-extension
  --uninstall-extension <ext-id>      Uninstalls an extension.
  --enable-proposed-api <ext-id>      Enables proposed API features for
                                      extensions. Can receive one or more
                                      extension IDs to enable individually.

Troubleshooting
  -v --version                    Print version.
  --verbose                       Print verbose output (implies --wait).
  --log <level>                   Log level to use. Default is 'info'. Allowed
                                  values are 'critical', 'error', 'warn',
                                  'info', 'debug', 'trace', 'off'. You can
                                  also configure the log level of an extension
                                  by passing extension id and log level in the
                                  following format:
                                  '${publisher}.${name}:${logLevel}'. For
                                  example: 'vscode.csharp:trace'. Can receive
                                  one or more such entries.
  -s --status                     Print process usage and diagnostics
                                  information.
  --prof-startup                  Run CPU profiler during startup.
  --disable-extensions            Disable all installed extensions. This option
                                  is not persisted and is effective only when
                                  the command opens a new window.
  --disable-extension <ext-id>    Disable the provided extension. This option
                                  is not persisted and is effective only when
                                  the command opens a new window.
  --sync <on | off>               Turn sync on or off.
  --inspect-extensions <port>     Allow debugging and profiling of extensions.
                                  Check the developer tools for the connection
                                  URI.
  --inspect-brk-extensions <port> Allow debugging and profiling of extensions
                                  with the extension host being paused after
                                  start. Check the developer tools for the
                                  connection URI.
  --disable-gpu                   Disable GPU hardware acceleration.
  --disable-chromium-sandbox      Use this option only when there is
                                  requirement to launch the application as
                                  sudo user on Linux or when running as an
                                  elevated user in an applocker environment on
                                  Windows.
  --telemetry                     Shows all telemetry events which VS code
                                  collects.

Subcommands
  tunnel       Make the current machine accessible from vscode.dev or other
               machines through a secure tunnel
  serve-web    Run a server that displays the editor UI in browsers.
/usr/bin/code-server
i18next: languageChanged en
i18next: initialized {
  debug: true,
  initImmediate: true,
  ns: [ 'translation' ],
  defaultNS: [ 'translation' ],
  fallbackLng: [ 'en' ],
  fallbackNS: false,
  supportedLngs: false,
  nonExplicitSupportedLngs: false,
  load: 'all',
  preload: false,
  simplifyPluralSuffix: true,
  keySeparator: '.',
  nsSeparator: ':',
  pluralSeparator: '_',
  contextSeparator: '_',
  partialBundledLanguages: false,
  saveMissing: false,
  updateMissing: false,
  saveMissingTo: 'fallback',
  saveMissingPlurals: true,
  missingKeyHandler: false,
  missingInterpolationHandler: false,
  postProcess: false,
  postProcessPassResolved: false,
  returnNull: false,
  returnEmptyString: true,
  returnObjects: false,
  joinArrays: false,
  returnedObjectHandler: false,
  parseMissingKeyHandler: false,
  appendNamespaceToMissingKey: false,
  appendNamespaceToCIMode: false,
  overloadTranslationOptionHandler: [Function: handle],
  interpolation: {
    escapeValue: true,
    format: [Function: bound format],
    prefix: '{{',
    suffix: '}}',
    formatSeparator: ',',
    unescapePrefix: '-',
    nestingPrefix: '$t(',
    nestingSuffix: ')',
    nestingOptionsSeparator: ',',
    maxReplaces: 1000,
    skipOnVariables: true
  },
  lng: 'en',
  lowerCaseLng: true,
  resources: {
    en: { translation: [Object] },
    'zh-cn': { translation: [Object] },
    th: { translation: [Object] },
    ja: { translation: [Object] },
    ur: { translation: [Object] }
  },
  ignoreJSONStructure: true
}
4.20.0 d0215eca8804d0be5d3551c39404e336032c3141 with Code 1.85.1
/usr/bin/coffee
CoffeeScript version 2.7.0
/ext/data/homer/configureHomer.pl

	Current base directory for HOMER is /ext/data/homer/

/ext/data/homer//update.txt: Read-only file system
	Updating Settings...
Packages with name conflicts have a trailing -o, -p, or -g
Version Installed	Package	Version	Description
SOFTWARE
v4.9.1	homer	v4.11.1	Code/Executables, ontologies, motifs for HOMER
ORGANISMS
v5.10	human-o	v6.3	Homo sapiens (human) accession and ontology information
-	tomato	v6.3	Solanum lycopersicum (tomato) accession and ontology information
-	ncrassa	v6.3	Neurospora crassa (ncrassa) accession and ontology information
-	mushroom	v6.3	Agaricus bisporus (mushroom) accession and ontology information
-	bee	v6.3	Apis mellifera (bee) accession and ontology information
-	yeast-o	v6.3	Saccharomyces cerevisiae (yeast) accession and ontology information
-	seahare	v6.3	Aplysia californica (seahare) accession and ontology information
-	pig	v6.3	Sus scrofa (pig) accession and ontology information
-	chlamy	v6.3	Chlamydomonas reinhardtii (chlamy) accession and ontology information
-	ascomycetes	v6.0	Neurospora crassa (ascomycetes) accession and ontology information
-	worm-o	v6.3	Caenorhabditis elegans (worm) accession and ontology information
-	rat-o	v6.3	Rattus norvegicus (rat) accession and ontology information
-	laevis	v6.3	Xenopus laevis (laevis) accession and ontology information
-	fugu	v6.3	Takifugu rubripes (fugu) accession and ontology information
-	zebrafish-o	v6.3	Danio rerio (zebrafish) accession and ontology information
-	pombe	v6.3	Schizosaccharomyces pombe (pombe) accession and ontology information
-	rice	v6.3	Oryza sativa (rice) accession and ontology information
-	urchin	v6.3	Strongylocentrotus purpuratus (urchin) accession and ontology information
-	patens	v6.3	Physcomitrella patens (patens) accession and ontology information
-	balbc_cocci	v5.2	Balbc/J mouse and Coccidioides genome combined
-	pseudonana	v6.3	Thalassiosira pseudonana (pseudonana) accession and ontology information
-	cow	v5.4	Bos taurus (cow) accession and ontology information
-	dicty	v6.3	Dictyostelium discoideum (dicty) accession and ontology information
-	fly-o	v6.3	Drosophila melanogaster (fly) accession and ontology information
-	cocci	v6.3	Coccidioides immitis RS (cocci) accession and ontology information
-	diatom	v6.3	Phaeodactylum tricornutum (diatom) accession and ontology information
-	mosquito	v6.3	Anopheles gambiae (mosquito) accession and ontology information
-	mouse-o	v6.3	Mus musculus (mouse) accession and ontology information
-	lamprey	v6.3	Petromyzon marinus (lamprey) accession and ontology information
-	corn	v6.3	Zea mays (corn) accession and ontology information
-	selaginella	v6.3	Selaginella moellendorffii (selaginella) accession and ontology information
-	hydra	v6.3	Hydra vulgaris (hydra) accession and ontology information
-	rhesus	v6.3	Macaca mulatta (rhesus) accession and ontology information
-	zebrafinch	v6.3	Taeniopygia guttata (zebrafinch) accession and ontology information
-	arabidopsis-o	v6.3	Arabidopsis thaliana (arabidopsis) accession and ontology information
-	volvox	v6.3	Volvox carteri (volvox) accession and ontology information
-	ciona	v6.3	Ciona intestinalis (ciona) accession and ontology information
-	ciliate	v6.3	Tetrahymena thermophila (ciliate) accession and ontology information
-	frog-o	v6.3	Xenopus tropicalis (frog) accession and ontology information
-	chicken-o	v6.3	Gallus gallus (chicken) accession and ontology information
-	anemone	v6.3	Nematostella vectensis (anemone) accession and ontology information
-	dog	v6.3	Canis lupus familiaris (dog) accession and ontology information
PROMOTERS
-	zebrafish-p	v5.5	zebrafish promoters (zebrafish)
-	chicken-p	v5.5	chicken promoters (chicken)
-	frog-p	v5.5	frog promoters (frog)
-	yeast-p	v5.5	yeast promoters (yeast)
-	worm-p	v5.5	worm promoters (worm)
-	fly-p	v5.5	fly promoters (fly)
-	arabidopsis-p	v6.3	arabidopsis promoters (arabidopsis)
-	rat-p	v5.5	rat promoters (rat)
-	human-p	v5.5	human promoters (human)
-	mouse-p	v5.5	mouse promoters (mouse)
GENOMES
v5.10	hg18	v6.4	human genome and annotation for UCSC hg18
-	canFam3	v6.4	dog genome and annotation for UCSC canFam3
-	rheMac2	v6.4	rhesus genome and annotation for UCSC rheMac2
-	rheMac8	v6.4	rhesus genome and annotation for UCSC rheMac8
-	apiMel2	v6.4	bee genome and annotation for UCSC apiMel2
-	ce6	v6.4	worm genome and annotation for UCSC ce6
-	rice.IRGSP-1.0	v5.10	rice genome and annotation (rice.IRGSP-1.0)
-	panPan2	v6.4	human genome and annotation for UCSC panPan2
-	fr3	v6.4	fugu genome and annotation for UCSC fr3
-	galGal5	v6.4	chicken genome and annotation for UCSC galGal5
-	papAnu2	v6.4	human genome and annotation for UCSC papAnu2
-	susScr3	v6.4	pig genome and annotation for UCSC susScr3
-	hg38	v6.4	human genome and annotation for UCSC hg38
-	taeGut2	v6.4	zebrafinch genome and annotation for UCSC taeGut2
-	gorGor5	v6.4	human genome and annotation for UCSC gorGor5
-	anoGam1	v6.4	mosquito genome and annotation for UCSC anoGam1
-	danRer11	v6.4	zebrafish genome and annotation for UCSC danRer11
-	ci2	v6.4	ciona genome and annotation for UCSC ci2
-	tetNig2	v6.4	fugu genome and annotation for UCSC tetNig2
-	corn.AGPv3	v5.10	corn genome and annotation (corn.AGPv3)
-	galGal6	v6.4	chicken genome and annotation for UCSC galGal6
-	apiMel3	v6.4	bee genome and annotation for UCSC apiMel3
-	rheMac3	v6.4	rhesus genome and annotation for UCSC rheMac3
-	rn5	v6.4	rat genome and annotation for UCSC rn5
-	panPan1	v6.4	human genome and annotation for UCSC panPan1
-	aplCal1	v6.4	seahare genome and annotation for UCSC aplCal1
-	tair10	v6.0	arabidopsis genome and annotation (tair10)
-	rn6	v6.4	rat genome and annotation for UCSC rn6
-	sacCer3	v6.4	yeast genome and annotation for UCSC sacCer3
-	ce11	v6.4	worm genome and annotation for UCSC ce11
-	susScr11	v6.4	pig genome and annotation for UCSC susScr11
-	strPur2	v6.0	urchin genome and annotation for UCSC strPur2
-	xenTro2	v6.4	frog genome and annotation for UCSC xenTro2
-	xenTro3	v6.4	frog genome and annotation for UCSC xenTro3
-	hg19	v6.4	human genome and annotation for UCSC hg19
-	mm10	v6.4	mouse genome and annotation for UCSC mm10
-	gorGor3	v6.4	human genome and annotation for UCSC gorGor3
-	hg17	v6.4	human genome and annotation for UCSC hg17
-	sacCer2	v6.4	yeast genome and annotation for UCSC sacCer2
-	panTro4	v6.4	human genome and annotation for UCSC panTro4
-	dm3	v6.0	fly genome and annotation for UCSC dm3
-	rn4	v6.4	rat genome and annotation for UCSC rn4
-	petMar3	v6.4	lamprey genome and annotation for UCSC petMar3
-	xenTro9	v6.4	frog genome and annotation for UCSC xenTro9
-	danRer10	v6.4	zebrafish genome and annotation for UCSC danRer10
-	panTro5	v6.4	human genome and annotation for UCSC panTro5
-	petMar2	v6.4	lamprey genome and annotation for UCSC petMar2
-	ci3	v6.4	ciona genome and annotation for UCSC ci3
-	panTro6	v6.4	human genome and annotation for UCSC panTro6
-	mm8	v6.4	mouse genome and annotation for UCSC mm8
-	mm9	v6.4	mouse genome and annotation for UCSC mm9
-	patens.ASM242v1	v5.10	patens genome and annotation (patens.ASM242v1)
-	AGPv3	v5.10	corn genome and annotation (AGPv3)
-	xenTro7	v6.4	frog genome and annotation for UCSC xenTro7
-	dm6	v6.4	fly genome and annotation for UCSC dm6
-	danRer7	v6.4	zebrafish genome and annotation for UCSC danRer7
-	panTro3	v6.4	human genome and annotation for UCSC panTro3
-	ce10	v6.4	worm genome and annotation for UCSC ce10
-	galGal4	v6.4	chicken genome and annotation for UCSC galGal4
-	gorGor4	v6.4	human genome and annotation for UCSC gorGor4
SETTINGS
/usr/bin/convert
Version: ImageMagick 6.9.11-60 Q16 x86_64 2021-01-25 https://imagemagick.org
Copyright: (C) 1999-2021 ImageMagick Studio LLC
License: https://imagemagick.org/script/license.php
Features: Cipher DPC Modules OpenMP(4.5) 
Delegates (built-in): bzlib djvu fftw fontconfig freetype heic jbig jng jp2 jpeg lcms lqr ltdl lzma openexr pangocairo png tiff webp wmf x xml zlib
/usr/bin/coqc
The Coq Proof Assistant, version 8.15.0
compiled with OCaml 4.13.1
/usr/bin/cpp
cpp (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/cpulimit
CPUlimit version 2.4
Usage: cpulimit TARGET [OPTIONS...] [-- PROGRAM]
   TARGET must be exactly one of these:
      -p, --pid=N        pid of the process
      -e, --exe=FILE     name of the executable program file
                         The -e option only works when
                         cpulimit is run with admin rights.
      -P, --path=PATH    absolute path name of the
                         executable program file
   OPTIONS
      -b  --background   run in background
      -f  --foreground   launch target process in foreground and wait for it to exit
      -c  --cpu=N        override the detection of CPUs on the machine.
      -l, --limit=N      percentage of cpu allowed from 1 up.
                         Usually 1 - 800, but can be higher
                         on multi-core CPUs (mandatory)
      -m, --monitor-forks  Watch children/forks of the target process
      -q, --quiet        run in quiet mode (only print errors).
      -k, --kill         kill processes going over their limit
                         instead of just throttling them.
      -r, --restore      Restore processes after they have
                         been killed. Works with the -k flag.
      -s, --signal=SIG   Send this signal to the watched process when cpulimit exits.
                         Signal should be specificed as a number or 
                         SIGTERM, SIGCONT, SIGSTOP, etc. SIGCONT is the default.
      -v, --verbose      show control statistics
      -z, --lazy         exit if there is no suitable target process,
                         or if it dies
          --             This is the final CPUlimit option. All following
                         options are for another program we will launch.
      -h, --help         display this help and exit
/usr/bin/csdp
CSDP 6.2.0
 
Usage: 

csdp <input problem> [<final solution>] [<initial solution>]
/usr/bin/cvs

Concurrent Versions System (CVS) 1.12.13-MirDebian-28 (client/server)

Copyright (C) 2005 Free Software Foundation, Inc.
Copyright (c) 2021 mirabilos <[email protected]>

Senior no longer active maintainers include Larry Jones, Derek R. Price,
and Mark D. Baushke.  Please see the AUTHORS and README files from the CVS
distribution kit for a complete list of contributors and copyrights.

CVS may be copied only under the terms of the GNU General Public License,
a copy of which can be found with the CVS distribution kit.

Specify the --help option for further information about CVS
/usr/local/bin/cython
Cython version 0.29.30
/usr/bin/data
0.10.1
/usr/bin/dbar
usage: dbar [-w <characters>] [-s <symbol>] [-min <minvalue>] [-max <maxvalue>] [-l <string>] [-nonl]
/usr/bin/dia
Dia version 0.97+git, compiled 20:11:23 Mar  9 2022
/usr/bin/diff3
diff3 (GNU diffutils) 3.8
Copyright (C) 2021 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Randy Smith.
/usr/bin/docbook2pdf
DocBook-utils version 0.6.14 (jw version 1.1)
/ext/bin/docker
                                                         
╔═══════════════════════════════════════════════════════╗
║   ⚠ DOCKER NOT AVAILABLE -> USE COMPUTE SERVERS  ⚠    ║
╠═══════════════════════════════════════════════════════╣
║ CoCalc projects have a managed software environment   ║
║ and do not offer elevated privileges for using docker ║
╟───────────────────────────────────────────────────────╢
║ But, you can become a full admin in a 𝗖𝗢𝗠𝗣𝗨𝗧𝗘 𝗦𝗘𝗥𝗩𝗘𝗥! ║
║ More info: https://doc.cocalc.com/compute_server.html ║
╚═══════════════════════════════════════════════════════╝
                                                         
/usr/local/bin/docx2txt
usage: docx2txt [-h] [-i IMG_DIR] docx

A pure python-based utility to extract text and images from docx files.

positional arguments:
  docx                  path of the docx file

options:
  -h, --help            show this help message and exit
  -i IMG_DIR, --img_dir IMG_DIR
                        path of directory to extract images
/usr/bin/dot
dot - graphviz version 2.43.0 (0)
/usr/bin/dotty
dotty version 96c (09-24-96)
Error: Can't open display: 
/usr/bin/dvips
This is dvips(k) 2021.1 (TeX Live 2022/dev)  Copyright 2021 Radical Eye Software
kpathsea version 6.3.4/dev
Copyright 2021 Radical Eye Software.
There is NO warranty.  You may redistribute this software
under the terms of the GNU General Public License
and the Dvips copyright.
For more information about these matters, see the files
named COPYING and dvips.h.
Primary author of Dvips: T. Rokicki.
/usr/bin/ed
GNU ed 1.18
Copyright (C) 1994 Andrew L. Moore.
Copyright (C) 2022 Antonio Diaz Diaz.
License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
/usr/bin/emacs
GNU Emacs 27.1
Copyright (C) 2020 Free Software Foundation, Inc.
GNU Emacs comes with ABSOLUTELY NO WARRANTY.
You may redistribute copies of GNU Emacs
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.
/usr/bin/encfs
encfs version 1.9.5
/usr/bin/erl
Erlang (SMP,ASYNC_THREADS) (BEAM) emulator version 12.2.1
/usr/local/bin/f2py
1.23.5
/usr/bin/f77
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/f95
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/fastp
fastp 0.20.1
/usr/bin/fastqc
Picked up _JAVA_OPTIONS: -Xms64m
FastQC v0.11.9
/usr/bin/fenics-version
2019.2.0.dev0
/usr/bin/feynmf
This is feynmf: $Id: feynmf.pl,v 1.5 1996/12/02 01:38:45 ohl Exp $
/usr/bin/ffmpeg
ffmpeg version 4.4.2-0ubuntu0.22.04.1 Copyright (c) 2000-2021 the FFmpeg developers
  built with gcc 11 (Ubuntu 11.2.0-19ubuntu1)
  configuration: --prefix=/usr --extra-version=0ubuntu0.22.04.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --enable-gnutls --enable-ladspa --enable-libaom --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libdav1d --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-libpulse --enable-librabbitmq --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libsrt --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzimg --enable-libzmq --enable-libzvbi --enable-lv2 --enable-omx --enable-openal --enable-opencl --enable-opengl --enable-sdl2 --enable-pocketsphinx --enable-librsvg --enable-libmfx --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
  WARNING: library configuration mismatch
  avcodec     configuration: --prefix=/usr --extra-version=0ubuntu0.22.04.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --enable-gnutls --enable-ladspa --enable-libaom --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libdav1d --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-libpulse --enable-librabbitmq --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libsrt --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzimg --enable-libzmq --enable-libzvbi --enable-lv2 --enable-omx --enable-openal --enable-opencl --enable-opengl --enable-sdl2 --enable-pocketsphinx --enable-librsvg --enable-libmfx --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared --enable-version3 --disable-doc --disable-programs --enable-libaribb24 --enable-libopencore_amrnb --enable-libopencore_amrwb --enable-libtesseract --enable-libvo_amrwbenc --enable-libsmbclient
  libavutil      56. 70.100 / 56. 70.100
  libavcodec     58.134.100 / 58.134.100
  libavformat    58. 76.100 / 58. 76.100
  libavdevice    58. 13.100 / 58. 13.100
  libavfilter     7.110.100 /  7.110.100
  libswscale      5.  9.100 /  5.  9.100
  libswresample   3.  9.100 /  3.  9.100
  libpostproc    55.  9.100 / 55.  9.100
Unrecognized option '-version'.
Error splitting the argument list: Option not found
/usr/bin/firefox
Mozilla Firefox 122.0
/usr/bin/fish
fish, version 3.3.1
/usr/bin/flex
flex 2.6.4
/ext/bin/fscip

syntax: fscip fscip_param_file problem_file_name [-l <logfile>] [-q] [-sl <settings>] [-s <settings>] [-sr <root_settings>] [-w <prefix_warm>] [-sth <number>] [-fsol <solution_file>] [-isol <initial solution file]
  -l <logfile>           : copy output into log file
  -q                     : suppress screen messages
  -sl <settings>         : load parameter settings (.set) file for LC presolving
  -s <settings>          : load parameter settings (.set) file for solvers
  -sr <root_settings>    : load parameter settings (.set) file for root
  -w <prefix_warm>       : warm start file prefix ( prefix_warm_nodes.gz and prefix_warm_solution.txt are read )
  -sth <number>          : the number of solver threads used
  -fsol <solution file> : specify output solution file
  -isol <intial solution file> : specify initial solution file
/usr/bin/g++
g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/g++-10
g++-10 (Ubuntu 10.5.0-1ubuntu1~22.04) 10.5.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/g++-11
g++-11 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/ext/bin/gap
 ┌───────┐   GAP 4.12.1 of 2022-10-20
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv8
 Configuration:  gmp 6.2.1, GASMAN
 Loading the library and packages ...

 Packages:   AClib 1.3.2, Alnuth 3.2.1, AtlasRep 2.1.6, AutoDoc 2022.10.20, 
             AutPGrp 1.11, Browse 1.8.18, CaratInterface 2.3.4, CRISP 1.4.5, 
             Cryst 4.1.25, CrystCat 1.1.10, CTblLib 1.3.4, 
             curlInterface 2.3.1, FactInt 1.6.3, FGA 1.4.0, Forms 1.2.9, 
             GAPDoc 1.6.6, genss 1.6.8, IO 4.8.0, IRREDSOL 1.4.3, 
             LAGUNA 3.9.5, orb 4.9.0, Polenta 1.3.10, Polycyclic 2.16, 
             PrimGrp 3.4.2, RadiRoot 2.9, recog 1.4.2, ResClasses 4.7.3, 
             SmallGrp 1.5, Sophus 1.27, SpinSym 1.5.2, TomLib 1.2.9, 
             TransGrp 3.6.3, utils 0.77
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
gap> 
/usr/local/bin/gap-sage
 ┌───────┐   GAP 4.12.2 of 2022-12-18
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv8
 Configuration:  gmp 6.2.1, GASMAN
 Loading the library and packages ...
 Packages:   AClib 1.3.2, Alnuth 3.2.1, AtlasRep 2.1.6, AutPGrp 1.11, 
             CRISP 1.4.6, Cryst 4.1.25, CrystCat 1.1.10, CTblLib 1.3.4, 
             FactInt 1.6.3, FGA 1.4.0, GAPDoc 1.6.6, IO 4.8.0, IRREDSOL 1.4.4, 
             LAGUNA 3.9.5, Polenta 1.3.10, Polycyclic 2.16, PrimGrp 3.4.3, 
             RadiRoot 2.9, ResClasses 4.7.3, SmallGrp 1.5.1, Sophus 1.27, 
             TomLib 1.2.9, TransGrp 3.6.3, utils 0.81
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
gap> 
/ext/bin/gap3
             ########            Lehrstuhl D fuer Mathematik, RWTH Aachen
           ###    ####             #######            #########
          ##         ##           #      ##          ## #     ##
         ##          #           #       ##             #      ##
        ##           #           ##       #             #      ##
        ####        ##            #########             #######
         #####     ###  Version 3 Release 4.4 18 Apr 97 #
           ######### #                                  # Martin Schoenert
                    ##  Alice Niemeyer, Werner Nickel   # Erzsebet Horvath
                   ###  Bettina Eick,   Frank Celler,   # Udo Polis
                  ## #  Johannes Meier, Alex Wegner,    # Goetz Pfeiffer
                 ##  #  Juergen Mnich,  Thomas Breuer   # Heiko Theissen
                ##   #  Hans U. Besche, Volkmar Felsch  # Ansgar Kaup
               ##    #  Akos Seress,    Alexander Hulpke, Thomas Bischops
              ##    ##  
               ######   For help enter: ?<return>
 lib: 29 May 2017, src: 22 feb 2017, sys: linux gcc64
 for this GAP3 distribution see webusers.imj-prg.fr/~jmichel/gap3
--- Loading package arep -------- version 1.0 of 1998 Jul 22 ----------------
(C) Sebastian Egner, Markus Pueschel -- Abstract REPresentations
--- Loading package guava ------- version 1.3 -------------------------------
(C) Jasper Cramwinckel, Erik Roijackers, Reinald Baart, Eric Minkes
--- Loading package autag ------- version of 1997 Jan -----------------------
--- Loading package cryst ------- version of 1997 ---------------------------
--- Loading package dce --------- version of 1995 ---------------------------
--- Loading package gliss ------- version 1.0 of 1996 Sep 27 ----------------
(C) Christof Noebauer -- Glissando: small semigroups and near rings
--- Loading package grim -------- version 1.0 -------------------------------
(C) [email protected] -- Groups of Rational and Integer Matrices
--- Loading package matrix ------ version 1.0 -------------------------------
(C) Frank Celler, Derek Holt, Charles Leedham-Green, Alice Niemeyer
    Eamon O'Brien, Cheryl Praeger, Anthony Pye, Sarah Rees
--- Loading package monoid ------ version 2.2 -------------------------------
--- Loading package xmod -------- version 1.3.1 of 1997 Jan -----------------
(C) Chris Wensley, Murat Alp -- Crossed-modules, Cat1-groups
--- Loading package algebra ----- version of 2010 Oct -----------------------
(C) C'edric Bonnaf'e -- Finite dimensional algebras
--- Loading package specht ------ version 3.1 - unofficial (development) ----
    Decomposition numbers of Hecke algebras of type A and q-Schur algebras.
(C) Andrew Mathas  [email protected]     Sydney
--- Loading package chevie ------ version of 2017 Jun 30 --------------------
    If you use CHEVIE in your work please cite the authors as follows:
    [Jean Michel] The development version of the CHEVIE package of GAP3
     Journal of algebra 435 (2015) 308--336
    [Meinolf Geck, Gerhard Hiss, Frank Luebeck, Gunter Malle, Goetz Pfeiffer]
     CHEVIE -- a system for computing and processing generic character tables
     Applicable Algebra in Engineering Comm. and Computing 7 (1996) 175--210
--- Loading package vkcurve ----- version 1.2 of 2009 Mar -------------------
(C) David Bessis, Jean Michel -- compute Pi_1 of hypersurface complements
gap> 
/usr/bin/gcc
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/gcc-10
gcc-10 (Ubuntu 10.5.0-1ubuntu1~22.04) 10.5.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/gcc-11
gcc-11 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/geckodriver
2024-02-12T17:20:55.745Z INFO geckodriver: Detected Geckodriver v0.34.0 to be latest
2024-02-12T17:20:55.746Z INFO geckodriver: Downloading Geckodriver from https://github.com/mozilla/geckodriver/releases/download/v0.34.0/geckodriver-v0.34.0-linux64.tar.gz
geckodriver 0.34.0 (c44f0d09630a 2024-01-02 15:36 +0000)

The source code of this program is available from
testing/geckodriver in https://hg.mozilla.org/mozilla-central.

This program is subject to the terms of the Mozilla Public License 2.0.
You can obtain a copy of the license at https://mozilla.org/MPL/2.0/.
/usr/bin/gfortran
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/gh
gh version 2.42.1 (2024-01-16)
https://github.com/cli/cli/releases/tag/v2.42.1
/usr/bin/ghc
The Glorious Glasgow Haskell Compilation System, version 8.8.4
/ext/bin/giac
// Maximum number of parallel threads 8
// (c) 2001, 2021 B. Parisse & others
1.9.0
/usr/bin/git
git version 2.34.1
/usr/local/bin/git-trac
usage: git-trac [-h] [--debug] [--log LOG]
                {create,checkout,search,fetch,pull,push,get,depends,print,browse,review,find,try,log,config,cheat-sheet,help}
                ...

The trac command extension for git

positional arguments:
  {create,checkout,search,fetch,pull,push,get,depends,print,browse,review,find,try,log,config,cheat-sheet,help}
    create              Create new ticket
    checkout            Download branch
    search              Search trac
    fetch               Fetch branch from trac ticket
    pull                Get updates
    push                Upload changes
    get                 Print trac page
    depends             Print trac dependencies
    print               Print trac page
    browse              Open trac page in browser
    review              Show code to review
    find                Find trac ticket from SHA1
    try                 Try out trac ticket in "detached HEAD"
    log                 Commit log for ticket
    config              Configure git-trac
    cheat-sheet         Show the git trac cheat sheet
    help                Show the git trac help

options:
  -h                    show this help message and exit
  --debug               debug
  --log LOG             one of [DEBUG, INFO, ERROR, WARNING, CRITICAL]
/usr/bin/gnat
GNAT 10.5.0
Copyright (C) 1996-2020, Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/gnatmake
GNATMAKE 10.5.0
Copyright (C) 1995-2020, Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/go
go version go1.18.1 linux/amd64
/usr/bin/google-chrome
Google Chrome 121.0.6167.85 
/usr/bin/gp
                                          GP/PARI CALCULATOR Version 2.13.3 (released)
                                  amd64 running linux (x86-64/GMP-6.2.1 kernel) 64-bit version
                              compiled: Oct 25 2021, gcc version 11.2.0 (Ubuntu 11.2.0-10ubuntu1)
                                                   threading engine: pthread
                                        (readline v8.1 disabled, extended help enabled)
/usr/bin/gradle
Picked up _JAVA_OPTIONS: -Xms64m

------------------------------------------------------------
Gradle 8.3
------------------------------------------------------------

Build time:   2023-08-17 07:06:47 UTC
Revision:     8afbf24b469158b714b36e84c6f4d4976c86fcd5

Kotlin:       1.9.0
Groovy:       3.0.17
Ant:          Apache Ant(TM) version 1.10.13 compiled on January 4 2023
JVM:          18.0.2-ea (Private Build 18.0.2-ea+9-Ubuntu-222.04)
OS:           Linux 5.15.0-1046-gcp amd64
/usr/bin/grass
GRASS GIS 7.8.7

Geographic Resources Analysis Support System (GRASS) is Copyright,
1999-2022 by the GRASS Development Team, and licensed under terms of the
GNU General Public License (GPL) version >=2.
 
This GRASS GIS 7.8.7 release is coordinated and produced by
the GRASS Development Team with contributions from all over the world.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.
/usr/bin/grepcidr
grepcidr 2.0
Copyright (C) 2004 - 2014  Jem E. Berkes <[email protected]>
/usr/bin/gringo
gringo version 5.4.1
Address model: 64-bit

libgringo version 5.4.1
Configuration: with Python 3.10.2, with Lua 5.4.3
License: The MIT License <https://opensource.org/licenses/MIT>
/usr/bin/gst
GNU Smalltalk version 3.2.5
Copyright 2009 Free Software Foundation, Inc.
Written by Steve Byrne ([email protected]) and Paolo Bonzini ([email protected])

GNU Smalltalk comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Smalltalk under the terms of the
GNU General Public License.  For more information, see the file named
COPYING.

Using default kernel path: /usr/share/gnu-smalltalk/kernel
Using default image path: /usr/lib/gnu-smalltalk
/usr/bin/guile
guile (GNU Guile) 3.0.7
Packaged by Debian (3.0.7-deb+3.0.7-1)
Copyright (C) 2021 Free Software Foundation, Inc.

License LGPLv3+: GNU LGPL 3 or later <http://gnu.org/licenses/lgpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
/usr/bin/gyoto
Gyoto 1.4.4
ABI compatibility version: 8
 Copyright (c) 2011-2019 Frédéric Vincent, Thibaut Paumard,
                         Odele Straub and Frédéric Lamy.
 GYOTO is distributed under the terms of the GPL v. 3 license.
 We request that use of Gyoto in scientific publications be  properly 
 acknowledged. Please cite:
  GYOTO: a new general relativistic ray-tracing code,
  F. H. Vincent, T. Paumard, E. Gourgoulhon & G. Perrin 2011,
  Classical and Quantum Gravity 28, 225011 (2011) [arXiv:1109.4769]
/usr/bin/h5dump
h5dump: Version 1.10.7
/usr/bin/hardlink
hardlink from util-linux 2.37.2
/usr/bin/haskell-compiler
The Glorious Glasgow Haskell Compilation System, version 8.8.4
/usr/bin/haxe
4.3.3
/usr/bin/haxelib
Unknown command --help
Haxe Library Manager 4.1.0 - (c)2006-2019 Haxe Foundation
  Usage: haxelib [command] [options]
  Basic
    install            : install a given library, or all libraries from a hxml file
    update             : update a single library (if given) or all installed libraries
    remove             : remove a given library/version
    list               : list all installed libraries
    set                : set the current version for a library
  Information
    search             : list libraries matching a word
    info               : list information on a given library
    user               : list information on a given user
    config             : print the repository path
    path               : give paths to libraries' sources and necessary build definitions
    libpath            : returns the root path of a library
    version            : print the currently used haxelib version
    help               : display this list of options
  Development
    submit             : submit or update a library package
    register           : register a new user
    dev                : set the development directory for a given library
    git                : use Git repository as library
    hg                 : use Mercurial (hg) repository as library
  Miscellaneous
    setup              : set the haxelib repository path
    newrepo            : create a new local repository
    deleterepo         : delete the local repository
    convertxml         : convert haxelib.xml file to haxelib.json
    run                : run the specified library with parameters
    proxy              : setup the Http proxy
  Available switches
    --flat             : do not use --recursive cloning for git
    --always           : answer all questions with yes
    --debug            : run in debug mode, imply not --quiet
    --quiet            : print less messages, imply not --debug
    --system           : run bundled haxelib version instead of latest update
    --skip-dependencies: do not install dependencies
    --never            : answer all questions with no
    --global           : force global repo if a local one exists
/usr/bin/head
mglconv convert mgl script to image file (default PNG).
Current version is 8.0.1
/usr/bin/heroku
heroku/8.7.1 linux-x64 node-v16.19.0
/usr/bin/hg
Mercurial Distributed SCM (version 6.1.1)
(see https://mercurial-scm.org for more information)

Copyright (C) 2005-2022 Olivia Mackall and others
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/hisat2
/usr/bin/hisat2-align-s version 2.2.1
64-bit
Built on Debian
28 September 2021
Compiler: gcc version 11.2.0 (Ubuntu 11.2.0-7ubuntu2) 
Options: -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
/usr/bin/htop
htop 3.0.5
/usr/bin/ijs
ijavascript 5.2.1
jmp 2.0.0
jp-kernel 2.0.0
nel 1.3.0
uuid 3.4.0
zeromq 5.3.1
/usr/bin/inkscape
Warning: Option --without-gui= is deprecated
Inkscape 1.1.2 (0a00cf5339, 2022-02-04)
/ext/bin/ipopt
Ipopt 3.14.12 (Linux x86_64), ASL(20160307)
/ext/anaconda2022.05/bin/ipython
8.14.0
/ext/miniforge2023/bin/ipython
8.19.0
/usr/local/bin/ipython
7.34.0
/usr/local/bin/ipython3
7.34.0
/usr/bin/irssi
irssi 1.2.3-1ubuntu4 (20210409 0011)
/usr/bin/iverilog
Icarus Verilog version 11.0 (stable) ()

Copyright 1998-2020 Stephen Williams

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License along
  with this program; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

Icarus Verilog Preprocessor version 11.0 (stable) ()

Copyright (c) 1999-2020 Stephen Williams ([email protected])
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License along
  with this program; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

Icarus Verilog Parser/Elaborator version 11.0 (stable) ()

Copyright (c) 1998-2020 Stephen Williams ([email protected])

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License along
  with this program; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

 FLAGS DLL vvp.tgt
vvp.tgt: Icarus Verilog VVP Code Generator 11.0 (stable) ()

Copyright (c) 2001-2020 Stephen Williams ([email protected])

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License along
  with this program; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
/usr/bin/jags
Welcome to JAGS 4.3.2 on Mon Feb 12 17:21:17 2024
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok
/usr/bin/java
Picked up _JAVA_OPTIONS: -Xms64m
openjdk version "18.0.2-ea" 2022-07-19
OpenJDK Runtime Environment (build 18.0.2-ea+9-Ubuntu-222.04)
OpenJDK 64-Bit Server VM (build 18.0.2-ea+9-Ubuntu-222.04, mixed mode, sharing)
/usr/bin/javac
Picked up _JAVA_OPTIONS: -Xms64m
javac 18.0.2-ea
/ext/bin/julia
julia version 1.10.0
/ext/bin/julia-1.10
julia version 1.10.0
/ext/bin/julia-1.8
julia version 1.8.4
/ext/bin/julia-1.9
julia version 1.9.4
/usr/local/bin/jupyter-book
Jupyter Book      : 0.15.1
External ToC      : 0.3.1
MyST-Parser       : 0.18.1
MyST-NB           : 0.17.2
Sphinx Book Theme : 1.0.1
Jupyter-Cache     : 0.6.1
NbClient          : 0.6.3
/usr/local/bin/jupyter-lab
3.6.5
/usr/local/bin/jupyter-nbconvert
7.2.7
/usr/local/bin/jupyter-notebook
6.5.2
/usr/local/bin/jupyterhub
2.3.1
/usr/local/bin/jupytext
/usr/local/lib/python3.10/dist-packages/jupytext/cell_reader.py:20: UserWarning: Sphinx Gallery in version 0.13.0 is not supported by Jupytext. Please use sphinx-gallery<=0.7.0 instead. If that is an issue, feel free to report it at https://github.com/mwouts/jupytext/issues, or even better, prepare a PR to handle the new signature of sphinx_gallery.notebook.rst2md.
  warnings.warn(
usage: jupytext [-h] [--from INPUT_FORMAT] [--to OUTPUT_FORMAT] [-o OUTPUT]
                [--update] [--set-formats SET_FORMATS] [--sync]
                [--paired-paths] [--format-options FORMAT_OPTIONS]
                [--update-metadata UPDATE_METADATA] [--use-source-timestamp]
                [--warn-only] [--test] [--test-strict] [--stop] [--pipe PIPE]
                [--diff] [--diff-format DIFF_FORMAT] [--check CHECK]
                [--pipe-fmt PIPE_FMT] [--set-kernel SET_KERNEL] [--execute]
                [--run-path RUN_PATH] [--quiet] [--show-changes] [--version]
                [--pre-commit] [--pre-commit-mode]
                [notebooks ...]

Jupyter Notebooks as Markdown Documents, Julia, Python or R Scripts

positional arguments:
  notebooks             One or more notebook(s). Notebook is read from stdin
                        when this argument is empty. (default: None)

options:
  -h, --help            show this help message and exit
  --from INPUT_FORMAT   Jupytext format for the input(s). Inferred from the
                        file extension and content when missing. (default:
                        None)
  --to OUTPUT_FORMAT    The destination format: 'ipynb', 'markdown' or
                        'script', or a file extension: 'md', 'Rmd', 'jl',
                        'py', 'R', ..., 'auto' (script extension matching the
                        notebook language), or a combination of an extension
                        and a format name, e.g. md:markdown, md:pandoc,
                        md:myst or py:hydrogen, py:percent, py:nomarker,
                        py:light, py:sphinx. The default format for scripts is
                        the 'light' format, which uses few cell markers (none
                        when possible). Alternatively, a format compatible
                        with many editors is the 'percent' format, which uses
                        '# %%' as cell markers. The main formats (markdown,
                        light, percent) preserve notebooks and text documents
                        in a roundtrip. Use the --test and and --test-strict
                        commands to test the roundtrip on your files. Read
                        more about the available formats at
                        https://jupytext.readthedocs.io/en/latest/formats.html
                        (default: None)
  -o OUTPUT, --output OUTPUT
                        Destination file. Defaults to the original file, with
                        prefix/suffix/extension changed according to the
                        destination format. Use '-' to print the notebook on
                        stdout. (default: None)
  --update              Preserve the output cells when the destination
                        notebook is an .ipynb file that already exists
                        (default: False)
  --set-formats SET_FORMATS
                        Turn the notebook or text document to one or more
                        alternative representations with e.g. '--set-formats
                        ipynb,py:light'. The --set-formats option also
                        triggers the creation/update of all paired files
                        (default: None)
  --sync, -s            Synchronize the content of the paired representations
                        of the given notebook. Input cells are taken from the
                        file that was last modified, and outputs are read from
                        the ipynb file, if present. (default: False)
  --paired-paths, -p    List the locations of the alternative representations
                        for this notebook. (default: False)
  --format-options FORMAT_OPTIONS, --opt FORMAT_OPTIONS
                        Set format options with e.g. '--opt
                        comment_magics=true' or '--opt
                        notebook_metadata_filter=-kernelspec'. (default: None)
  --update-metadata UPDATE_METADATA
                        Update the notebook metadata with the desired
                        dictionary. Argument must be given in JSON format. For
                        instance, if you want to activate a pairing in the
                        generated file, use e.g. --update-metadata
                        '{"jupytext":{"formats":"ipynb,py:light"}}' See also
                        the --opt and --set-formats options for other ways to
                        operate on the Jupytext metadata. (default: {})
  --use-source-timestamp
                        Set the modification timestamp of the output file(s)
                        equalto that of the source file, and keep the source
                        file and its timestamp unchanged. (default: False)
  --warn-only, -w       Only issue a warning and continue processing other
                        notebooks when the conversion of a given notebook
                        fails (default: False)
  --test                Test that the notebook is stable under a round trip
                        conversion, up to the expected changes (default:
                        False)
  --test-strict         Test that the notebook is strictly stable under a
                        round trip conversion (default: False)
  --stop, -x            In --test mode, stop on first round trip conversion
                        error, and report stack traceback (default: False)
  --pipe PIPE           Pipe the text representation (in format --pipe-fmt) of
                        the notebook into another program, and read the
                        notebook back. For instance, reformat your notebook
                        with: 'jupytext notebook.ipynb --pipe black' If you
                        want to reformat it and sync the paired
                        representation, execute: 'jupytext notebook.ipynb
                        --sync --pipe black' In case the program that you want
                        to execute does not accept pipes, use {} as a
                        placeholder for a temporary file name into which
                        jupytext will write the text representation of the
                        notebook, e.g.: jupytext notebook.ipynb --pipe 'black
                        {}' (default: None)
  --diff, -d            Show the differences between (the inputs) of two
                        notebooks (default: False)
  --diff-format DIFF_FORMAT
                        The text format used to show differences in --diff
                        (default: None)
  --check CHECK         Pipe the text representation (in format --pipe-fmt) of
                        the notebook into another program, and test that the
                        returned value is non zero. For instance, test that
                        your notebook is pep8 compliant with: 'jupytext
                        notebook.ipynb --check flake8' or run pytest on your
                        notebook with: 'jupytext notebook.ipynb --check
                        pytest' In case the program that you want to execute
                        does not accept pipes, use {} as a placeholder for a
                        temporary file name into which jupytext will write the
                        text representation of the notebook, e.g.: jupytext
                        notebook.ipynb --check 'pytest {}' (default: None)
  --pipe-fmt PIPE_FMT   The format in which the notebook should be piped to
                        other programs, when using the --pipe and/or --check
                        commands. (default: auto:percent)
  --set-kernel SET_KERNEL, -k SET_KERNEL
                        Set the kernel with the given name on the notebook.
                        Use '--set-kernel -' to set a kernel matching the
                        current environment on Python notebooks, and matching
                        the notebook language otherwise (get the list of
                        available kernels with 'jupyter kernelspec list')
                        (default: None)
  --execute             Execute the notebook with the given kernel. In the
                        --pre-commit-mode, the notebook is executed only if a
                        code cell changed, or if some execution outputs are
                        missing or not ordered. (default: False)
  --run-path RUN_PATH   Execute the notebook at the given path (defaults to
                        the notebook parent directory) (default: None)
  --quiet, -q           Quiet mode: do not comment about files being updated
                        or created (default: False)
  --show-changes        Display the diff for each output file (default: False)
  --version, -v         Show jupytext's version number and exit (default:
                        False)
  --pre-commit          Ignore the notebook argument, and instead apply
                        Jupytext on the notebooks found in the git index,
                        which have an extension that matches the (optional)
                        --from argument. (default: False)
  --pre-commit-mode     This is a mode that is compatible with the pre-commit
                        framework. In this mode, --sync won't use timestamp
                        but instead will determines the source notebook as the
                        element of the pair that is added to the git index. An
                        alert is raised if multiple inconsistent
                        representations are in the index. It also raises an
                        alert after updating the paired files or outputs if
                        those files need to be added to the index. Finally,
                        filepaths that aren't in the source format you are
                        trying to convert from are ignored. (default: False)
/usr/bin/jurism
Jurism Jurism 6.0.22m6, Copyright (c) 2006-2020 Contributors
/usr/bin/latex
pdfTeX 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian)
kpathsea version 6.3.4/dev
Copyright 2021 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.37; using libpng 1.6.37
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 4.03
/usr/bin/latexmk

Latexmk, John Collins, 20 November 2021. Version 4.76
/ext/bin/lean
Lean (version 3.11.0, commit fb3f3e88be8a, Release)
/usr/bin/lfm
usage: lfm [-h] [-d] [-w] [--restore-config] [--restore-keys]
           [--restore-theme] [--delete-history]
           [path1] [path2]

lfm v3.0 - (C) 2001-17, by Iñigo Serna <[email protected]>

positional arguments:
  path1                 Path to show in left pane (default: ".")
  path2                 Path to show in right pane (default: ".")

options:
  -h, --help            show this help message and exit
  -d, --debug           Enable debug level in log file
  -w, --use-wide-chars  Enable support for wide chars
  --restore-config      Restore default configuration
  --restore-keys        Restore default key bindings
  --restore-theme       Restore default theme
  --delete-history      Delete history

'Last File Manager' is a powerful file manager for UNIX console.
It has a curses interface and it's written in Python version 3.4+.
Released under GNU Public License, read COPYING file for more details.
/usr/bin/libreoffice
LibreOffice 7.3.7.2 30(Build:2)
/usr/bin/lilypond
GNU LilyPond 2.22.1

Copyright (c) 1996--2021 by
  Han-Wen Nienhuys <[email protected]>
  Jan Nieuwenhuizen <[email protected]>
  and others.

This program is free software.  It is covered by the GNU General Public
License and you are welcome to change it and/or distribute copies of it
under certain conditions.  Invoke as `lilypond --warranty' for more
information.
/usr/bin/lneato
lneato version 95 (04-18-95)
Error: Can't open display: 
/usr/bin/lrzip
lrzip version 0.651
/usr/bin/lsb_release
22.04
/usr/bin/lua
Lua 5.2.4  Copyright (C) 1994-2015 Lua.org, PUC-Rio
/usr/bin/lua5.4
Lua 5.4.4  Copyright (C) 1994-2022 Lua.org, PUC-Rio
/usr/bin/luatex
This is LuaTeX, Version 1.14.0 (TeX Live 2022/dev/Debian)

Execute  'luatex --credits'  for credits and version details.

There is NO warranty. Redistribution of this software is covered by
the terms of the GNU General Public License, version 2 or (at your option)
any later version. For more information about these matters, see the file
named COPYING and the LuaTeX source.

LuaTeX is Copyright 2021 Taco Hoekwater and the LuaTeX Team.
/usr/bin/lzma
xz (XZ Utils) 5.2.5
liblzma 5.2.5
/usr/bin/M2
1.22
/usr/bin/m4
m4 (GNU M4) 1.4.18
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Rene' Seindal.
/ext/bin/macs2
macs2 2.2.9.1
/ext/bin/mageck
0.5.9.5
/usr/bin/make
GNU Make 4.3
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
/usr/bin/markdown

This is Markdown, version 1.0.1.
Copyright 2004 John Gruber
http://daringfireball.net/projects/markdown/
/usr/bin/materialized
materialized v0.26.6 (5ad960ec7)
/ext/bin/mathics
mathics 6.0.1
/usr/bin/maxima
Maxima 5.45.1
/usr/local/bin/maxima-sage
;;; Loading #P"/usr/lib/x86_64-linux-gnu/ecl-21.2.1/sb-bsd-sockets.fas"
;;; Loading #P"/usr/lib/x86_64-linux-gnu/ecl-21.2.1/sockets.fas"
Maxima 5.46.0
/usr/bin/mc
GNU Midnight Commander 4.8.27
Built with GLib 2.68.4
Built with S-Lang 2.3.2 with terminfo database
With builtin Editor and Aspell support
With subshell support as default
With support for background operations
With mouse support on xterm and Linux console
With support for X11 events
With internationalization support
With multiple codepages support
With ext2fs attributes support
Virtual File Systems:
 cpiofs, tarfs, sfs, extfs, ext2undelfs, ftpfs, sftpfs, fish
Data types:
 char: 8; int: 32; long: 64; void *: 64; size_t: 64; off_t: 64;
/usr/local/bin/meson
0.63.0
/usr/bin/mono
Mono JIT compiler version 6.8.0.105 (Debian 6.8.0.105+dfsg-3.2 Wed Jun 30 05:34:49 UTC 2021)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
	TLS:           __thread
	SIGSEGV:       altstack
	Notifications: epoll
	Architecture:  amd64
	Disabled:      none
	Misc:          softdebug 
	Interpreter:   yes
	LLVM:          supported, not enabled.
	Suspend:       hybrid
	GC:            sgen (concurrent by default)
/usr/bin/mpiexec
mpiexec (OpenRTE) 4.1.2

Report bugs to http://www.open-mpi.org/community/help/
/usr/local/bin/mzcli
Version: 3.0.0
/usr/bin/nano
 GNU nano, version 6.2
 (C) 1999-2011, 2013-2022 Free Software Foundation, Inc.
 (C) 2014-2022 the contributors to nano
 Compiled options: --disable-libmagic --enable-utf8
/usr/local/bin/nasm
NASM version 2.15.05 compiled on Sep 13 2022
/usr/local/bin/nbdime
3.1.1
/usr/bin/neofetch
Neofetch 7.1.0
/usr/bin/nettle-hash
nettle-hash (nettle 3.7.3)
/ext/bin/nim
Nim Compiler Version 1.6.10 [Linux: amd64]
Compiled at 2022-11-21
Copyright (c) 2006-2021 by Andreas Rumpf

git hash: f1519259f85cbdf2d5ff617c6a5534fcd2ff6942
active boot switches: -d:release
/usr/local/bin/ninja
1.10.2.git.kitware.jobserver-1
/usr/bin/nnn
4.3
/home/user/bin/node
v18.17.1
/usr/bin/nosetests3
/usr/lib/python3/dist-packages/nose/plugins/manager.py:394: RuntimeWarning: Unable to load plugin warnaserror = bayespy.testing:WarnAsError: `scipy.optimize.optimize` has no attribute `_epsilon`; furthermore, `scipy.optimize.optimize` is deprecated and will be removed in SciPy 2.0.0.
  warn("Unable to load plugin %s: %s" % (ep, e),
nosetests3 version 1.3.7
/usr/local/bin/notedown
1.5.1
/home/user/bin/npm
10.4.0
/usr/bin/nvim
NVIM v0.6.1
Build type: Release
LuaJIT 2.1.0-beta3
Compiled by [email protected]

Features: +acl +iconv +tui
See ":help feature-compile"

   system vimrc file: "$VIM/sysinit.vim"
  fall-back for $VIM: "/usr/share/nvim"

Run :checkhealth for more info
/usr/bin/ocaml
The OCaml toplevel, version 4.13.1
/usr/local/bin/octave
GNU Octave, version 8.2.0
Copyright (C) 1993-2023 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
/usr/local/bin/octave-7.3.0
GNU Octave, version 7.3.0
Copyright (C) 1993-2022 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
/usr/local/bin/octave-8.2.0
GNU Octave, version 8.2.0
Copyright (C) 1993-2023 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
/usr/local/bin/octave-cli
GNU Octave, version 8.2.0
Copyright (C) 1993-2023 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
/usr/local/bin/octave-cli-7.3.0
GNU Octave, version 7.3.0
Copyright (C) 1993-2022 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
/usr/local/bin/octave-cli-8.2.0
GNU Octave, version 8.2.0
Copyright (C) 1993-2023 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
/ext/bin/ok
okpy==v1.18.1
/usr/bin/oligotm
USAGE: oligotm OPTIONS oligo

where oligo is a DNA sequence of between 2 and 36 bases

and

OPTIONS can include any of the the following:

-mv monovalent_conc - concentration of monovalent cations in mM, by default 50mM

-dv divalent_conc   - concentration of divalent cations in mM, by default 1.5mM

-n  dNTP_conc       - concentration of deoxynycleotide triphosphate in mM, by default 0.6mM

-d  dna_conc        - concentration of DNA strands in nM, by default 50nM

-tp [0|1]     - Specifies the table of thermodynamic parameters and
                the method of melting temperature calculation:
                 0  Breslauer et al., 1986 and Rychlik et al., 1990
                    (used by primer3 up to and including release 1.1.0).
                 1  Use nearest neighbor parameters from SantaLucia 1998
                    *This is the default and recommended value*

-sc [0..2]    - Specifies salt correction formula for the melting 
                 temperature calculation
                  0  Schildkraut and Lifson 1965, used by primer3 up to 
                     and including release 1.1.0.
                  1  SantaLucia 1998
                     *This is the default and recommended value*
                  2  Owczarzy et al., 2004



Prints oligo's melting temperature on stdout.
/usr/bin/opam
2.1.2
/usr/bin/openscad
OpenSCAD version 2021.01
/usr/bin/pandoc
pandoc 3.1.11.1
Features: +server +lua
Scripting engine: Lua 5.4
User data directory: /home/user/.local/share/pandoc
Copyright (C) 2006-2023 John MacFarlane. Web: https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
/usr/local/bin/papermill
2.3.4 from /usr/local/lib/python3.10/dist-packages/papermill/cli.py (3.10.12)
/usr/bin/pdflatex
pdfTeX 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian)
kpathsea version 6.3.4/dev
Copyright 2021 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.37; using libpng 1.6.37
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 4.03
/usr/bin/pdftk
Picked up _JAVA_OPTIONS: -Xms64m
pdftk port to java 3.2.2 a Handy Tool for Manipulating PDF Documents
Copyright (c) 2017-2018 Marc Vinyals - https://gitlab.com/pdftk-java/pdftk
Copyright (c) 2003-2013 Steward and Lee, LLC.
pdftk includes a modified version of the iText library.
Copyright (c) 1999-2009 Bruno Lowagie, Paulo Soares, et al.
This is free software; see the source code for copying conditions. There is
NO warranty, not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/bin/pdftotext
pdftotext version 22.02.0
Copyright 2005-2022 The Poppler Developers - http://poppler.freedesktop.org
Copyright 1996-2011 Glyph & Cog, LLC
/usr/bin/perl

This is perl 5, version 34, subversion 0 (v5.34.0) built for x86_64-linux-gnu-thread-multi
(with 60 registered patches, see perl -V for more detail)

Copyright 1987-2021, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
/usr/bin/perldoc
Perldoc v3.2801, under perl v5.034000 for linux
/usr/bin/phc
PHCv2.4.85 released 2020-06-30
/usr/bin/php
PHP 8.1.2-1ubuntu2.14 (cli) (built: Aug 18 2023 11:41:11) (NTS)
Copyright (c) The PHP Group
Zend Engine v4.1.2, Copyright (c) Zend Technologies
    with Zend OPcache v8.1.2-1ubuntu2.14, Copyright (c), by Zend Technologies
/ext/bin/phylip
Starting main
running main
['/ext/bin/phylip', 'test']
/ext/miniforge2023/share/phylip-3.697-0/exe
testing dnapars...
passed; cleaning up
testing dnaml...
passed; cleaning up
testing dnadist...
passed; cleaning up
testing dnapenny...
passed; cleaning up
testing dnacomp...
passed; cleaning up
testing dnamlk...
passed; cleaning up
testing protpars...
passed; cleaning up
testing protdist...
passed; cleaning up
testing proml...
passed; cleaning up
testing promlk...
passed; cleaning up
testing pars...
passed; cleaning up
testing penny...
passed; cleaning up
testing dollop...
passed; cleaning up
testing dolpenny...
passed; cleaning up
testing clique...
passed; cleaning up
testing mix...
passed; cleaning up
testing restml...
passed; cleaning up
testing restdist...
passed; cleaning up
testing fitch...
passed; cleaning up
testing kitsch...
passed; cleaning up
testing neighbor...
passed; cleaning up
testing drawtree...
passed; cleaning up
testing drawgram...
passed; cleaning up
/usr/bin/pigz
pigz 2.6
/usr/local/bin/pip-upgrade
1.4.15
/usr/local/bin/pipenv
pipenv, version 2023.11.15
/ext/bin/plink

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Mon Feb 12 17:23:20 2024

Options in effect:
	--noweb

Before frequency and genotyping pruning, there are 0 SNPs
0 founders and 0 non-founders found
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 0 SNPs

ERROR: Stopping as there are no SNPs left for analysis
/usr/bin/pm2
pm2 launched in no-daemon mode (you can add DEBUG="*" env variable to get more messages)
2024-02-12T17:23:24: PM2 log: Launching in no daemon mode
5.3.0
/usr/bin/pngnq
pngnq 1.0
   Compiled with libpng 1.6.23; using libpng 1.6.37.
   Compiled with zlib 1.2.8; using zlib 1.2.11.
/usr/bin/pnpm
8.15.1
/usr/local/bin/poetry
Poetry (version 1.7.1)
/usr/bin/polymake
polymake version 4.4
Copyright (c) 1997-2021
Ewgenij Gawrilow, Michael Joswig, and the polymake team
Technische Universität Berlin, Germany
https://polymake.org

This is free software licensed under GPL; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/home/user/bin/postgres
postgres (PostgreSQL) 15.5 (Ubuntu 15.5-1.pgdg22.04+1)
/usr/local/bin/pretext
2.3.4
/usr/bin/prettier
3.2.5
/usr/bin/primecount
primecount 7.2, <https://github.com/kimwalisch/primecount>
Copyright (C) 2013 - 2021 Kim Walisch
BSD 2-Clause License <https://opensource.org/licenses/BSD-2-Clause>
/usr/bin/primer3_core

Copyright (c) 1996-2019
Whitehead Institute for Biomedical Research, Steve Rozen
(http://purl.com/STEVEROZEN/), Andreas Untergasser and Helen Skaletsky
All rights reserved.

    This file is part of the primer3 suite and libraries.

    The primer3 suite and libraries are free software;
    you can redistribute them and/or modify them under the terms
    of the GNU General Public License as published by the Free
    Software Foundation; either version 2 of the License, or (at
    your option) any later version.

    This software is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this software (file gpl-2.0.txt in the source
    distribution); if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



USAGE: primer3_core [--format_output] [--default_version=1|--default_version=2] [--io_version=4] [--p3_settings_file=<file_path>] [--echo_settings_file] [--strict_tags] [--output=<file_path>] [--error=<file_path>] [input_file]
This is primer3 (libprimer3 release 2.5.0)
Input can also be provided on standard input.
For example:
$ primer3_core < my_input_file
/usr/bin/primesieve
primesieve 7.8, <https://github.com/kimwalisch/primesieve>
Copyright (C) 2010 - 2022 Kim Walisch
BSD 2-Clause License <https://opensource.org/licenses/BSD-2-Clause>
/usr/bin/prolog
SWI-Prolog version 8.4.2 for x86_64-linux
/usr/bin/protoc
libprotoc 3.12.4
/usr/local/bin/py.test
pytest 7.1.3
/usr/local/bin/pytest
pytest 7.1.3
/ext/anaconda2022.05/bin/python
Python 3.9.15
/ext/miniforge2023/bin/python
Python 3.10.13
/usr/bin/python2
Python 2.7.18
/ext/anaconda2022.05/bin/python3
Python 3.9.15
/ext/bin/python3-sage
Python 3.11.1
/ext/miniforge2023/bin/python3
Python 3.10.13
/usr/bin/python3
Python 3.10.12
/usr/bin/pythontex
PythonTeX 0.18
/usr/bin/pythontex3
PythonTeX 0.18
/usr/local/bin/pytype
2024.01.05
/usr/bin/qgis
QGIS 3.34.3-Prizren 'Prizren' (47373234acd)
/usr/local/bin/quarto
1.3.450
/usr/bin/R
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
/usr/local/bin/R-sage
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
/ext/bin/RRA
RRA - Robust Rank Aggreation v 0.5.9.
usage:
-i <input data file>. Format: <item id> <group id> <list id> <value> [<probability>] [<chosen>]
-o <output file>. Format: <group id> <number of items in the group> <lo-value> <false discovery rate>
-p <maximum percentile>. RRA only consider the items with percentile smaller than this parameter. Default=0.1
-P <minimum percentile>. RRA only consider the items with percentile greater than this parameter. Default=-1.0
--control <control_sgrna list>. A list of control sgRNA names.
--permutation <int>. The number of rounds of permutation. Increase this value if the number of genes is small. Default 100.
--no-permutation-by-group. By default, gene permutation is performed separately, by their number of sgRNAs. Turning this option will perform permutation on all genes together. This makes the program faster, but the p value estimation is accurate only if the number of sgRNAs per gene is approximately the same.
--skip-gene <gene_name>. Genes to skip from doing permutation. Specify it multiple times if you need to skip more than 1 genes.
--min-percentage-goodsgrna <min percentage>. Filter genes that have too few percentage of 'good sgrnas', or sgrnas that fall below the -p threshold. Must be a number between 0-1. Default 0 (do not filter genes).
--min-number-goodsgrna <min number>. Filter genes that have too few number of 'good sgrnas', or sgrnas that fall below the -p threshold. Must be an integer. Default 0 (do not filter genes). 
--max-sgrnapergene-permutation <max number>. Only permute genes by group if the number of sgRNAs per gene is smaller than this number. This will save a lot of time if some regions are targeted by a large number of sgRNAs (usually hundreds). Must be an integer. Default 100. 
example:
RRA -i input.txt -o output.txt -p 0.1 
/usr/bin/racket
Welcome to Racket v8.6 [cs].
/usr/bin/ranger
ranger version: ranger 1.9.3
Python version: 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]
Locale: en_US.UTF-8
/usr/bin/rclone
rclone v1.63.1
- os/version: ubuntu 22.04 (64 bit)
- os/kernel: 5.15.0-1046-gcp (x86_64)
- os/type: linux
- os/arch: amd64
- go/version: go1.20.6
- go/linking: static
- go/tags: none
/usr/bin/rdfind
This is rdfind version 1.5.0
/usr/bin/reveal-md
6.0.0
/usr/bin/rg
ripgrep 13.0.0
-SIMD -AVX (compiled)
+SIMD +AVX (runtime)
/usr/bin/ros
roswell 21.10.14.111(NO-GIT-REVISION)
/usr/bin/Rscript
Rscript (R) version 4.3.2 (2023-10-31)
/ext/bin/rstudio
RStudio is a trademarks of RStudio, Inc.

CoCalc provides RStudio in unmodified form supplied by RStudio, Inc.
primarily to foster the use of R or RStudio products in teaching
for internal use in courses. RStudio, Inc. is in no way
affiliated with CoCalc.   Do not use RStudio in CoCalc if
your use is not covered under Automatic Permitted Use:
https://www.rstudio.com/about/trademark/.

Launching RStudio...
[4422:0212/172403.579715:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
2023.06.2+561
/usr/bin/rsync
rsync  version 3.2.7  protocol version 31
Copyright (C) 1996-2022 by Andrew Tridgell, Wayne Davison, and others.
Web site: https://rsync.samba.org/
Capabilities:
    64-bit files, 64-bit inums, 64-bit timestamps, 64-bit long ints,
    socketpairs, symlinks, symtimes, hardlinks, hardlink-specials,
    hardlink-symlinks, IPv6, atimes, batchfiles, inplace, append, ACLs,
    xattrs, optional secluded-args, iconv, prealloc, stop-at, no crtimes
Optimizations:
    SIMD-roll, no asm-roll, openssl-crypto, no asm-MD5
Checksum list:
    xxh128 xxh3 xxh64 (xxhash) md5 md4 sha1 none
Compress list:
    zstd lz4 zlibx zlib none
Daemon auth list:
    sha512 sha256 sha1 md5 md4

rsync comes with ABSOLUTELY NO WARRANTY.  This is free software, and you
are welcome to redistribute it under certain conditions.  See the GNU
General Public Licence for details.
/usr/bin/ruby
ruby 3.0.2p107 (2021-07-07 revision 0db68f0233) [x86_64-linux-gnu]
/usr/bin/run-one
x
/ext/bin/rustc
rustc 1.71.1 (eb26296b5 2023-08-03)
/ext/bin/rustfmt
rustfmt 1.5.2-stable (eb26296 2023-08-03)
/ext/bin/rustup
rustup 1.26.0 (5af9b9484 2023-04-05)
info: This is the version for the rustup toolchain manager, not the rustc compiler.
info: The currently active `rustc` version is `rustc 1.71.1 (eb26296b5 2023-08-03)`
/usr/bin/rvim
VIM - Vi IMproved 8.2 (2019 Dec 12, compiled Dec 05 2023 17:58:57)
Included patches: 1-579, 1969, 580-1848, 4975, 5016, 5023, 5072, 2068, 1849-1854, 1857, 1855-1857, 1331, 1858, 1858-1859, 1873, 1860-1969, 1992, 1970-1992, 2010, 1993-2068, 2106, 2069-2106, 2108, 2107-2109, 2109-3995, 4563, 4646, 4774, 4895, 4899, 4901, 4919, 213, 1840, 1846-1847, 2110-2112, 2121
Modified by [email protected]
Compiled by [email protected]
Huge version with GTK3 GUI.  Features included (+) or not (-):
+acl               +file_in_path      +mouse_urxvt       -tag_any_white
+arabic            +find_in_path      +mouse_xterm       +tcl
+autocmd           +float             +multi_byte        +termguicolors
+autochdir         +folding           +multi_lang        +terminal
-autoservername    -footer            -mzscheme          +terminfo
+balloon_eval      +fork()            +netbeans_intg     +termresponse
+balloon_eval_term +gettext           +num64             +textobjects
+browse            -hangul_input      +packages          +textprop
++builtin_terms    +iconv             +path_extra        +timers
+byte_offset       +insert_expand     +perl              +title
+channel           +ipv6              +persistent_undo   +toolbar
+cindent           +job               +popupwin          +user_commands
+clientserver      +jumplist          +postscript        +vartabs
+clipboard         +keymap            +printer           +vertsplit
+cmdline_compl     +lambda            +profile           +vim9script
+cmdline_hist      +langmap           -python            +viminfo
+cmdline_info      +libcall           +python3           +virtualedit
+comments          +linebreak         +quickfix          +visual
+conceal           +lispindent        +reltime           +visualextra
+cryptv            +listcmds          +rightleft         +vreplace
+cscope            +localmap          +ruby              +wildignore
+cursorbind        +lua               +scrollbind        +wildmenu
+cursorshape       +menu              +signs             +windows
+dialog_con_gui    +mksession         +smartindent       +writebackup
+diff              +modify_fname      +sodium            +X11
+digraphs          +mouse             +sound             -xfontset
+dnd               +mouseshape        +spell             +xim
-ebcdic            +mouse_dec         +startuptime       +xpm
+emacs_tags        +mouse_gpm         +statusline        +xsmp_interact
+eval              -mouse_jsbterm     -sun_workshop      +xterm_clipboard
+ex_extra          +mouse_netterm     +syntax            -xterm_save
+extra_search      +mouse_sgr         +tag_binary        
-farsi             -mouse_sysmouse    -tag_old_static    
   system vimrc file: "$VIM/vimrc"
     user vimrc file: "$HOME/.vimrc"
 2nd user vimrc file: "~/.vim/vimrc"
      user exrc file: "$HOME/.exrc"
  system gvimrc file: "$VIM/gvimrc"
    user gvimrc file: "$HOME/.gvimrc"
2nd user gvimrc file: "~/.vim/gvimrc"
       defaults file: "$VIMRUNTIME/defaults.vim"
    system menu file: "$VIMRUNTIME/menu.vim"
  fall-back for $VIM: "/usr/share/vim"
Compilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -DFEAT_GUI_GTK -pthread -I/usr/include/gtk-3.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib/x86_64-linux-gnu/dbus-1.0/include -I/usr/include/gtk-3.0 -I/usr/include/gio-unix-2.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Wdate-time -g -O2 -ffile-prefix-map=/build/vim-gVT2fw/vim-8.2.3995=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -D_REENTRANT -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 
Linking: gcc -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vim -lgtk-3 -lgdk-3 -lpangocairo-1.0 -lpango-1.0 -lharfbuzz -latk-1.0 -lcairo-gobject -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lSM -lICE -lXpm -lXt -lX11 -lXdmcp -lSM -lICE -lm -ltinfo -lselinux -lcanberra -lsodium -lacl -lattr -lgpm -L/usr/lib -llua5.2 -Wl,-E -fstack-protector-strong -L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/perl/5.34/CORE -lperl -ldl -lm -lpthread -lcrypt -L/usr/lib/python3.10/config-3.10-x86_64-linux-gnu -lpython3.10 -lcrypt -ldl -lm -lm -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -lruby-3.0 -lm -L/usr/lib 
/ext/bin/sage
SageMath version 10.2, Release Date: 2023-12-03
/ext/bin/sage-10.0
SageMath version 10.0, Release Date: 2023-05-20
/ext/bin/sage-10.1
SageMath version 10.1, Release Date: 2023-08-20
/ext/bin/sage-10.2
SageMath version 10.2, Release Date: 2023-12-03
/ext/bin/sage-9.6
SageMath version 9.6, Release Date: 2022-05-15
/ext/bin/sage-9.7
SageMath version 9.7, Release Date: 2022-09-19
/ext/bin/sage-9.8
SageMath version 9.8, Release Date: 2023-02-11
/ext/bin/samtools
samtools 1.19
Using htslib 1.19
Copyright (C) 2023 Genome Research Ltd.

Samtools compilation details:
    Features:       build=configure curses=yes 
    CC:             /opt/conda/conda-bld/samtools_1702426945528/_build_env/bin/x86_64-conda-linux-gnu-cc
    CPPFLAGS:       -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /ext/miniforge2023/include
    CFLAGS:         -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2023/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1702426945528/work=/usr/local/src/conda/samtools-1.19 -fdebug-prefix-map=/ext/miniforge2023=/usr/local/src/conda-prefix
    LDFLAGS:        -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/ext/miniforge2023/lib -Wl,-rpath-link,/ext/miniforge2023/lib -L/ext/miniforge2023/lib
    HTSDIR:         
    LIBS:           
    CURSES_LIB:     -ltinfow -lncursesw

HTSlib compilation details:
    Features:       build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/ext/miniforge2023/libexec/htslib htscodecs=1.6.0
    CC:             /opt/conda/conda-bld/htslib_1702415411511/_build_env/bin/x86_64-conda-linux-gnu-cc
    CPPFLAGS:       -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /ext/miniforge2023/include
    CFLAGS:         -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2023/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1702415411511/work=/usr/local/src/conda/htslib-1.19 -fdebug-prefix-map=/ext/miniforge2023=/usr/local/src/conda-prefix -fvisibility=hidden
    LDFLAGS:        -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/ext/miniforge2023/lib -Wl,-rpath-link,/ext/miniforge2023/lib -L/ext/miniforge2023/lib -fvisibility=hidden -rdynamic

HTSlib URL scheme handlers present:
    built-in:	 preload, data, file
    S3 Multipart Upload:	 s3w, s3w+https, s3w+http
    Amazon S3:	 s3+https, s3+http, s3
    libcurl:	 imaps, pop3, gophers, http, smb, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict
    Google Cloud Storage:	 gs+http, gs+https, gs
    crypt4gh-needed:	 crypt4gh
    mem:	 mem
/usr/bin/sbcl
SBCL 2.1.11.debian
/usr/bin/scala
Picked up _JAVA_OPTIONS: -Xms64m
Welcome to Scala 2.11.12 (OpenJDK 64-Bit Server VM, Java 18.0.2-ea).
Type in expressions for evaluation. Or try :help.

scala> :quit
/usr/bin/scheme
MIT/GNU Scheme 11.2
Copyright (C) 2020 Massachusetts Institute of Technology
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Image saved on Thursday March 17, 2022 at 6:50:34 PM
  Release 11.2 || SF || LIAR/x86-64

Happy happy joy joy!
/usr/bin/scilab-cli-bin
Scilab version "6.1.1.988271013"
scilab-branch-6.1
/ext/bin/scip
SCIP version 8.0.3 [precision: 8 byte] [memory: block] [mode: optimized] [LP solver: Soplex 6.0.3] [GitHash: 62fab8a2e3]
Copyright (C) 2002-2022 Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB)

External libraries: 
  Soplex 6.0.3         Linear Programming Solver developed at Zuse Institute Berlin (soplex.zib.de) [GitHash: f900e3d0]
  CppAD 20180000.0     Algorithmic Differentiation of C++ algorithms developed by B. Bell (github.com/coin-or/CppAD)
  ZLIB 1.2.11          General purpose compression library by J. Gailly and M. Adler (zlib.net)
  GMP 6.2.1            GNU Multiple Precision Arithmetic Library developed by T. Granlund (gmplib.org)
  ZIMPL 3.5.3          Zuse Institute Mathematical Programming Language developed by T. Koch (zimpl.zib.de)
  AMPL/MP 4e2d45c4     AMPL .nl file reader library (github.com/ampl/mp)
  PaPILO 2.1.2         parallel presolve for integer and linear optimization (github.com/scipopt/papilo) [GitHash: 2fe2543]
  bliss 0.77           Computing Graph Automorphism Groups by T. Junttila and P. Kaski (www.tcs.hut.fi/Software/bliss/)
  Ipopt 3.13.2         Interior Point Optimizer developed by A. Waechter et.al. (github.com/coin-or/Ipopt)

Compiler: gcc 9.4.0

Build options:
 ARCH=x86_64
 OSTYPE=Linux-4.19.0-21-amd64
 COMP=GNU 9.4.0
 BUILD=Release
 DEBUGSOL=OFF
 EXPRINT=cppad
 SYM=bliss
 GMP=ON
 IPOPT=ON
 WORHP=OFF
 LPS=spx
 LPSCHECK=OFF
 NOBLKBUFMEM=OFF
 NOBLKMEM=OFF
 NOBUFMEM=OFF
 THREADSAFE=ON
 READLINE=off
 SANITIZE_ADDRESS=OFF
 SANITIZE_MEMORY=OFF
 SANITIZE_UNDEFINED=OFF
 SANITIZE_THREAD=OFF
 SHARED=ON
 VERSION=8.0.3.0
 API_VERSION=104
 ZIMPL=ON
 ZLIB=ON
/usr/bin/scons
SCons by Steven Knight et al.:
	SCons: v4.0.1.c289977f8b34786ab6c334311e232886da7e8df1, 2020-07-17 01:50:03, by bdbaddog on ProDog2020
	SCons path: ['/usr/lib/python3/dist-packages/SCons']
Copyright (c) 2001 - 2020 The SCons Foundation
/usr/bin/sed
sed (GNU sed) 4.8
Packaged by Debian
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Jay Fenlason, Tom Lord, Ken Pizzini,
Paolo Bonzini, Jim Meyering, and Assaf Gordon.

This sed program was built with SELinux support.
SELinux is disabled on this system.

GNU sed home page: <https://www.gnu.org/software/sed/>.
General help using GNU software: <https://www.gnu.org/gethelp/>.
E-mail bug reports to: <[email protected]>.
/usr/bin/sha1sum
sha1sum (GNU coreutils) 8.32
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Ulrich Drepper, Scott Miller, and David Madore.
/usr/bin/sha256sum
sha256sum (GNU coreutils) 8.32
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Ulrich Drepper, Scott Miller, and David Madore.
/usr/local/bin/shiny
Usage: shiny [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  cells-to-app    Convert a JSON file with code cells to a py file.
  create          Create a Shiny application from a template.
  get-shiny-deps  Get Shiny's HTML dependencies as JSON.
  run             Run a Shiny app (press Ctrl+C to stop).
  static          The functionality from `shiny static` has been moved to...
  static-assets   Manage local copy of assets for static app deployment.
/usr/bin/Singular
Singular for x86_64-Linux version 4.2.1 (4212, 64 bit) Dec 17 2021 20:20:53
with
	GMP(6.2.1),NTL(11.5.1),FLINT(2.8.0),
	omalloc,static readline(8),Plural,vspace(2),DBM,
	dynamic modules,OM_NDEBUG,SING_NDEBUG,
	CC:OPTIMIZE,GenericAdd,TableMult,no invTable,
	eigenvalues,Gauss-Manin system,random=1707758375
built-in modules: {}
AC_CONFIGURE_ARGS =  '--build=x86_64-linux-gnu' '--prefix=/usr' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-option-checking' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--libexecdir=/usr/libexec/x86_64-linux-gnu' '--enable-streamio' 'build_alias=x86_64-linux-gnu' 'CFLAGS=-g -O2 -ffile-prefix-map=/build/singular-pPci2W/singular-4.2.1-p3+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/singular-pPci2W/singular-4.2.1-p3+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security' 'PYTHON=/usr/bin/python3' --enable-omalloc  OMALLOC_LIBS='/build/singular-pPci2W/singular-4.2.1-p3+ds/omalloc/libsingular-omalloc.la' OMALLOC_INCLUDES='-I/build/singular-pPci2W/singular-4.2.1-p3+ds' --with-Singular RESOURCES_LIBS='/build/singular-pPci2W/singular-4.2.1-p3+ds/resources/libsingular-resources.la' RESOURCES_INCLUDES='-I/build/singular-pPci2W/singular-4.2.1-p3+ds ' FACTORY_LIBS='/build/singular-pPci2W/singular-4.2.1-p3+ds/factory/libsingular-factory.la' FACTORY_INCLUDES='-I/build/singular-pPci2W/singular-4.2.1-p3+ds -I/build/singular-pPci2W/singular-4.2.1-p3+ds/factory -I/build/singular-pPci2W/singular-4.2.1-p3+ds/factory/include',
CC = gcc,FLAGS :  -g -O2 -ffile-prefix-map=/build/singular-pPci2W/singular-4.2.1-p3+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pipe -fno-common -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -pthread -pthread,
CXX = g++,FLAGS : -g -O2 -ffile-prefix-map=/build/singular-pPci2W/singular-4.2.1-p3+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pipe -fno-common -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -fno-rtti -fno-delete-null-pointer-checks -pthread,
DEFS : ,CPPFLAGS : -Wdate-time -D_FORTIFY_SOURCE=2,
LDFLAGS : -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -pipe -fno-common -g -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops  -rdynamic -Wl,-undefined,dynamic_lookup,LIBS : -lcddgmp -lreadline -lncurses -lmpfr  -lgmp -lrt  -lpthread (ver: 11.2.0)
argv[0]   :	Singular
SearchPath:	/usr/bin/../share/singular/LIB:/usr/bin/../share/singular/factory:/usr/libexec/x86_64-linux-gnu/singular/MOD:/usr/bin
Singular  :	/usr/bin/Singular
BinDir    :	/usr/bin
ProcDir   :	/usr/libexec/x86_64-linux-gnu/singular/MOD
RootDir   :	/usr/bin/..
DataDir   :	/usr/bin/../share
DefaultDir:	/usr
InfoFile  :	
IdxFile   :	
HtmlDir   :	
ManualUrl :	https://www.singular.uni-kl.de/Manual/
ExDir     :	
Path      :	/usr/bin:/usr/libexec/x86_64-linux-gnu/singular/MOD:/home/user/bin:/cocalc/bin:/ext/bin/nosudo:/ext/bin:/usr/lib/xpra:/usr/local/sbin:/usr/local/bin:/usr/sbin:/sbin:/bin:/ext/data/homer/bin:/ext/data/weblogo:/usr/lib/postgresql/15/bin:/home/user/.gem/ruby/2.3.0/bin
emacs     :	/usr/bin/emacs
xemacs    :	
SingularEmacs:	/usr/bin/Singular
EmacsLoad :	
EmacsDir  :	
SingularXterm:	/usr/bin/Singular
xterm     :	/usr/bin/xterm
EmacsDir  :	
Available HelpBrowsers: lynx-www, dummy, emacs, 
Current HelpBrowser: lynx-www 
                     SINGULAR                                 /  Development
 A Computer Algebra System for Polynomial Computations       /   version 4.2.1
                                                           0<
 by: W. Decker, G.-M. Greuel, G. Pfister, H. Schoenemann     \   May 2021
FB Mathematik der Universitaet, D-67653 Kaiserslautern        \  Debian 1:4.2.1-p3+ds-1
// ** Can not open /dev/null
Auf Wiedersehen.
/usr/local/bin/Singular-sage
Singular for x86_64-Linux version 4.3.2 (4328, 64 bit) Dec  4 2023 22:14:48
with
	GMP(6.2.1),NTL(11.4.3),FLINT(2.9.0),
	omalloc,static readline(8),Plural,vspace(2),DBM,
	dynamic modules,OM_NDEBUG,SING_NDEBUG,
	CC:OPTIMIZE,GenericAdd,TableMult,no invTable,
	eigenvalues,Gauss-Manin system,random=1707758376
built-in modules: {}
AC_CONFIGURE_ARGS =  '--prefix=/ext/sage/10.2/local' '--libdir=/ext/sage/10.2/local/lib' '--disable-maintainer-mode' '--disable-dependency-tracking' '--exec-prefix=/ext/sage/10.2/local' '--bindir=/ext/sage/10.2/local/bin' '--with-ntl=/ext/sage/10.2/local' '--with-flint=/ext/sage/10.2/local' '--enable-gfanlib' '--enable-Singular' '--enable-factory' '--disable-doc' '--disable-polymake' '--without-python' '--without-pythonmodule' '--disable-python' '--disable-python_module' '--disable-python-module' '--disable-static' '--with-libparse' 'CC=gcc' 'CFLAGS=-g -O2' 'LDFLAGS=-Wl,-rpath-link,/ext/sage/10.2/local/lib -L/ext/sage/10.2/local/lib -Wl,-rpath,/ext/sage/10.2/local/lib -Wl,-rpath-link,/ext/sage/10.2/local/lib -L/ext/sage/10.2/local/lib -Wl,-rpath,/ext/sage/10.2/local/lib ' 'CXX=g++ -std=gnu++11' 'CXXFLAGS=-g -O2' --enable-omalloc  OMALLOC_LIBS='/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src/omalloc/libomalloc.la' OMALLOC_INCLUDES='-I/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src' --htmldir=${prefix}/share/doc/singular --with-Singular RESOURCES_LIBS='/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src/resources/libsingular_resources.la' RESOURCES_INCLUDES='-I/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src ' FACTORY_LIBS='/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src/factory/libfactory.la' FACTORY_INCLUDES='-I/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src -I/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src/factory -I/ext/sage/10.2/local/var/tmp/sage/build/singular-4.3.2p8/src/factory/include',
CC = gcc,FLAGS :  -g -O2  -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fconserve-space -funroll-loops -pthread -pthread,
CXX = g++ -std=gnu++11,FLAGS : -g -O2 -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -fno-rtti -fno-delete-null-pointer-checks -pthread,
DEFS : ,CPPFLAGS : ,
LDFLAGS : -Wl,-rpath-link,/ext/sage/10.2/local/lib -L/ext/sage/10.2/local/lib -Wl,-rpath,/ext/sage/10.2/local/lib -Wl,-rpath-link,/ext/sage/10.2/local/lib -L/ext/sage/10.2/local/lib -Wl,-rpath,/ext/sage/10.2/local/lib  -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fconserve-space -funroll-loops  -rdynamic -Wl,-undefined,dynamic_lookup,LIBS : -lreadline -lncurses  -lgmp -lrt   (ver: 11.4.0)
argv[0]   :	Singular
SearchPath:	/ext/sage/10.2/local/bin/../share/singular/LIB:/ext/sage/10.2/local/bin/../share/factory:/ext/sage/10.2/local/bin/../libexec/singular/MOD:/ext/sage/10.2/local/libexec/singular/MOD:/ext/sage/10.2/local/bin:/ext/sage/10.2/local/bin/..
Singular  :	/ext/sage/10.2/local/bin/Singular
BinDir    :	/ext/sage/10.2/local/bin
ProcDir   :	/ext/sage/10.2/local/bin/..:/ext/sage/10.2/local/bin/../libexec/singular/MOD:/ext/sage/10.2/local/libexec/singular/MOD
RootDir   :	/ext/sage/10.2/local/bin/..
DataDir   :	/ext/sage/10.2/local/bin/../share
DefaultDir:	/ext/sage/10.2/local
InfoFile  :	/ext/sage/10.2/local/bin/../share/info/singular.info
IdxFile   :	/ext/sage/10.2/local/bin/../share/singular/singular.idx
HtmlDir   :	/ext/sage/10.2/local/bin/../share/doc/singular
ManualUrl :	https://www.singular.uni-kl.de/Manual/
ExDir     :	
Path      :	/ext/sage/10.2/local/bin:/ext/sage/10.2/local/bin/..:/ext/sage/10.2/local/bin/../libexec/singular/MOD:/ext/sage/10.2/local/libexec/singular/MOD:/ext/sage/10.2/src/bin:/ext/sage/10.2/local/libexec/ccache:/ext/sage/10.2/build/bin:/ext/sage/10.2/local/var/lib/sage/venv-python3.11.1/bin:/home/user/bin:/cocalc/bin:/ext/bin/nosudo:/ext/bin:/usr/lib/xpra:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/ext/data/homer/bin:/ext/data/weblogo:/usr/lib/postgresql/15/bin:/home/user/.gem/ruby/2.3.0/bin
emacs     :	/usr/bin/emacs-gtk
xemacs    :	
SingularEmacs:	/ext/sage/10.2/local/bin/Singular
EmacsLoad :	/ext/sage/10.2/local/bin/../share/singular/emacs/.emacs-singular
EmacsDir  :	/ext/sage/10.2/local/bin/../share/singular/emacs
SingularXterm:	/ext/sage/10.2/local/bin/Singular
xterm     :	/usr/bin/xterm
EmacsDir  :	/ext/sage/10.2/local/bin/../share/singular/emacs
Available HelpBrowsers: info, lynx, lynx-www-idx, lynx-www, builtin, dummy, emacs, 
Current HelpBrowser: info 
                     SINGULAR                                 /  Development
 A Computer Algebra System for Polynomial Computations       /   version 4.3.2
                                                           0<
 by: W. Decker, G.-M. Greuel, G. Pfister, H. Schoenemann     \   Feb 2023
FB Mathematik der Universitaet, D-67653 Kaiserslautern        \
// ** Can not open /dev/null
Auf Wiedersehen.
/usr/bin/sml
sml 110.79
/ext/bin/soplex
SoPlex version 6.0.3 [mode: optimized] [precision: 8 byte] [rational: GMP 6.2.1] [PaPILO  2.1.2 {2fe2543}]
 [githash: f900e3d0]
Copyright (c) 1996-2022 Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB)

Error parsing setting string: no ':' separating parameter type and name.
invalid option "--version"

usage: soplex [options] <lpfile>
  <lpfile>               linear program as .mps[.gz] or .lp[.gz] file

general options:
  --readbas=<basfile>    read starting basis from file
  --writebas=<basfile>   write terminal basis to file
  --writefile=<lpfile>   write LP to file in LP or MPS format depending on extension
  --writedual=<lpfile>   write the dual LP to a file in LP or MPS formal depending on extension
  --<type>:<name>=<val>  change parameter value using syntax of settings file entries
  --loadset=<setfile>    load parameters from settings file (overruled by command line parameters)
  --saveset=<setfile>    save parameters to settings file
  --diffset=<setfile>    save modified parameters to settings file
  --extsol=<value>       external solution for soplex to use for validation

limits and tolerances:
  -t<s>                  set time limit to <s> seconds
  -i<n>                  set iteration limit to <n>
  -f<eps>                set primal feasibility tolerance to <eps>
  -o<eps>                set dual feasibility (optimality) tolerance to <eps>
  -l<eps>                set validation tolerance to <eps>

algorithmic settings (* indicates default):
  --readmode=<value>     choose reading mode for <lpfile> (0* - floating-point, 1 - rational)
  --solvemode=<value>    choose solving mode (0 - floating-point solve, 1* - auto, 2 - force iterative refinement)
  --arithmetic=<value>   choose base arithmetic type (0 - double, 1 - quadprecision, 2 - higher multiprecision)
  --precision=<value>    choose precision for multiprecision solve (only active when arithmetic=2, possible values 50,100,200, compile with mpfr for arbitrary precision)
  -s<value>              choose simplifier/presolver (0 - off, 1* - internal, 2*- PaPILO)
  -g<value>              choose scaling (0 - off, 1 - uni-equilibrium, 2* - bi-equilibrium, 3 - geometric, 4 - iterated geometric, 5 - least squares, 6 - geometric-equilibrium)
  -p<value>              choose pricing (0* - auto, 1 - dantzig, 2 - parmult, 3 - devex, 4 - quicksteep, 5 - steep)
  -r<value>              choose ratio tester (0 - textbook, 1 - harris, 2 - fast, 3* - boundflipping)

display options:
  -v<level>              set verbosity to <level> (0 - error, 3 - normal, 5 - high)
  -x                     print primal solution
  -y                     print dual multipliers
  -X                     print primal solution in rational numbers
  -Y                     print dual multipliers in rational numbers
  -q                     display detailed statistics
  -c                     perform final check of optimal solution in original problem
/usr/bin/sqlite
2.8.17
/usr/bin/sqlite3
3.37.2 2022-01-06 13:25:41 872ba256cbf61d9290b571c0e6d82a20c224ca3ad82971edc46b29818d5dalt1
/usr/bin/sqlline
                                                               
╔═════════════════════════════════════════════════════════════╗
║  ⚠  SYSTEM UTILITY NOT AVAILABLE -> USE COMPUTE SERVERS  ⚠  ║
╠═════════════════════════════════════════════════════════════╣
║ It is not possible to run this utility in a CoCalc project. ║
╟─────────────────────────────────────────────────────────────╢
║ However, you can become an admin in a 𝗖𝗢𝗠𝗣𝗨𝗧𝗘 𝗦𝗘𝗥𝗩𝗘𝗥!       ║
║ Learn more here: https://doc.cocalc.com/compute_server.html ║
╚═════════════════════════════════════════════════════════════╝
                                                               
[warning] /usr/bin/sqlline: Unable to locate mariadb-java-client in /usr/share/java
[warning] /usr/bin/sqlline: Unable to locate hsqldb in /usr/share/java
[warning] /usr/bin/sqlline: Unable to locate jtds in /usr/share/java
Picked up _JAVA_OPTIONS: -Xms64m
Usage: java sqlline.SqlLine 
   -u <database url>               the JDBC URL to connect to
   -n <username>                   the username to connect as
   -p <password>                   the password to connect as
   -d <driver class>               the driver class to use
   --color=[true/false]            control whether color is used for display
   --showHeader=[true/false]       show column names in query results
   --headerInterval=ROWS;          the interval between which heades are displayed
   --fastConnect=[true/false]      skip building table/column list for tab-completion
   --autoCommit=[true/false]       enable/disable automatic transaction commit
   --verbose=[true/false]          show verbose error messages and debug info
   --showWarnings=[true/false]     display connection warnings
   --force=[true/false]            continue running script even after errors
   --maxWidth=MAXWIDTH             the maximum width of the terminal
   --maxColumnWidth=MAXCOLWIDTH    the maximum width to use when displaying columns
   --silent=[true/false]           be more silent
   --autosave=[true/false]         automatically save preferences
   --outputformat=[table/vertical/csv/tsv]   format mode for result display
   --isolation=LEVEL               set the transaction isolation level
   --help                          display this message
/usr/bin/ssh
OpenSSH_8.9p1 Ubuntu-3ubuntu0.6, OpenSSL 3.0.2 15 Mar 2022
/usr/bin/stack
2.3.3 x86_64
Compiled with:
- Cabal-3.0.1.0
- Glob-0.10.1
- StateVar-1.2
- aeson-1.4.7.1
- annotated-wl-pprint-0.7.0
- ansi-terminal-0.10.3
- ansi-wl-pprint-0.6.9
- array-0.5.4.0
- asn1-encoding-0.9.6
- asn1-parse-0.9.5
- asn1-types-0.3.4
- async-2.2.2
- attoparsec-0.13.2.4
- attoparsec-iso8601-1.0.1.0
- auto-update-0.1.6
- base-4.13.0.0
- base-compat-0.11.1
- base-compat-batteries-0.11.1
- base-orphans-0.8.2
- base16-bytestring-0.1.1.7
- base64-bytestring-1.0.0.3
- basement-0.0.11
- bifunctors-5.5.7
- binary-0.8.7.0
- bitarray-0.0.1.1
- blaze-builder-0.4.1.0
- blaze-html-0.9.1.2
- blaze-markup-0.8.2.7
- bytestring-0.10.10.1
- casa-client-0.0.1
- casa-types-0.0.1
- case-insensitive-1.2.1.0
- cereal-0.5.8.1
- clock-0.8
- colour-2.3.5
- comonad-5.0.6
- conduit-1.3.2
- conduit-extra-1.3.5
- connection-0.3.1
- constraints-0.12
- containers-0.6.2.1
- contravariant-1.5.2
- cookie-0.4.5
- cryptohash-sha256-0.11.101.0
- cryptonite-0.26
- cryptonite-conduit-0.2.2
- data-default-class-0.1.2.0
- deepseq-1.4.4.0
- digest-0.0.1.2
- directory-1.3.6.0
- distributive-0.6.2
- dlist-0.8.0.8
- easy-file-0.2.2
- echo-0.1.3
- ed25519-0.0.5.0
- either-5.0.1.1
- enclosed-exceptions-1.0.3
- exceptions-0.10.4
- extra-1.7.4
- fast-logger-3.0.1
- file-embed-0.0.12.0
- filelock-0.1.1.5
- filepath-1.4.2.1
- fsnotify-0.3.0.1
- generic-deriving-1.13.1
- ghc-boot-th-8.8.4
- ghc-prim-0.5.3
- hackage-security-0.6.0.1
- hashable-1.3.0.0
- hi-file-parser-0.1.0.0
- hinotify-0.4
- hourglass-0.2.12
- hpack-0.34.2
- hpc-0.6.0.3
- http-api-data-0.4.1.1
- http-client-0.6.4.1
- http-client-tls-0.3.5.3
- http-conduit-2.3.7.3
- http-download-0.2.0.0
- http-types-0.12.3
- infer-license-0.2.0
- integer-gmp-1.0.2.0
- integer-logarithms-1.0.3
- libyaml-0.1.2
- lifted-async-0.10.1.2
- lifted-base-0.2.3.12
- megaparsec-8.0.0
- memory-0.15.0
- microlens-0.4.11.2
- microlens-mtl-0.2.0.1
- microlens-th-0.4.3.5
- mime-types-0.1.0.9
- monad-control-1.0.2.3
- monad-logger-0.3.34
- monad-loops-0.4.3
- mono-traversable-1.0.15.1
- mtl-2.2.2
- mustache-2.3.1
- neat-interpolation-0.3.2.6
- network-3.1.1.1
- network-uri-2.6.3.0
- old-locale-1.0.0.7
- old-time-1.1.0.3
- open-browser-0.2.1.0
- optparse-applicative-0.15.1.0
- pantry-0.4.0.2
- parsec-3.1.14.0
- parser-combinators-1.2.1
- path-0.7.0
- path-io-1.6.0
- path-pieces-0.2.1
- pem-0.2.4
- persistent-2.10.5.2
- persistent-sqlite-2.10.6.2
- persistent-template-2.8.2.3
- pretty-1.1.3.6
- primitive-0.7.0.1
- process-1.6.9.0
- profunctors-5.5.2
- project-template-0.2.1.0
- random-1.1
- regex-applicative-0.3.3.1
- regex-applicative-text-0.1.0.1
- resource-pool-0.2.3.2
- resourcet-1.2.4.2
- retry-0.8.1.2
- rio-0.1.18.0
- rio-orphans-0.1.1.0
- rio-prettyprint-0.1.1.0
- rts-1.0
- safe-0.3.19
- safe-exceptions-0.1.7.0
- scientific-0.3.6.2
- semigroupoids-5.3.4
- semigroups-0.19.1
- shelly-1.9.0
- silently-1.2.5.1
- socks-0.6.1
- split-0.2.3.4
- stm-2.5.0.0
- stm-chans-3.0.0.4
- streaming-commons-0.2.2.1
- syb-0.7.1
- tagged-0.8.6
- tar-0.5.1.1
- tar-conduit-0.3.2
- template-haskell-2.15.0.0
- temporary-1.3
- text-1.2.4.0
- text-metrics-0.3.0
- th-abstraction-0.3.2.0
- th-expand-syns-0.4.6.0
- th-lift-0.8.1
- th-lift-instances-0.1.17
- th-reify-many-0.1.9
- time-1.9.3
- time-compat-1.9.3
- tls-1.5.4
- transformers-0.5.6.2
- transformers-base-0.4.5.2
- transformers-compat-0.6.5
- type-equality-1
- typed-process-0.2.6.0
- unicode-transforms-0.3.6
- unix-2.7.2.2
- unix-compat-0.5.2
- unix-time-0.4.7
- unliftio-0.2.13
- unliftio-core-0.1.2.0
- unordered-containers-0.2.10.0
- uuid-types-1.0.3
- vector-0.12.1.2
- vector-algorithms-0.8.0.3
- x509-1.7.5
- x509-store-1.6.7
- x509-system-1.6.6
- x509-validation-1.6.11
- yaml-0.11.4.0
- zip-archive-0.4.1
- zlib-0.6.2.2

Warning: this is an unsupported build that may use different versions of
dependencies and GHC than the officially released binaries, and therefore may
not behave identically.  If you encounter problems, please try the latest
official build by running 'stack upgrade --force-download'.
/usr/local/bin/stapler
usage: usage: stapler [options] mode (input.pdf|input handle) ... [output.pdf]

Modes:
cat/sel: <inputfile>|<input handle> [<pagerange>[<rotation>]] ... (output needed)
    Select the given pages/ranges from input files.
    No range means all pages.
del: <inputfile> [<pagerange>[<rotation>]] ... (output needed)
    Select all but the given pages/ranges from input files.
burst/split: <inputfile> ... (no output needed)
    Create one file per page in input pdf files (no output needed)
zip: <inputfile>|<input handle> [<pagerange>[<rotation>]] ... (output needed)
    Merge/Collate the given input files interleaved.
background: <inputfile> [<pagerange>[<rotation>]] ... (output needed)
    Merge/Overlay the given input files interleaved.
info: <inputfile> ... (no output needed)
    Display PDF metadata
list-log(ical): <inputfile>
    Display the logical names of each page.

Input handle:
    A single, upper-case letter as an alias to a file
    For example: A=input1.pdf B=input2.pdf

Page ranges:
    n - single numbers mean single pages (e.g., 15)
    n-m - page ranges include the entire specified range (e.g. 1-6)
    m-n - negative ranges sort pages backwards (e.g., 6-3)

Extended page range options:
    ...-end will be replaced with the last page in the file
    R, L, or D will rotate the respective range +90, -90, or 180 degrees,
        respectively. (e.g., 1-15R)

positional arguments:
  mode                  requested stapler mode

options:
  -h, --help            show this help message and exit
  -o OWNERPW, --ownerpw OWNERPW
                        Set owner password to encrypt output file with
  -u USERPW, --userpw USERPW
                        Set user password to encrypt output file with
  -v, --verbose
  -f, --force           Overwrite output file if it exists
  -d DESTDIR, --destdir DESTDIR
                        directory where to store output file
/usr/bin/sumo
Eclipse SUMO sumo Version 1.19.0
 Build features: Linux-5.4.0-164-generic x86_64 GNU 11.4.0 Release FMI Proj GUI Intl SWIG GDAL GL2PS Eigen
 Copyright (C) 2001-2023 German Aerospace Center (DLR) and others; https://sumo.dlr.de

Eclipse SUMO sumo Version 1.19.0 is part of SUMO.
This program and the accompanying materials
are made available under the terms of the Eclipse Public License v2.0
which accompanies this distribution, and is available at
http://www.eclipse.org/legal/epl-v20.html
This program may also be made available under the following Secondary
Licenses when the conditions for such availability set forth in the Eclipse
Public License 2.0 are satisfied: GNU General Public License, version 2
or later which is available at
https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
SPDX-License-Identifier: EPL-2.0 OR GPL-2.0-or-later
/usr/bin/syco
EMBOSS:6.6.0.0
/usr/bin/symphony

==  Welcome to the SYMPHONY MILP Solver 
==  Copyright 2000-2019 Ted Ralphs and others 
==  All Rights Reserved. 
==  Distributed under the Eclipse Public License 1.0 
==  Version: 5.6.17 
==  Build Date: Oct 16 2021 
/usr/bin/synctex
This is SyncTeX command line utility, version 1.5
usage: synctex <subcommand> [options] [args]
Synchronize TeXnology command-line client, version 1.21

The Synchronization TeXnology by Jérôme Laurens is a rather new feature of recent TeX engines.
It allows to synchronize between input and output, which means to
navigate from the source document to the typeset material and vice versa.

Available subcommands:
   view     to perform forwards synchronization
   edit     to perform backwards synchronization
   update   to update a synctex file after a dvi/xdv to pdf filter
   help     this help

Type 'synctex help <subcommand>' for help on a specific subcommand.
There is also an undocumented test subcommand.
/usr/bin/t1asm
t1asm (LCDF t1utils) 1.41
Copyright (C) 1992-2017 I. Lee Hetherington, Eddie Kohler et al.
This is free software; see the source for copying conditions.
There is NO warranty, not even for merchantability or fitness for a
particular purpose.
/usr/bin/tclsh
8.6
/usr/local/bin/texsurgery
usage: texsurgery [-h] [-pdf] [-tex] [-replace REPLACE REPLACE] [-find FIND]
                  [-shuffle SHUFFLE SHUFFLE] [-randomseed RANDOMSEED]
                  [--output_file OUTPUT_FILE] [--pdflatex-options ...]
                  [input_file]

TexSurgery passes code from latex files to jupyter kernels, and substitutes it
by the corresponding output.

positional arguments:
  input_file            file to parse. Uses stdin if none given.

options:
  -h, --help            show this help message and exit
  -pdf                  create a pdf file from the modified latex (requires
                        pdflatex installed).
  -tex                  just produce the modified latex (default).
  -replace REPLACE REPLACE
                        finds a selector, replaces the first match with the
                        replacement text, outputs the result
  -find FIND            finds a selector, output the code for the innermost
                        part of the selector
  -shuffle SHUFFLE SHUFFLE
                        finds a parent selector, and shuffles all matches of
                        the children selector within the parent, then outputs
                        the result
  -randomseed RANDOMSEED
                        randomseed for -shuffle
  --output_file OUTPUT_FILE, -o OUTPUT_FILE
                        file to write the output to.
  --pdflatex-options ...
                        options to pass to pdflatex (requires the -pdf option)
/usr/bin/tidy
HTML Tidy for Linux version 5.6.0
/usr/bin/tmux
tmux 3.2a
/usr/local/bin/tmuxp
tmuxp 1.11.1, libtmux 0.11.0
/usr/sbin/traceroute
Modern traceroute for Linux, version 2.1.0
Copyright (c) 2016  Dmitry Butskoy,   License: GPL v2 or any later
/usr/bin/tsc
Version 5.3.3
/usr/bin/valgrind
valgrind-3.18.1
/usr/bin/vim
VIM - Vi IMproved 8.2 (2019 Dec 12, compiled Dec 05 2023 17:58:57)
Included patches: 1-579, 1969, 580-1848, 4975, 5016, 5023, 5072, 2068, 1849-1854, 1857, 1855-1857, 1331, 1858, 1858-1859, 1873, 1860-1969, 1992, 1970-1992, 2010, 1993-2068, 2106, 2069-2106, 2108, 2107-2109, 2109-3995, 4563, 4646, 4774, 4895, 4899, 4901, 4919, 213, 1840, 1846-1847, 2110-2112, 2121
Modified by [email protected]
Compiled by [email protected]
Huge version with GTK3 GUI.  Features included (+) or not (-):
+acl               +file_in_path      +mouse_urxvt       -tag_any_white
+arabic            +find_in_path      +mouse_xterm       +tcl
+autocmd           +float             +multi_byte        +termguicolors
+autochdir         +folding           +multi_lang        +terminal
-autoservername    -footer            -mzscheme          +terminfo
+balloon_eval      +fork()            +netbeans_intg     +termresponse
+balloon_eval_term +gettext           +num64             +textobjects
+browse            -hangul_input      +packages          +textprop
++builtin_terms    +iconv             +path_extra        +timers
+byte_offset       +insert_expand     +perl              +title
+channel           +ipv6              +persistent_undo   +toolbar
+cindent           +job               +popupwin          +user_commands
+clientserver      +jumplist          +postscript        +vartabs
+clipboard         +keymap            +printer           +vertsplit
+cmdline_compl     +lambda            +profile           +vim9script
+cmdline_hist      +langmap           -python            +viminfo
+cmdline_info      +libcall           +python3           +virtualedit
+comments          +linebreak         +quickfix          +visual
+conceal           +lispindent        +reltime           +visualextra
+cryptv            +listcmds          +rightleft         +vreplace
+cscope            +localmap          +ruby              +wildignore
+cursorbind        +lua               +scrollbind        +wildmenu
+cursorshape       +menu              +signs             +windows
+dialog_con_gui    +mksession         +smartindent       +writebackup
+diff              +modify_fname      +sodium            +X11
+digraphs          +mouse             +sound             -xfontset
+dnd               +mouseshape        +spell             +xim
-ebcdic            +mouse_dec         +startuptime       +xpm
+emacs_tags        +mouse_gpm         +statusline        +xsmp_interact
+eval              -mouse_jsbterm     -sun_workshop      +xterm_clipboard
+ex_extra          +mouse_netterm     +syntax            -xterm_save
+extra_search      +mouse_sgr         +tag_binary        
-farsi             -mouse_sysmouse    -tag_old_static    
   system vimrc file: "$VIM/vimrc"
     user vimrc file: "$HOME/.vimrc"
 2nd user vimrc file: "~/.vim/vimrc"
      user exrc file: "$HOME/.exrc"
  system gvimrc file: "$VIM/gvimrc"
    user gvimrc file: "$HOME/.gvimrc"
2nd user gvimrc file: "~/.vim/gvimrc"
       defaults file: "$VIMRUNTIME/defaults.vim"
    system menu file: "$VIMRUNTIME/menu.vim"
  fall-back for $VIM: "/usr/share/vim"
Compilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -DFEAT_GUI_GTK -pthread -I/usr/include/gtk-3.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib/x86_64-linux-gnu/dbus-1.0/include -I/usr/include/gtk-3.0 -I/usr/include/gio-unix-2.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Wdate-time -g -O2 -ffile-prefix-map=/build/vim-gVT2fw/vim-8.2.3995=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -D_REENTRANT -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 
Linking: gcc -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -fstack-protector-strong -rdynamic -Wl,-export-dynamic -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vim -lgtk-3 -lgdk-3 -lpangocairo-1.0 -lpango-1.0 -lharfbuzz -latk-1.0 -lcairo-gobject -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lSM -lICE -lXpm -lXt -lX11 -lXdmcp -lSM -lICE -lm -ltinfo -lselinux -lcanberra -lsodium -lacl -lattr -lgpm -L/usr/lib -llua5.2 -Wl,-E -fstack-protector-strong -L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/perl/5.34/CORE -lperl -ldl -lm -lpthread -lcrypt -L/usr/lib/python3.10/config-3.10-x86_64-linux-gnu -lpython3.10 -lcrypt -ldl -lm -lm -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -lruby-3.0 -lm -L/usr/lib 
/usr/bin/vis
vis v0.7 +curses +lua +tre +acl +selinux
/usr/bin/wdiff
wdiff (GNU wdiff) 1.2.2

Copyright (C) 1992, 1997, 1998, 1999, 2009, 2010, 2011, 2012 Free Software
Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Written by Franc,ois Pinard <[email protected]>.
/usr/local/bin/weasyprint
WeasyPrint version 60.2
/usr/bin/which
/usr/sbin/rpcinfo
/usr/bin/wordmatch
EMBOSS:6.6.0.0
/usr/bin/xclip
xclip version 0.13
Copyright (C) 2001-2008 Kim Saunders et al.
Distributed under the terms of the GNU GPL
/usr/bin/xdotool
xdotool version 3.20160805.1
/usr/bin/xelatex
XeTeX 3.141592653-2.6-0.999993 (TeX Live 2022/dev/Debian)
kpathsea version 6.3.4/dev
Copyright 2021 SIL International, Jonathan Kew and Khaled Hosny.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the XeTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the XeTeX source.
Primary author of XeTeX: Jonathan Kew.
Compiled with ICU version 70.1; using 70.1
Compiled with zlib version 1.2.11; using 1.2.11
Compiled with FreeType2 version 2.11.1; using 2.11.1
Compiled with Graphite2 version 1.3.14; using 1.3.14
Compiled with HarfBuzz version 2.7.4; using 2.7.4
Compiled with libpng version 1.6.37; using 1.6.37
Compiled with pplib version v2.05 less toxic i hope
Compiled with fontconfig version 2.13.1; using 2.13.1
/usr/bin/xindy
xindy release: unknown
xindy script version: 1.18
xindy kernel version: 3.0
CLISP version 2.49.93+ (2018-02-18) (built on lcy02-amd64-013.buildd [127.0.1.1])
    architecture: X86_64
/usr/bin/xpra
xpra v3.1
/usr/bin/xsel
xsel version 1.2.0 by Conrad Parker <[email protected]>
/usr/bin/xz
xz (XZ Utils) 5.2.5
liblzma 5.2.5
/usr/bin/yacc
bison (GNU Bison) 3.8.2
Written by Robert Corbett and Richard Stallman.

Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/usr/local/bin/yapf
yapf 0.40.2
/usr/bin/z3
Z3 version 4.8.12 - 64 bit
/ext/bin/zig
0.11.0
/ext/bin/zimpl
3.5.3
/usr/bin/zotero
Zotero Zotero 6.0.30, Copyright (c) 2006-2018 Contributors
/usr/bin/zsh
zsh 5.8.1 (x86_64-ubuntu-linux-gnu)
This information was collected at 20240212-1717.