Executables in CoCalc (Ubuntu 24.04)

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 24.04.

Showing 291 executables

Path	Information
`/usr/bin/4ti2-zsolve`	------------------------------------------------- 4ti2 version 1.6.10 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 23.01 (x64) : Copyright (c) 1999-2023 Igor Pavlov : 2023-06-20 64-bit locale=C.UTF-8 Threads:4 OPEN_MAX:10000 Usage: 7z <command> [<switches>...] <archive_name> [<file_names>...] [@listfile] <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 and @listfile 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 -mx[N] : set compression level: -mx1 (fastest) ... -mx9 (ultra) -o{Directory} : set Output directory -p{Password} : set Password -r[-\|0] : Recurse subdirectories for name search -sa{a\|e\|s} : set Archive name mode -scc{UTF-8\|WIN\|DOS} : set charset 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[2] : use fully qualified file paths -ssc[-] : set sensitive case mode -sse : stop archive creating, if it can't open some input file -ssp : do not change Last Access Time of source files while archiving -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 pcre version 10.42 2022-12-11 Features: +jit +pcre2 +lzma +zlib
`/usr/bin/ant`	Picked up _JAVA_OPTIONS: -Xms64m Apache Ant(TM) version 1.10.14 compiled on September 25 2023
`/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 2.8.3 (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 - automatically remove 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 2.8.3 (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.
`/ext/venvs/cocalc/bin/asciidoc`	asciidoc 10.2.1
`/usr/bin/aspell`	@(#) International Ispell Version 3.1.20 (but really Aspell 0.60.8.1)
`/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]>.
`/ext/venvs/cocalc/bin/autopep8`	autopep8 2.3.2 (pycodestyle: 2.13.0)
`/usr/bin/bash`	GNU bash, version 5.2.21(1)-release (x86_64-pc-linux-gnu) Copyright (C) 2022 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`	WARNING: ignoring _JAVA_OPTIONS in environment. OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [bazel development version] Usage: bazel <command> <options> ... Available commands: analyze-profile Analyzes build profile data. aquery Analyzes the given targets and queries the action graph. build Builds the specified targets. canonicalize-flags Canonicalizes a list of bazel options. clean Removes output files and optionally stops the server. coverage Generates code coverage report for specified test targets. cquery Loads, analyzes, and queries the specified targets w/ configurations. dump Dumps the internal state of the bazel server process. fetch Fetches external repositories that are prerequisites to the targets. help Prints help for commands, or the index. info Displays runtime info about the bazel server. license Prints the license of this software. print_action Prints the command line args for compiling a file. query Executes a dependency graph query. run Runs the specified target. shutdown Stops the bazel server. sync Syncs all repositories specified in the workspace file test Builds and runs the specified test targets. version Prints version information for bazel. Getting more help: bazel help <command> Prints help and options for <command>. bazel help startup_options Options for the JVM hosting bazel. bazel help target-syntax Explains the syntax for specifying targets. bazel help info-keys Displays a list of keys used by the info command.
`/usr/bin/bc`	bc 1.07.1 Copyright 1991-1994, 1997, 1998, 2000, 2004, 2006, 2008, 2012-2017 Free Software Foundation, Inc.
`/ext/bin/bedtools`	bedtools v2.31.1
`/ext/texlive/2025/bin/x86_64-linux/biber`	biber version: 2.20
`/ext/texlive/2025/bin/x86_64-linux/bibtex`	BibTeX 0.99d (TeX Live 2025) kpathsea version 6.4.1 Copyright 2025 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.
`/ext/venvs/cocalc/bin/black`	black, 25.1.0 (compiled: yes) Python (CPython) 3.12.10
`/usr/bin/bliss`	bliss version 0.77 (Debian ) Copyright (C) 2003-2015 Tommi Junttila. License LGPLv3+: GNU LGPL version 3 or later, <http://gnu.org/licenses/lgpl.html>. This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions; see COPYING and COPYING.LESSER for details.
`/usr/bin/bun`	1.2.17
`/usr/bin/bup`	0.33.3
`/usr/bin/cabal`	cabal-install version 3.8.1.0 compiled using version 3.8.1.0 of the Cabal library
`/usr/bin/cal`	June 2025 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 30
`/usr/bin/calc`	C-style arbitrary precision calculator w/custom functions (version 2.15.0.4)
`/ext/bin/cargo`	cargo 1.83.0 (5ffbef321 2024-10-29)
`/usr/bin/cbc`	Welcome to the CBC MILP Solver Version: 2.10.11 Build Date: Jan 21 2024 command line - cbc -help (default strategy 1) Cbc version 2.10.11, build Jan 21 2024 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): 0.01 (Wallclock seconds): 0.01
`/usr/bin/ccache`	ccache version 4.9.1 Features: file-storage http-storage redis+unix-storage redis-storage Copyright (C) 2002-2007 Andrew Tridgell Copyright (C) 2009-2024 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 4.0.2 CMake suite maintained and supported by Kitware (kitware.com/cmake).
`/ext/bin/cdo`	Climate Data Operators version 2.4.4 (https://mpimet.mpg.de/cdo) System: x86_64-conda-linux-gnu CXX Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1733367957166/_build_env/bin/x86_64-conda-linux-gnu-c++ -std=gnu++20 -fPIC -DPIC -g -O2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/venvs/miniforge2025/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1733367957166/work=/usr/local/src/conda/cdo-2.4.4 -fdebug-prefix-map=/ext/venvs/miniforge2025=/usr/local/src/conda-prefix -fopenmp -pthread CXX version : x86_64-conda-linux-gnu-c++ (conda-forge gcc 13.3.0-1) 13.3.0 CXX library : span ranges C Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1733367957166/_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/venvs/miniforge2025/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1733367957166/work=/usr/local/src/conda/cdo-2.4.4 -fdebug-prefix-map=/ext/venvs/miniforge2025=/usr/local/src/conda-prefix -fopenmp -pthread -pthread C version : x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0 F77 Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1733367957166/_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/venvs/miniforge2025/include -I/home/conda/feedstock_root/build_artifacts/cdo_1733367957166/_build_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1733367957166/work=/usr/local/src/conda/cdo-2.4.4 -fdebug-prefix-map=/ext/venvs/miniforge2025=/usr/local/src/conda-prefix F77 version : GNU Fortran (conda-forge gcc 13.3.0-1) 13.3.0 Features: 31GB 4threads c++20 OpenMP45 Fortran pthreads HDF5 NC4/HDF5/threadsafe OPeNDAP udunits2 proj xml2 magics curl fftw3 sse3 Libraries: yac/3.1.0 NetCDF/4.9.2 HDF5/1.14.3 proj/9.5.1 xml2/2.13.5 curl/8.13.0(h8.10.1) magics/4.15.5 CDI data types: SizeType=size_t CDI file types: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5 nczarr CDI library version : 2.4.4 cgribex library version : 2.3.0 ecCodes library version : 2.41.0 NetCDF library version : 4.9.2 of Dec 3 2024 13:20:46 $ exse library version : 2.0.0 FILE library version : 1.9.1
`/usr/bin/chafa`	Chafa version 1.14.0 Loaders: AVIF GIF JPEG PNG QOI SVG TIFF WebP XWD Features: mmx sse4.1 popcnt avx2 Applying: mmx sse4.1 popcnt avx2 Copyright (C) 2018-2023 Hans Petter Jansson et al. Incl. libnsgif copyright (C) 2004 Richard Wilson, copyright (C) 2008 Sean Fox Incl. LodePNG copyright (C) 2005-2018 Lode Vandevenne Incl. QOI decoder copyright (C) 2021 Dominic Szablewski 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/venvs/cocalc/bin/cheetah`	3.2.6.post1
`/usr/bin/chromedriver`	ChromeDriver 137.0.7151.119 (e0ac9d12dff5f2d33c935958b06bf1ded7f1c08c-refs/branch-heads/7151@{#2356})
`/usr/bin/clang`	Ubuntu clang version 18.1.3 (1ubuntu1) Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin
`/usr/bin/clang-format`	Ubuntu clang-format version 18.1.3 (1ubuntu1)
`/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 "1.11.1"
`/usr/bin/clp`	Coin LP version 1.17.9, build Jan 21 2024 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/bin/cmake`	cmake version 4.0.2 CMake suite maintained and supported by Kitware (kitware.com/cmake).
`/usr/bin/cobc`	cobc (GnuCOBOL) 3.1.2.0 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; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Written by Keisuke Nishida, Roger While, Ron Norman, Simon Sobisch, Edward Hart Built Apr 14 2024 07:59:15 Packaged Dec 23 2020 12:04:58 UTC C version "13.2.0"
`/usr/bin/code-server`	4.100.2 9dd999ba78032163d606fadd531de5e1fcae5443 with Code 1.100.2
`/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 - selaginella v6.3 Selaginella moellendorffii (selaginella) 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 - lamprey v6.3 Petromyzon marinus (lamprey) accession and ontology information - dog v6.3 Canis lupus familiaris (dog) accession and ontology information - chicken-o v6.3 Gallus gallus (chicken) accession and ontology information - patens v6.3 Physcomitrella patens (patens) accession and ontology information - bee v6.3 Apis mellifera (bee) accession and ontology information - corn v6.3 Zea mays (corn) accession and ontology information - zebrafinch v6.3 Taeniopygia guttata (zebrafinch) accession and ontology information - balbc_cocci v5.2 Balbc/J mouse and Coccidioides genome combined - tomato v6.3 Solanum lycopersicum (tomato) accession and ontology information - zebrafish-o v6.3 Danio rerio (zebrafish) accession and ontology information - hydra v6.3 Hydra vulgaris (hydra) accession and ontology information - rice v6.3 Oryza sativa (rice) accession and ontology information - mosquito v6.3 Anopheles gambiae (mosquito) accession and ontology information - laevis v6.3 Xenopus laevis (laevis) accession and ontology information - rat-o v6.3 Rattus norvegicus (rat) accession and ontology information - chlamy v6.3 Chlamydomonas reinhardtii (chlamy) accession and ontology information - mouse-o v6.3 Mus musculus (mouse) accession and ontology information - ncrassa v6.3 Neurospora crassa (ncrassa) accession and ontology information - yeast-o v6.3 Saccharomyces cerevisiae (yeast) accession and ontology information - arabidopsis-o v6.3 Arabidopsis thaliana (arabidopsis) accession and ontology information - fugu v6.3 Takifugu rubripes (fugu) accession and ontology information - mushroom v6.3 Agaricus bisporus (mushroom) 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 - urchin v6.3 Strongylocentrotus purpuratus (urchin) accession and ontology information - frog-o v6.3 Xenopus tropicalis (frog) accession and ontology information - pig v6.3 Sus scrofa (pig) accession and ontology information - seahare v6.3 Aplysia californica (seahare) accession and ontology information - ciliate v6.3 Tetrahymena thermophila (ciliate) accession and ontology information - pseudonana v6.3 Thalassiosira pseudonana (pseudonana) accession and ontology information - ciona v6.3 Ciona intestinalis (ciona) accession and ontology information - diatom v6.3 Phaeodactylum tricornutum (diatom) accession and ontology information - pombe v6.3 Schizosaccharomyces pombe (pombe) accession and ontology information - anemone v6.3 Nematostella vectensis (anemone) accession and ontology information - volvox v6.3 Volvox carteri (volvox) accession and ontology information - cow v5.4 Bos taurus (cow) accession and ontology information - rhesus v6.3 Macaca mulatta (rhesus) accession and ontology information - dicty v6.3 Dictyostelium discoideum (dicty) accession and ontology information PROMOTERS - mouse-p v5.5 mouse promoters (mouse) - zebrafish-p v5.5 zebrafish promoters (zebrafish) - arabidopsis-p v6.3 arabidopsis promoters (arabidopsis) - yeast-p v5.5 yeast promoters (yeast) - frog-p v5.5 frog promoters (frog) - rat-p v5.5 rat promoters (rat) - chicken-p v5.5 chicken promoters (chicken) - worm-p v5.5 worm promoters (worm) - fly-p v5.5 fly promoters (fly) - human-p v5.5 human promoters (human) GENOMES v5.10 hg18 v6.4 human genome and annotation for UCSC hg18 - susScr3 v6.4 pig genome and annotation for UCSC susScr3 - apiMel2 v6.4 bee genome and annotation for UCSC apiMel2 - anoGam1 v6.4 mosquito genome and annotation for UCSC anoGam1 - AGPv3 v5.10 corn genome and annotation (AGPv3) - apiMel3 v6.4 bee genome and annotation for UCSC apiMel3 - hg17 v6.4 human genome and annotation for UCSC hg17 - mm10 v6.4 mouse genome and annotation for UCSC mm10 - canFam3 v6.4 dog genome and annotation for UCSC canFam3 - susScr11 v6.4 pig genome and annotation for UCSC susScr11 - panPan1 v6.4 human genome and annotation for UCSC panPan1 - mm9 v6.4 mouse genome and annotation for UCSC mm9 - galGal4 v6.4 chicken genome and annotation for UCSC galGal4 - tetNig2 v6.4 fugu genome and annotation for UCSC tetNig2 - taeGut2 v6.4 zebrafinch genome and annotation for UCSC taeGut2 - rice.IRGSP-1.0 v5.10 rice genome and annotation (rice.IRGSP-1.0) - panTro6 v6.4 human genome and annotation for UCSC panTro6 - panTro5 v6.4 human genome and annotation for UCSC panTro5 - mm8 v6.4 mouse genome and annotation for UCSC mm8 - rheMac8 v6.4 rhesus genome and annotation for UCSC rheMac8 - rn4 v6.4 rat genome and annotation for UCSC rn4 - ci2 v6.4 ciona genome and annotation for UCSC ci2 - xenTro9 v6.4 frog genome and annotation for UCSC xenTro9 - galGal5 v6.4 chicken genome and annotation for UCSC galGal5 - ce11 v6.4 worm genome and annotation for UCSC ce11 - galGal6 v6.4 chicken genome and annotation for UCSC galGal6 - fr3 v6.4 fugu genome and annotation for UCSC fr3 - ci3 v6.4 ciona genome and annotation for UCSC ci3 - petMar3 v6.4 lamprey genome and annotation for UCSC petMar3 - rheMac2 v6.4 rhesus genome and annotation for UCSC rheMac2 - panPan2 v6.4 human genome and annotation for UCSC panPan2 - rn5 v6.4 rat genome and annotation for UCSC rn5 - petMar2 v6.4 lamprey genome and annotation for UCSC petMar2 - panTro4 v6.4 human genome and annotation for UCSC panTro4 - panTro3 v6.4 human genome and annotation for UCSC panTro3 - rheMac3 v6.4 rhesus genome and annotation for UCSC rheMac3 - papAnu2 v6.4 human genome and annotation for UCSC papAnu2 - tair10 v6.0 arabidopsis genome and annotation (tair10) - ce6 v6.4 worm genome and annotation for UCSC ce6 - hg38 v6.4 human genome and annotation for UCSC hg38 - danRer10 v6.4 zebrafish genome and annotation for UCSC danRer10 - gorGor5 v6.4 human genome and annotation for UCSC gorGor5 - hg19 v6.4 human genome and annotation for UCSC hg19 - aplCal1 v6.4 seahare genome and annotation for UCSC aplCal1 - xenTro3 v6.4 frog genome and annotation for UCSC xenTro3 - rn6 v6.4 rat genome and annotation for UCSC rn6 - sacCer3 v6.4 yeast genome and annotation for UCSC sacCer3 - corn.AGPv3 v5.10 corn genome and annotation (corn.AGPv3) - dm6 v6.4 fly genome and annotation for UCSC dm6 - xenTro7 v6.4 frog genome and annotation for UCSC xenTro7 - ce10 v6.4 worm genome and annotation for UCSC ce10 - sacCer2 v6.4 yeast genome and annotation for UCSC sacCer2 - xenTro2 v6.4 frog genome and annotation for UCSC xenTro2 - gorGor3 v6.4 human genome and annotation for UCSC gorGor3 - danRer7 v6.4 zebrafish genome and annotation for UCSC danRer7 - strPur2 v6.0 urchin genome and annotation for UCSC strPur2 - gorGor4 v6.4 human genome and annotation for UCSC gorGor4 - dm3 v6.0 fly genome and annotation for UCSC dm3 - patens.ASM242v1 v5.10 patens genome and annotation (patens.ASM242v1) - danRer11 v6.4 zebrafish genome and annotation for UCSC danRer11 SETTINGS
`/usr/bin/convert`	Version: ImageMagick 6.9.12-98 Q16 x86_64 18038 https://legacy.imagemagick.org Copyright: (C) 1999 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 raw tiff webp wmf x xml zlib
`/usr/bin/coqc`	The Coq Proof Assistant, version 8.18.0 compiled with OCaml 4.14.1
`/usr/bin/coqchk`	The Coq Proof Checker, version 8.18.0
`/usr/bin/cpp`	cpp (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 Copyright (C) 2023 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 3.0 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 - 400, 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-30 (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
`/ext/venvs/cocalc/bin/cython`	Cython version 3.1.1
`/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 0.98.0, compiled 14:38:19 Apr 8 2024
`/usr/bin/diff3`	diff3 (GNU diffutils) 3.10 Copyright (C) 2023 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/dig`	DiG 9.18.30-0ubuntu0.24.04.2-Ubuntu
`/usr/bin/docbook2pdf`	DocBook-utils version 0.6.14 (jw version 1.1)
`/ext/bin/nosudo/docker`	╔═════════════════════════════════════════════════════════════╗ ║ ⚠ 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 ║ ╚═════════════════════════════════════════════════════════════╝ ╔═══════════════════════════════════════════════════════╗ ║ ⚠ 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/bin/docx2txt`	Usage: /usr/bin/docx2txt [infile.docx\|-\|-h] [outfile.txt\|-] /usr/bin/docx2txt < infile.docx /usr/bin/docx2txt < infile.docx > outfile.txt In second usage, output is dumped on STDOUT. Use '-h' as the first argument to get this usage information. Use '-' as the infile name to read the docx file from STDIN. Use '-' as the outfile name to dump the text on STDOUT. Output is saved in infile.txt if second argument is omitted. Note: infile.docx can also be a directory name holding the unzipped content of concerned .docx file.
`/usr/bin/dot`	dot - graphviz version 2.43.0 (0)
`/usr/bin/dotty`	dotty version 96c (09-24-96) Error: Can't open display:
`/ext/bin/dust`	Dust 1.2.0
`/ext/texlive/2025/bin/x86_64-linux/dvips`	This is dvips(k) 2025.1 (TeX Live 2025) Copyright 2025 Radical Eye Software kpathsea version 6.4.1 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 1.20.1 Copyright (C) 1994 Andrew L. Moore. Copyright (C) 2024 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 29.3 Copyright (C) 2024 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 13.2.2.5
`/ext/venvs/cocalc/bin/f2py`	2.2.6
`/usr/bin/f77`	GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 Copyright (C) 2023 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 13.3.0-6ubuntu2~24.04) 13.3.0 Copyright (C) 2023 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 0.23.4
`/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 6.1.1-3ubuntu5 Copyright (c) 2000-2023 the FFmpeg developers built with gcc 13 (Ubuntu 13.2.0-23ubuntu3) configuration: --prefix=/usr --extra-version=3ubuntu5 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --disable-omx --enable-gnutls --enable-libaom --enable-libass --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libdav1d --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libglslang --enable-libgme --enable-libgsm --enable-libharfbuzz --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzimg --enable-openal --enable-opencl --enable-opengl --disable-sndio --enable-libvpl --disable-libmfx --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-chromaprint --enable-frei0r --enable-ladspa --enable-libbluray --enable-libjack --enable-libpulse --enable-librabbitmq --enable-librist --enable-libsrt --enable-libssh --enable-libsvtav1 --enable-libx264 --enable-libzmq --enable-libzvbi --enable-lv2 --enable-sdl2 --enable-libplacebo --enable-librav1e --enable-pocketsphinx --enable-librsvg --enable-libjxl --enable-shared WARNING: library configuration mismatch avcodec configuration: --prefix=/usr --extra-version=3ubuntu5 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --disable-omx --enable-gnutls --enable-libaom --enable-libass --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libdav1d --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libglslang --enable-libgme --enable-libgsm --enable-libharfbuzz --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzimg --enable-openal --enable-opencl --enable-opengl --disable-sndio --enable-libvpl --disable-libmfx --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-chromaprint --enable-frei0r --enable-ladspa --enable-libbluray --enable-libjack --enable-libpulse --enable-librabbitmq --enable-librist --enable-libsrt --enable-libssh --enable-libsvtav1 --enable-libx264 --enable-libzmq --enable-libzvbi --enable-lv2 --enable-sdl2 --enable-libplacebo --enable-librav1e --enable-pocketsphinx --enable-librsvg --enable-libjxl --enable-shared --enable-version3 --disable-doc --disable-programs --disable-static --enable-libaribb24 --enable-libopencore_amrnb --enable-libopencore_amrwb --enable-libtesseract --enable-libvo_amrwbenc --enable-libsmbclient libavutil 58. 29.100 / 58. 29.100 libavcodec 60. 31.102 / 60. 31.102 libavformat 60. 16.100 / 60. 16.100 libavdevice 60. 3.100 / 60. 3.100 libavfilter 9. 12.100 / 9. 12.100 libswscale 7. 5.100 / 7. 5.100 libswresample 4. 12.100 / 4. 12.100 libpostproc 57. 3.100 / 57. 3.100 Unrecognized option '-version'. Error splitting the argument list: Option not found
`/usr/bin/fish`	fish, version 3.7.0
`/usr/bin/flex`	flex 2.6.4
`/usr/bin/fortls`	2.13.0
`/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 -qsol : quit to output solution file -isol <intial solution file> : specify initial solution file
`/usr/bin/g++`	g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 Copyright (C) 2023 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 10.5.0-4ubuntu2) 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++-14`	g++-14 (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0 Copyright (C) 2024 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/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 13.3.0-6ubuntu2~24.04) 13.3.0 Copyright (C) 2023 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 10.5.0-4ubuntu2) 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-14`	gcc-14 (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0 Copyright (C) 2024 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`	2025-06-25T11:52:45.673Z INFO geckodriver: Detected Geckodriver v0.36.0 to be latest 2025-06-25T11:52:45.691Z INFO geckodriver: Downloading Geckodriver from https://github.com/mozilla/geckodriver/releases/download/v0.36.0/geckodriver-v0.36.0-linux64.tar.gz geckodriver 0.36.0 (a3d508507022 2025-02-24 15:57 +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 13.3.0-6ubuntu2~24.04) 13.3.0 Copyright (C) 2023 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 2.74.0 (2025-05-29) https://github.com/cli/cli/releases/tag/v2.74.0
`/usr/bin/ghc`	The Glorious Glasgow Haskell Compilation System, version 9.4.7
`/usr/bin/giac`	// Using locale /usr/share/locale/ // C.UTF-8 // /usr/share/locale/ // giac // UTF-8 // Maximum number of parallel threads 4 // (c) 2001, 2021 B. Parisse & others 1.9.0
`/usr/bin/git`	git version 2.43.0
`/usr/bin/gnat`	GNAT 13.3.0 Copyright (C) 1996-2023, 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 13.3.0 Copyright (C) 1995-2023, 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 go1.22.2 linux/amd64
`/usr/bin/google-chrome`	Google Chrome 137.0.7151.68
`/usr/bin/gp`	GP/PARI CALCULATOR Version 2.15.4 (released) amd64 running linux (x86-64/GMP-6.3.0 kernel) 64-bit version compiled: Apr 1 2024, gcc version 13.2.0 (Ubuntu 13.2.0-23ubuntu3) threading engine: pthread (readline v8.2 disabled, extended help enabled)
`/usr/bin/gradle`	Picked up _JAVA_OPTIONS: -Xms64m openjdk version "21.0.7" 2025-04-15 OpenJDK Runtime Environment (build 21.0.7+6-Ubuntu-0ubuntu124.04) OpenJDK 64-Bit Server VM (build 21.0.7+6-Ubuntu-0ubuntu124.04, mixed mode, sharing) Picked up _JAVA_OPTIONS: -Xms64m ------------------------------------------------------------ Gradle 4.4.1 ------------------------------------------------------------ Build time: 2012-12-21 00:00:00 UTC Revision: none Groovy: 2.4.21 Ant: Apache Ant(TM) version 1.10.14 compiled on September 25 2023 JVM: 21.0.7 (Ubuntu 21.0.7+6-Ubuntu-0ubuntu124.04) OS: Linux 5.15.0-1074-gcp amd64
`/usr/bin/grass`	/usr/bin/grass:298: SyntaxWarning: invalid escape sequence '\.' "%([#0 +-])([0-9])(\.[0-9]*)?([hlL]?[diouxXeEfFgGcrsa%])", fmt GRASS GIS 8.3.2 Geographic Resources Analysis Support System (GRASS) is Copyright, 1999-2024 by the GRASS Development Team, and licensed under terms of the GNU General Public License (GPL) version >=2. This GRASS GIS 8.3.2 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 5.6.2 Address model: 64-bit libgringo version 5.6.2 Configuration: without Python, with Lua 5.4.6 License: The MIT License <https://opensource.org/licenses/MIT>
`/usr/bin/guile`	guile (GNU Guile) 2.2.7 Packaged by Debian (2.2.7-deb+1-9build3) Copyright (C) 2020 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 2.0.2 ABI compatibility version: 9 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 1.10.10
`/usr/bin/hardlink`	hardlink from util-linux 2.39.3 (features: reflink, cryptoapi)
`/usr/bin/haskell-compiler`	The Glorious Glasgow Haskell Compilation System, version 9.4.7
`/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
`/ext/venvs/cocalc/bin/hg`	Mercurial Distributed SCM (version 7.0.2) (see https://mercurial-scm.org for more information) Copyright (C) 2005-2025 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 14 October 2022 Compiler: gcc version 12.2.0 (Ubuntu 12.2.0-9ubuntu1) 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 3.3.0
`/usr/bin/inkscape`	Warning: Option --without-gui= is deprecated Inkscape 1.2.2 (b0a8486541, 2022-12-01)
`/ext/bin/ipopt`	Ipopt 3.14.17 (Linux x86_64), ASL(20231111)
`/ext/venvs/cocalc/bin/ipython`	9.2.0
`/ext/venvs/miniforge2025/bin/ipython`	9.2.0
`/ext/venvs/cocalc/bin/ipython3`	9.2.0
`/usr/bin/irssi`	irssi 1.4.5 (20231003 1405)
`/usr/bin/iverilog`	Icarus Verilog version 12.0 (stable) () Copyright (c) 2000-2021 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 Preprocessor version 12.0 (stable) () Copyright (c) 1999-2021 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 12.0 (stable) () Copyright (c) 1998-2021 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 12.0 (stable) () Copyright (c) 2001-2021 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 Wed Jun 25 11:52:55 2025 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 "21.0.7" 2025-04-15 OpenJDK Runtime Environment (build 21.0.7+6-Ubuntu-0ubuntu124.04) OpenJDK 64-Bit Server VM (build 21.0.7+6-Ubuntu-0ubuntu124.04, mixed mode, sharing)
`/usr/bin/javac`	Picked up _JAVA_OPTIONS: -Xms64m javac 21.0.7
`/ext/bin/julia`	julia version 1.11.2
`/ext/bin/julia-1.11`	julia version 1.11.2
`/ext/venvs/cocalc/bin/jupyter-book`	Jupyter Book : 1.0.4.post1 External ToC : 1.0.1 MyST-Parser : 3.0.1 MyST-NB : 1.2.0 Sphinx Book Theme : 1.1.4 Jupyter-Cache : 1.0.1 NbClient : 0.10.2
`/ext/venvs/cocalc/bin/jupyter-lab`	4.4.2
`/ext/venvs/cocalc/bin/jupyter-nbconvert`	7.16.6
`/ext/venvs/cocalc/bin/jupytext`	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:pandoc, md:markdown, md:myst or py:light, py:nomarker, py:percent, py:sphinx, py:hydrogen. The default format for scripts is the 'percent' format, which uses '# %%' as cell markers and is compatible with VS Code and PyCharm. Alternatively, you can also use the 'light' format, which uses fewer cell markers. The main formats (MyST Markdown, Markdown, percent, light) 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)
`/ext/texlive/2025/bin/x86_64-linux/latex`	pdfTeX 3.141592653-2.6-1.40.28 (TeX Live 2025) kpathsea version 6.4.1 Copyright 2025 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 1.6.46; using libpng 1.6.46 Compiled with zlib 1.3.1; using zlib 1.3.1 Compiled with xpdf version 4.04
`/ext/texlive/2025/bin/x86_64-linux/latexmk`	Latexmk, John Collins, 15 June 2025. Version 4.87
`/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 24.2.7.2 420(Build:2)
`/usr/bin/lilypond`	GNU LilyPond 2.24.3 (running Guile 2.2) Copyright (c) 1996--2023 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`	Distributor ID: Ubuntu Description: Ubuntu 24.04.2 LTS Release: 24.04 Codename: noble
`/usr/bin/lua`	Lua 5.1.5 Copyright (C) 1994-2012 Lua.org, PUC-Rio
`/usr/bin/lua5.4`	Lua 5.4.6 Copyright (C) 1994-2023 Lua.org, PUC-Rio
`/ext/texlive/2025/bin/x86_64-linux/luatex`	This is LuaTeX, Version 1.22.0 (TeX Live 2025) Development id: 7673 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 2025 Taco Hoekwater and the LuaTeX Team.
`/usr/bin/lzma`	xz (XZ Utils) 5.4.5 liblzma 5.4.5
`/usr/bin/M2`	1.25.06
`/usr/bin/m4`	m4 (GNU M4) 1.4.19 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 René Seindal.
`/usr/bin/macs3`	macs3 3.0.1
`/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/
`/ext/bin/mathics`	mathics 7.0.0
`/usr/bin/maxima`	Maxima 5.46.0
`/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 5.47.0
`/usr/bin/mc`	GNU Midnight Commander 4.8.30 Built with GLib 2.80.0 Built with S-Lang 2.3.3 with terminfo database Built with libssh2 1.11.0 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/bin/meson`	1.3.2
`/usr/bin/mono`	Mono JIT compiler version 6.8.0.105 (Debian 6.8.0.105+dfsg-3.6ubuntu2 Sun Mar 31 02:55:28 UTC 2024) 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) 4.1.6 Report bugs to http://www.open-mpi.org/community/help/
`/usr/bin/nano`	GNU nano, version 7.2 (C) 2023 the Free Software Foundation and various contributors Compiled options: --disable-libmagic --enable-utf8
`/usr/local/bin/nasm`	NASM version 2.16.03 compiled on Dec 12 2024
`/ext/venvs/cocalc/bin/nbdime`	4.0.2
`/usr/bin/neofetch`	Neofetch 7.1.0
`/usr/bin/nettle-hash`	nettle-hash (nettle 3.9.1)
`/usr/bin/nim`	Nim Compiler Version 1.6.14 [Linux: amd64] Compiled at 2024-04-01 Copyright (c) 2006-2023 by Andreas Rumpf active boot switches: -d:release
`/ext/venvs/cocalc/bin/ninja`	1.11.1.git.kitware.jobserver-1
`/usr/bin/nnn`	4.9
`/usr/bin/node`	v22.16.0
`/usr/bin/nosetests3`	nosetests3 version 1.3.7
`/ext/venvs/cocalc/bin/notedown`	1.5.1
`/usr/bin/npm`	11.4.2
`/ext/bin/nvidia-smi`	╔═══════════════════════════════════════╗ ║ ⚠ FOR GPUs: USE A COMPUTE SERVER ⚠ ║ ╠═══════════════════════════════════════╣ ║ CoCalc projects can be extended by ║ ║ compute servers offering GPUs: ║ ║ https://doc.cocalc.com/compute_server ║ ╚═══════════════════════════════════════╝
`/usr/bin/nvim`	NVIM v0.9.5 Build type: Release LuaJIT 2.1.0-beta3 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 4.14.1
`/ext/bin/octave`	GNU Octave, version 10.1.0 Copyright (C) 1993-2025 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". Home page: https://octave.org Support resources: https://octave.org/support Improve Octave: https://octave.org/get-involved
`/ext/bin/octave-10.1.0`	GNU Octave, version 10.1.0 Copyright (C) 1993-2025 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". Home page: https://octave.org Support resources: https://octave.org/support Improve Octave: https://octave.org/get-involved
`/ext/bin/octave-cli`	GNU Octave, version 10.1.0 Copyright (C) 1993-2025 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". Home page: https://octave.org Support resources: https://octave.org/support Improve Octave: https://octave.org/get-involved
`/ext/bin/octave-cli-10.1.0`	GNU Octave, version 10.1.0 Copyright (C) 1993-2025 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". Home page: https://octave.org Support resources: https://octave.org/support Improve Octave: https://octave.org/get-involved
`/ext/bin/octave-cli-systemwide`	GNU Octave, version 8.4.0 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/octave-systemwide`	GNU Octave, version 8.4.0 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 -dm dmso_conc - concentration of DMSO in %, by default 0 -df dmso_factor - correction factor for DMSO, by default 0.6 -fo formamide_conc - concentration of formamide in mol/l, by default 0 mol/l -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`	2.1.5
`/usr/bin/openscad`	OpenSCAD version 2021.01
`/usr/bin/pandoc`	pandoc 3.7.0.2 Features: +server +lua Scripting engine: Lua 5.4 User data directory: /home/user/.local/share/pandoc Copyright (C) 2006-2024 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.
`/ext/venvs/cocalc/bin/papermill`	2.6.0 from /ext/venvs/cocalc/lib/python3.12/site-packages/papermill/cli.py (3.12.10)
`/ext/texlive/2025/bin/x86_64-linux/pdflatex`	pdfTeX 3.141592653-2.6-1.40.28 (TeX Live 2025) kpathsea version 6.4.1 Copyright 2025 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 1.6.46; using libpng 1.6.46 Compiled with zlib 1.3.1; using zlib 1.3.1 Compiled with xpdf version 4.04
`/usr/bin/pdftk`	Picked up _JAVA_OPTIONS: -Xms64m pdftk port to java 3.3.3 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 24.02.0 Copyright 2005-2024 The Poppler Developers - http://poppler.freedesktop.org Copyright 1996-2011, 2022 Glyph & Cog, LLC
`/usr/bin/perl`	This is perl 5, version 38, subversion 2 (v5.38.2) built for x86_64-linux-gnu-thread-multi (with 45 registered patches, see perl -V for more detail) Copyright 1987-2023, 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 https://www.perl.org/, the Perl Home Page.
`/usr/bin/perldoc`	Perldoc v3.2801, under perl v5.038002 for linux
`/usr/bin/phc`	PHCv2.4.90 released 2024-03-20
`/usr/bin/php`	PHP 8.3.6 (cli) (built: Mar 19 2025 10:08:38) (NTS) Copyright (c) The PHP Group Zend Engine v4.3.6, Copyright (c) Zend Technologies with Zend OPcache v8.3.6, Copyright (c), by Zend Technologies
`/ext/bin/phylip`	Starting main running main ['/ext/bin/phylip', 'test'] /ext/venvs/miniforge2025/share/phylip-3.697-2/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 2.8
`/ext/venvs/cocalc/bin/pip`	pip 25.1.1 from /ext/venvs/cocalc/lib/python3.12/site-packages/pip (python 3.12)
`/ext/venvs/cocalc/bin/pip3`	pip 25.1.1 from /ext/venvs/cocalc/lib/python3.12/site-packages/pip (python 3.12)
`/ext/venvs/cocalc/bin/pipenv`	pipenv, version 2025.0.2
`/usr/bin/plink1`	@----------------------------------------------------------@ \| 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: Wed Jun 25 11:53:41 2025 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) 2025-06-25T11:53:43: PM2 log: Launching in no daemon mode 6.0.8
`/usr/bin/pngnq`	pngnq 1.1 Compiled with libpng 1.6.43; using libpng 1.6.43. Compiled with zlib 1.3; using zlib 1.3.
`/usr/bin/pnpm`	10.12.3
`/ext/venvs/cocalc/bin/poetry`	Poetry (version 2.1.3)
`/usr/bin/polymake`	polymake version 4.11 Copyright (c) 1997-2023 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.
`/usr/lib/postgresql/16/bin/postgres`	postgres (PostgreSQL) 16.9 (Ubuntu 16.9-1.pgdg24.04+1)
`/ext/venvs/cocalc/bin/pretext`	2.18.3
`/usr/bin/prettier`	3.6.0
`/usr/bin/primecount`	primecount 7.10, <https://github.com/kimwalisch/primecount> Copyright (C) 2013 - 2024 Kim Walisch BSD 2-Clause License <https://opensource.org/licenses/BSD-2-Clause>
`/usr/bin/primer3_core`	Copyright (c) 1996-2022 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 2.6.1) Input can also be provided on standard input. For example: $ primer3_core < my_input_file
`/usr/bin/primesieve`	primesieve 12.0, <https://github.com/kimwalisch/primesieve> Copyright (C) 2010 - 2024 Kim Walisch BSD 2-Clause License <https://opensource.org/licenses/BSD-2-Clause>
`/usr/bin/prolog`	SWI-Prolog version 9.0.4 for x86_64-linux
`/usr/bin/protoc`	libprotoc 3.21.12
`/ext/venvs/cocalc/bin/py.test`	pytest 8.3.5
`/ext/venvs/cocalc/bin/pytest`	pytest 8.3.5
`/ext/venvs/miniforge2025/bin/python`	Python 3.12.10
`/ext/bin/python3-sage`	Python 3.12.5
`/ext/venvs/cocalc/bin/python3`	Python 3.12.10
`/ext/venvs/miniforge2025/bin/python3`	Python 3.12.10
`/ext/texlive/2025/bin/x86_64-linux/pythontex`	/ext/texlive/2025/texmf-dist/scripts/pythontex/pythontex3.py:557: SyntaxWarning: invalid escape sequence '\s' the "\\usepackage{pythontex}": "\setpythontexworkingdir{<outputdir>}". /ext/texlive/2025/texmf-dist/scripts/pythontex/pythontex3.py:1810: SyntaxWarning: invalid escape sequence '\s' errgobble = match('(\s)', line).groups()[0] /ext/texlive/2025/texmf-dist/scripts/pythontex/pythontex3.py:2075: SyntaxWarning: invalid escape sequence '\s' errgobble = match('(\s)', line).groups()[0] PythonTeX 0.18
`/usr/bin/pythontex3`	/usr/share/texlive/texmf-dist/scripts/pythontex/pythontex3.py:549: SyntaxWarning: invalid escape sequence '\s' msg = ''' /usr/share/texlive/texmf-dist/scripts/pythontex/pythontex3.py:1810: SyntaxWarning: invalid escape sequence '\s' errgobble = match('(\s)', line).groups()[0] /usr/share/texlive/texmf-dist/scripts/pythontex/pythontex3.py:2075: SyntaxWarning: invalid escape sequence '\s' errgobble = match('(\s)', line).groups()[0] PythonTeX 0.18
`/ext/venvs/cocalc/bin/pytype`	2024.10.11
`/usr/bin/qgis`	QGIS 3.42.3-Münster 'Münster' (bb018e12fe6)
`/usr/local/bin/quarto`	1.7.31
`/usr/bin/R`	R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 v8.10 [cs].
`/usr/bin/ranger`	ranger version: ranger 1.9.3 Python version: 3.12.3 (main, Feb 4 2025, 14:48:35) [GCC 13.3.0] Locale: C.UTF-8
`/usr/bin/rclone`	rclone v1.68.2 - os/version: ubuntu 24.04 (64 bit) - os/kernel: 5.15.0-1074-gcp (x86_64) - os/type: linux - os/arch: amd64 - go/version: go1.23.3 - go/linking: static - go/tags: none
`/usr/bin/rdfind`	This is rdfind version 1.6.0
`/usr/bin/reveal-md`	6.1.4
`/usr/bin/rg`	ripgrep 14.1.0 features:-simd-accel,+pcre2 simd(compile):+SSE2,-SSSE3,-AVX2 simd(runtime):+SSE2,+SSSE3,+AVX2 PCRE2 10.42 is available (JIT is available)
`/usr/bin/ros`	roswell 24.10.115(NO-GIT-REVISION)
`/usr/bin/Rscript`	Rscript (R) version 4.5.0 (2025-04-11)
`/usr/lib/rstudio-server/bin/rserver`	command-line options: automation: --run-automation [=arg(=1)] (=0) Run RStudio's built-in automation tests. Requires a Google Chrome installation. --automation-filter arg A regular expression (ERE), indicating which automation test file(s) should be run. --automation-markers arg One or more test markers, indicating which tests should be run. Markers can be separated by spaces. verify: --verify-installation arg (=0) Runs verification mode to verify the current installation. server: --server-working-dir arg (=/) The default working directory of the rserver process. --server-user arg (=rstudio-server) The user account of the rserver process. --server-daemonize arg (=0) Indicates whether or not the rserver process should run as a daemon. --server-pid-file arg (=/var/run/rstudio-server.pid) The path to a file where the rserver daemon's pid is written. --server-app-armor-enabled arg (=0) Indicates whether or not to enable AppArmor profiles for the rserver process. --server-set-umask arg (=1) If enabled, sets the rserver process umask to `022` on startup, which causes new files to have `rw-r--r--` permissions. --secure-cookie-key-file arg If set, overrides the default path of the secure-cookie-key file used for encrypting cookies. --server-data-dir arg (=/var/run/rstudio-server) Path to the data directory where RStudio Server will write run-time state. --server-add-header arg Adds a header to all responses from RStudio Server. This option can be specified multiple times to add multiple headers. www: --www-address arg (=0.0.0.0) The network address that RStudio Server will listen on for incoming connections. --www-port arg The port that RStudio Server will bind to while listening for incoming connections. If left empty, the port will be automatically determined based on your SSL settings (443 for SSL, 80 for no SSL). --www-socket arg The socket that RStudio Server will bind to while listening for incoming connections. If left empty, a port will be used. --www-root-path arg (=/) The path prefix added by a proxy to the incoming RStudio URL. This setting is used so RStudio Server knows what path it is being served from. If running RStudio Server behind a path-modifying proxy, this should be changed to match the base RStudio Server URL. --www-local-path arg (=www) The relative path from the RStudio installation directory, or absolute path where web assets are stored. --www-symbol-maps-path arg (=www-symbolmaps) The relative path from the RStudio installation directory, or absolute path, where symbol maps are stored. --www-use-emulated-stack arg (=0) Indicates whether or not to use GWT's emulated stack. --www-thread-pool-size arg (=6) The size of the threadpool from which requests will be serviced. This needs to have enough threads to avoid bottlenecks due to certain requests that block the request thread (e.g. a login fail might run into a delay caused by the pam configuration). For systems with lots of users a larger value is recommended. For systems with only one or two users, a value of 2 will be slightly more efficient. --www-proxy-localhost arg (=1) Indicates whether or not to proxy requests to localhost ports over the main server port. This should generally be enabled, and is used to proxy HTTP traffic within a session that belongs to code running within the session (e.g. Shiny or Plumber APIs) --www-verify-user-agent arg (=1) Indicates whether or not to verify connecting browser user agents to ensure they are compatible with RStudio Server. --www-same-site arg The value of the 'SameSite' attribute on the cookies issued by RStudio Server. Accepted values are 'none' or 'lax'. The value 'none' should be used only when RStudio is hosted into an iframe. For compatibility with some browsers (i.e. Safari 12), duplicate cookies will be issued by RStudio Server when 'none' is used. --www-frame-origin arg (=none) Specifies the allowed origin for the iframe hosting RStudio if iframe embedding is enabled. --www-enable-origin-check arg (=0) If enabled, cause RStudio to enforce that incoming request origins are from the host domain. This can be added for additional security. See https://cheatsheetseries.owasp.org/chea tsheets/Cross-Site_Request_Forgery_Prev ention_Cheat_Sheet.html#verifying-origi n-with-standard-headers --www-allow-origin arg Specifies an additional origin that requests are allowed from, even if it does not match the host domain. Used if origin checking is enabled. May be specified multiple times for multiple origins. --session-use-file-storage arg (=1) Whether to use the file system to store metadata about the session storage or the internal database. Setting this to false may require special network configuration. See [Session Storage](../server_management/session_s torage.html) for more information. --www-stats-monitor-seconds arg (=0) The time interval in seconds to log info/debug messages with stats on server performance. Set to 0 to disable. rsession: --rsession-which-r arg The path to the main R program (e.g. /usr/bin/R). This should be set if no versions are specified in /etc/rstudio/r-versions and the default R installation is not available on the system path. --rsession-path arg (=rsession) The relative path from the RStudio installation directory, or absolute path to the rsession executable. --rldpath-path arg (=r-ldpath) The path to the r-ldpath script which specifies extra library paths for R versions. --rsession-ld-library-path arg Specifies additional LD_LIBRARY_PATHs to use for R sessions. --rsession-config-file arg If set, overrides the path to the /etc/rstudio/rsession.conf configuration file. The specified path may be a relative path from the RStudio installation directory, or an absolute path. --rsession-proxy-max-wait-secs arg (=30) The maximum time to wait in seconds for a successful response when proxying requests to rsession. --rsession-memory-limit-mb arg (=0) The limit in MB that an rsession process may consume. --rsession-stack-limit-mb arg (=0) The limit in MB that an rsession process may consume for its stack. --rsession-process-limit arg (=0) The maximum number of allowable rsession processes. database: --database-config-file arg If set, overrides the path to the /etc/rstudio/database.conf configuration file. --db-command arg Executes the shell command specified injecting the current database configuration in the command. --db-connection-timeout arg (=15) Specifies the number of seconds to wait for making a new db connection auth: --auth-none arg (=1) If set, disables multi-user authentication. Workbench/Pro features may not work in this mode. --auth-validate-users arg (=0) Indicates whether or not to validate that authenticated users exist on the target system. Disabling this option may cause issues to start or to run a session. --auth-stay-signed-in-days arg (=30) The number of days to keep a user signed in when using the "Stay Signed In" option. Will only take affect when auth-timeout-minutes is 0 (disabled). --auth-timeout-minutes arg (=60) The number of minutes a user will stay logged in while idle before required to sign in again. Set this to 0 (disabled) to enable legacy timeout auth-stay-signed-in-days. --auth-encrypt-password arg (=1) Indicates whether or not to encrypt the password sent from the login form. For security purposes, we strongly recommend you leave this enabled. --auth-login-page-html arg (=/etc/rstudio/login.html) The path to a file containing additional HTML customization for the login page. --auth-rdp-login-page-html arg (=/etc/rstudio/rdplogin.html) The path to a file containing additional HTML customization for the login page, as seen by RDP users. --auth-required-user-group arg Specifies a group that users must be in to be able to use RStudio. --auth-minimum-user-id arg (=auto) Specifies a minimum user id value. Users with a uid lower than this value may not use RStudio. --auth-pam-helper-path arg (=rserver-pam) The relative path from the RStudio installation directory, or absolute path where the PAM helper binary resides. --auth-pam-require-password-prompt arg (=1) Indicates whether or not to require the "Password: " prompt before sending the password via PAM. In most cases, this should be enabled. If using a custom PAM password prompt, you may need to disable this setting if PAM logins do not work correctly. --auth-pam-requires-priv arg (=1) Deprecated - will always be true. --auth-sign-in-throttle-seconds arg (=5) The minimum amount of time a user must wait before attempting to sign in again after signing out. --auth-revocation-list-dir arg If set, overrides the path to the directory which contains the revocation list to be used for storing expired tokens. As of RStudio Server 1.4, this has been moved to database storage, and so this setting is deprecated, but will be used to port over any existing file-based expired tokens. --auth-cookies-force-secure arg (=0) Indicates whether or not auth cookies should be forcefully marked as secure. This should be enabled if running an SSL terminator in front of RStudio Server. Otherwise, cookies will be marked secure if SSL is configured. monitor: --monitor-interval-seconds arg (=60) The interval in seconds at which the monitor is probed for new data. databricks: userProvisioning: snowflake: general: --help print help message --test-config test to ensure the config file is valid --config-file arg (=/etc/rstudio/rserver.conf) configuration file
`/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 3.2.3 (2024-01-18 revision 52bb2ac0a6) [x86_64-linux-gnu]
`/usr/bin/run-one`	x
`/ext/bin/rustc`	rustc 1.83.0 (90b35a623 2024-11-26)
`/ext/bin/rustfmt`	rustfmt 1.8.0-stable (90b35a6239 2024-11-26)
`/ext/bin/rustup`	rustup 1.27.1 (54dd3d00f 2024-04-24) info: This is the version for the rustup toolchain manager, not the rustc compiler. info: The currently active `rustc` version is `rustc 1.83.0 (90b35a623 2024-11-26)`
`/usr/bin/rvim`	VIM - Vi IMproved 9.1 (2024 Jan 02, compiled Apr 01 2025 20:12:31) Included patches: 1-16, 647, 678, 697 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 +xattr +dnd +mouseshape +spell -xfontset -ebcdic +mouse_dec +startuptime +xim +emacs_tags +mouse_gpm +statusline -xpm +eval -mouse_jsbterm -sun_workshop +xsmp_interact +ex_extra +mouse_netterm +syntax +xterm_clipboard +extra_search +mouse_sgr +tag_binary -xterm_save -farsi -mouse_sysmouse -tag_old_static system vimrc file: "/etc/vim/vimrc" user vimrc file: "$HOME/.vimrc" 2nd user vimrc file: "~/.vim/vimrc" user exrc file: "$HOME/.exrc" system gvimrc file: "/etc/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 -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I/usr/include/gio-unix-2.0 -I/usr/include/atk-1.0 -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 -pthread -Wdate-time -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/vim-AkQQan/vim-9.1.0016=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/vim-AkQQan/vim-9.1.0016=/usr/src/vim-2:9.1.0016-1ubuntu7.8 -DSYS_VIMRC_FILE=\"/etc/vim/vimrc\" -DSYS_GVIMRC_FILE=\"/etc/vim/gvimrc\" -D_REENTRANT -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 Linking: gcc -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vim -lgtk-3 -lgdk-3 -lz -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 -lXt -lX11 -lXdmcp -lSM -lICE -lm -ltinfo -lselinux -lcanberra -lsodium -lacl -lattr -lgpm -L/usr/lib -llua5.1 -Wl,-E -fstack-protector-strong -L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/perl/5.38/CORE -lperl -ldl -lm -lpthread -lcrypt -L/usr/lib/python3.12/config-3.12-x86_64-linux-gnu -lpython3.12 -ldl -lm -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -lruby-3.2 -lm -lpthread -L/usr/lib
`/ext/bin/sage`	SageMath version 10.6, Release Date: 2025-03-31
`/ext/bin/sage-10.5`	SageMath version 10.5, Release Date: 2024-12-04
`/ext/bin/sage-10.6`	SageMath version 10.6, Release Date: 2025-03-31
`/ext/bin/samtools`	samtools 1.21 Using htslib 1.21 Copyright (C) 2024 Genome Research Ltd. Samtools compilation details: Features: build=configure curses=yes CC: /opt/conda/conda-bld/samtools_1734249775320/_build_env/bin/x86_64-conda-linux-gnu-cc CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /ext/venvs/miniforge2025/include CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/venvs/miniforge2025/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1734249775320/work=/usr/local/src/conda/samtools-1.21 -fdebug-prefix-map=/ext/venvs/miniforge2025=/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/venvs/miniforge2025/lib -Wl,-rpath-link,/ext/venvs/miniforge2025/lib -L/ext/venvs/miniforge2025/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/venvs/miniforge2025/libexec/htslib htscodecs=1.6.1 CC: /opt/conda/conda-bld/htslib_1734145038589/_build_env/bin/x86_64-conda-linux-gnu-cc CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /ext/venvs/miniforge2025/include CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/venvs/miniforge2025/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1734145038589/work=/usr/local/src/conda/htslib-1.21 -fdebug-prefix-map=/ext/venvs/miniforge2025=/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/venvs/miniforge2025/lib -Wl,-rpath-link,/ext/venvs/miniforge2025/lib -L/ext/venvs/miniforge2025/lib -fvisibility=hidden -rdynamic HTSlib URL scheme handlers present: built-in: file, preload, data libcurl: gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, ftp, gopher, imap, http, https, sftp, smtps, dict, scp, mqtt, telnet Amazon S3: s3+https, s3, s3+http Google Cloud Storage: gs+http, gs+https, gs S3 Multipart Upload: s3w+https, s3w+http, s3w crypt4gh-needed: crypt4gh mem: mem
`/usr/bin/sbcl`	SBCL 2.2.9.debian
`/usr/bin/scala`	Picked up _JAVA_OPTIONS: -Xms64m Welcome to Scala 2.11.12 (OpenJDK 64-Bit Server VM, Java 21.0.7). Type in expressions for evaluation. Or try :help. Exception in thread "Thread-1" java.lang.NoClassDefFoundError: org/fusesource/jansi/AnsiOutputStream at jline.internal.Ansi.stripAnsi(Ansi.java:28) at jline.console.ConsoleReader.setPrompt(ConsoleReader.java:499) at jline.console.ConsoleReader.readLine(ConsoleReader.java:2425) at jline.console.ConsoleReader.readLine(ConsoleReader.java:2378) at jline.console.ConsoleReader.readLine(ConsoleReader.java:2366) at scala.tools.nsc.interpreter.jline.InteractiveReader.readOneLine(JLineReader.scala:59) at scala.tools.nsc.interpreter.InteractiveReader$class.readLine(InteractiveReader.scala:38) at scala.tools.nsc.interpreter.jline.InteractiveReader.readLine(JLineReader.scala:27) at scala.tools.nsc.interpreter.SplashReader.readLine(InteractiveReader.scala:142) at scala.tools.nsc.interpreter.SplashLoop.run(InteractiveReader.scala:71) at java.base/java.lang.Thread.run(Thread.java:1583) Caused by: java.lang.ClassNotFoundException: org.fusesource.jansi.AnsiOutputStream at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641) at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:526) ... 11 more Failed to initialize compiler: NoClassDefFoundError. This is most often remedied by a full clean and recompile. Otherwise, your classpath may continue bytecode compiled by different and incompatible versions of scala. java.lang.NoClassDefFoundError: org/fusesource/jansi/AnsiOutputStream at jline.internal.Ansi.stripAnsi(Ansi.java:28) at jline.console.ConsoleReader.setPrompt(ConsoleReader.java:499) at jline.console.ConsoleReader.readLine(ConsoleReader.java:2425) at jline.console.ConsoleReader.readLine(ConsoleReader.java:2378) at jline.console.ConsoleReader.readLine(ConsoleReader.java:2366) at scala.tools.nsc.interpreter.jline.InteractiveReader.readOneLine(JLineReader.scala:59) at scala.tools.nsc.interpreter.InteractiveReader$class.readLine(InteractiveReader.scala:38) at scala.tools.nsc.interpreter.jline.InteractiveReader.readLine(JLineReader.scala:27) at scala.tools.nsc.interpreter.ILoop.readOneLine(ILoop.scala:413) at scala.tools.nsc.interpreter.ILoop.loop(ILoop.scala:425) at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply$mcZ$sp(ILoop.scala:993) at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:891) at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:891) at scala.reflect.internal.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:97) at scala.tools.nsc.interpreter.ILoop.process(ILoop.scala:891) at scala.tools.nsc.MainGenericRunner.runTarget$1(MainGenericRunner.scala:74) at scala.tools.nsc.MainGenericRunner.run$1(MainGenericRunner.scala:87) at scala.tools.nsc.MainGenericRunner.process(MainGenericRunner.scala:98) at scala.tools.nsc.MainGenericRunner$.main(MainGenericRunner.scala:103) at scala.tools.nsc.MainGenericRunner.main(MainGenericRunner.scala) Caused by: java.lang.ClassNotFoundException: org.fusesource.jansi.AnsiOutputStream ... 20 more
`/usr/bin/scheme`	MIT/GNU Scheme 12.1 Copyright (C) 2022 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 Tuesday May 16, 2023 at 2:38:25 PM Release 12.1 \|\| SF \|\| LIAR/x86-64 Post proelium, praemium.
`/usr/bin/scilab-cli-bin`	Scilab version "2024.0.0.988271013" scilab-branch-main
`/ext/bin/scip`	SCIP version 9.2.0 [precision: 8 byte] [memory: block] [mode: optimized] [LP solver: Soplex 7.1.2] [GitHash: 74cea9222e] Copyright (c) 2002-2024 Zuse Institute Berlin (ZIB) External libraries: Soplex 7.1.2 Linear Programming Solver developed at Zuse Institute Berlin (soplex.zib.de) [GitHash: b040369c] CppAD 20180000.0 Algorithmic Differentiation of C++ algorithms developed by B. Bell (github.com/coin-or/CppAD) ZLIB 1.3 General purpose compression library by J. Gailly and M. Adler (zlib.net) TinyCThread 1.2 small portable implementation of the C11 threads API (tinycthread.github.io) GMP 6.3.0 GNU Multiple Precision Arithmetic Library developed by T. Granlund (gmplib.org) ZIMPL 3.6.2 Zuse Institute Mathematical Programming Language developed by T. Koch (zimpl.zib.de) AMPL/MP 690e9e7 AMPL .nl file reader library (github.com/ampl/mp) PaPILO 2.4.0 parallel presolve for integer and linear optimization (github.com/scipopt/papilo) (built with TBB) [GitHash: 2d9fe29f] Nauty 2.8.8 Computing Graph Automorphism Groups by Brendan D. McKay (users.cecs.anu.edu.au/~bdm/nauty) sassy 1.1 Symmetry preprocessor by Markus Anders (github.com/markusa4/sassy) Ipopt 3.14.16 Interior Point Optimizer developed by A. Waechter et.al. (github.com/coin-or/Ipopt) Compiler: gcc 13.2.0 Build options: ARCH=x86_64 OSTYPE=Linux-6.1.0-25-amd64 COMP=GNU 13.2.0 BUILD=Release DEBUGSOL=OFF EXPRINT=cppad SYM=snauty GMP=ON IPOPT=ON WORHP=OFF LPS=spx LPSCHECK=OFF NOBLKBUFMEM=OFF NOBLKMEM=OFF NOBUFMEM=OFF THREADSAFE=ON;FORCE READLINE=off SANITIZE_ADDRESS=OFF SANITIZE_MEMORY=OFF SANITIZE_UNDEFINED=OFF SANITIZE_THREAD=OFF SHARED=ON VERSION=9.2.0.0 API_VERSION=115 ZIMPL=ON ZLIB=ON
`/usr/bin/scons`	SCons by Steven Knight et al.: SCons: v4.5.2.120fd4f633e9ef3cafbc0fec35306d7555ffd1db, Tue, 21 Mar 2023 12:11:27 -0400, by bdbaddog on M1DOG2021 SCons path: ['/usr/lib/python3/dist-packages/SCons'] Copyright (c) 2001 - 2023 The SCons Foundation
`/usr/bin/sed`	sed (GNU sed) 4.9 Packaged by Debian Copyright (C) 2022 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) 9.4 Copyright (C) 2023 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) 9.4 Copyright (C) 2023 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.
`/ext/venvs/cocalc/bin/shiny`	shiny, version 1.4.0
`/usr/bin/Singular`	Singular for x86_64-Linux version 4.3.2 (4330, 64 bit) Apr 1 2024 04:44:00 with GMP(6.3.0),NTL(11.5.1),FLINT(3.0.1), 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=1750852318 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' '--htmldir=/usr/share/doc/singular/html' '--with-libparse' '--enable-streamio' 'build_alias=x86_64-linux-gnu' 'CFLAGS=-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=/usr/src/singular-1:4.3.2-p10+ds-1.1build1' 'LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=3' 'CXXFLAGS=-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=/usr/src/singular-1:4.3.2-p10+ds-1.1build1' 'PYTHON=/usr/bin/python3' --enable-omalloc OMALLOC_LIBS='/build/singular-HDHwVv/singular-4.3.2-p10+ds/omalloc/libsingular-omalloc.la' OMALLOC_INCLUDES='-I/build/singular-HDHwVv/singular-4.3.2-p10+ds' --with-Singular RESOURCES_LIBS='/build/singular-HDHwVv/singular-4.3.2-p10+ds/resources/libsingular-resources.la' RESOURCES_INCLUDES='-I/build/singular-HDHwVv/singular-4.3.2-p10+ds ' FACTORY_LIBS='/build/singular-HDHwVv/singular-4.3.2-p10+ds/factory/libsingular-factory.la' FACTORY_INCLUDES='-I/build/singular-HDHwVv/singular-4.3.2-p10+ds -I/build/singular-HDHwVv/singular-4.3.2-p10+ds/factory -I/build/singular-HDHwVv/singular-4.3.2-p10+ds/factory/include', CC = gcc,FLAGS : -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=/usr/src/singular-1:4.3.2-p10+ds-1.1build1 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/singular-HDHwVv/singular-4.3.2-p10+ds=/usr/src/singular-1:4.3.2-p10+ds-1.1build1 -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=3, LDFLAGS : -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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 : -lreadline -lncurses -lgmp -lrt -lpthread (ver: 13.2.0) 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:/cocalc/bin:/ext/venvs/cocalc/bin:/ext/venvs/cocalc/condabin:/ext/texlive/2025/bin/x86_64-linux:/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/rstudio-server/bin:/usr/lib/postgresql/16/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 4.3.2 0< by: W. Decker, G.-M. Greuel, G. Pfister, H. Schoenemann \ Feb 2023 FB Mathematik der Universitaet, D-67653 Kaiserslautern \ Debian 1:4.3.2-p10+ds-1.1build1 // ** Can not open /dev/null Auf Wiedersehen.
`/usr/local/bin/Singular-sage`	Singular for x86_64-Linux version 4.4.0 (44000, 64 bit) Apr 2024 with GMP(6.3.0),NTL(11.5.1),FLINT(3.0.1), 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=1750852319 built-in modules: {} AC_CONFIGURE_ARGS = '--prefix=/ext/sage/10.6/local' '--libdir=/ext/sage/10.6/local/lib' '--disable-maintainer-mode' '--disable-dependency-tracking' '--exec-prefix=/ext/sage/10.6/local' '--bindir=/ext/sage/10.6/local/bin' '--with-ntl=/ext/sage/10.6/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/10.6/local/lib -L/ext/sage/10.6/local/lib -Wl,-rpath,/ext/sage/10.6/local/lib -Wl,-rpath-link,/ext/sage/10.6/local/lib -L/ext/sage/10.6/local/lib -Wl,-rpath,/ext/sage/10.6/local/lib ' 'CXX=g++ -std=gnu++11' 'CXXFLAGS=-g -O2' --enable-omalloc OMALLOC_LIBS='/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src/omalloc/libomalloc.la' OMALLOC_INCLUDES='-I/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src' --htmldir=${prefix}/share/doc/singular --with-Singular RESOURCES_LIBS='/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src/resources/libsingular_resources.la' RESOURCES_INCLUDES='-I/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src ' FACTORY_LIBS='/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src/factory/libfactory.la' FACTORY_INCLUDES='-I/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src -I/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/src/factory -I/ext/sage/10.6/local/var/tmp/sage/build/singular-4.4.0/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/10.6/local/lib -L/ext/sage/10.6/local/lib -Wl,-rpath,/ext/sage/10.6/local/lib -Wl,-rpath-link,/ext/sage/10.6/local/lib -L/ext/sage/10.6/local/lib -Wl,-rpath,/ext/sage/10.6/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: 13.3.0) argv[0] : Singular SearchPath: /ext/sage/10.6/local/bin/../share/singular/LIB:/ext/sage/10.6/local/bin/../share/factory:/ext/sage/10.6/local/bin/../libexec/singular/MOD:/ext/sage/10.6/local/libexec/singular/MOD:/ext/sage/10.6/local/bin:/ext/sage/10.6/local/bin/.. Singular : /ext/sage/10.6/local/bin/Singular BinDir : /ext/sage/10.6/local/bin ProcDir : /ext/sage/10.6/local/bin/..:/ext/sage/10.6/local/bin/../libexec/singular/MOD:/ext/sage/10.6/local/libexec/singular/MOD RootDir : /ext/sage/10.6/local/bin/.. DataDir : /ext/sage/10.6/local/bin/../share DefaultDir: /ext/sage/10.6/local InfoFile : /ext/sage/10.6/local/bin/../share/info/singular.info IdxFile : /ext/sage/10.6/local/bin/../share/singular/singular.idx HtmlDir : /ext/sage/10.6/local/bin/../share/doc/singular ManualUrl : https://www.singular.uni-kl.de/Manual/ ExDir : Path : /ext/sage/10.6/local/bin:/ext/sage/10.6/local/bin/..:/ext/sage/10.6/local/bin/../libexec/singular/MOD:/ext/sage/10.6/local/libexec/singular/MOD:/ext/sage/10.6/src/bin:/ext/sage/10.6/local/libexec/ccache:/ext/sage/10.6/build/bin:/ext/sage/10.6/local/var/lib/sage/venv-python3.12.5/bin:/cocalc/bin:/ext/venvs/cocalc/bin:/ext/venvs/cocalc/condabin:/ext/texlive/2025/bin/x86_64-linux:/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/rstudio-server/bin:/usr/lib/postgresql/16/bin emacs : /usr/bin/emacs-gtk xemacs : SingularEmacs: /ext/sage/10.6/local/bin/Singular EmacsLoad : /ext/sage/10.6/local/bin/../share/singular/emacs/.emacs-singular EmacsDir : /ext/sage/10.6/local/bin/../share/singular/emacs SingularXterm: /ext/sage/10.6/local/bin/Singular xterm : /usr/bin/xterm EmacsDir : /ext/sage/10.6/local/bin/../share/singular/emacs Available HelpBrowsers: info, lynx, lynx-www-idx, lynx-www, builtin, dummy, emacs, Current HelpBrowser: info SINGULAR / A Computer Algebra System for Polynomial Computations / version 4.4.0 0< by: W. Decker, G.-M. Greuel, G. Pfister, H. Schoenemann \ Apr 2024 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 7.1.2 [mode: optimized] [precision: 8 byte] [rational: GMP 6.3.0] [PaPILO 2.4.0 {2d9fe29f}] [githash: b040369c] Copyright (c) 1996-2024 Zuse Institute 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 minimal value = 50) -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=<solfile> print primal solution to file (or just -x to print to terminal) -y=<solfile> print dual multipliers to file (or just -y to print to terminal) -X=<solfile> print primal solution in rational numbers to file (or just -X to print to terminal) -Y=<solfile> print dual multipliers in rational numbers to file (or just -Y to print to terminal) -q display detailed statistics -c perform final check of optimal solution in original problem
`/usr/bin/sqlite3`	3.45.1 2024-01-30 16:01:20 e876e51a0ed5c5b3126f52e532044363a014bc594cfefa87ffb5b82257ccalt1 (64-bit)
`/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_9.6p1 Ubuntu-3ubuntu13.11, OpenSSL 3.0.13 30 Jan 2024
`/usr/bin/stack`	2.9.3.1 x86_64 Compiled with: - Cabal-3.8.1.0 - Cabal-syntax-3.8.1.0 - Glob-0.10.2 - OneTuple-0.4.1.1 - QuickCheck-2.14.3 - StateVar-1.2.2 - aeson-2.1.2.1 - annotated-wl-pprint-0.7.0 - ansi-terminal-0.11.5 - ansi-terminal-types-0.11.5 - ansi-wl-pprint-0.6.9 - appar-0.1.8 - array-0.5.4.0 - asn1-encoding-0.9.6 - asn1-parse-0.9.5 - asn1-types-0.3.4 - assoc-1.1 - async-2.2.4 - attoparsec-0.14.4 - attoparsec-iso8601-1.1.0.0 - auto-update-0.1.6 - base-4.17.2.0 - base-compat-0.12.3 - base-compat-batteries-0.12.3 - base-orphans-0.9.1 - base16-bytestring-1.0.2.0 - base64-bytestring-1.2.1.0 - basement-0.0.16 - bifunctors-5.5.15 - binary-0.8.9.1 - bitvec-1.1.5.0 - blaze-builder-0.4.2.3 - blaze-html-0.9.1.2 - blaze-markup-0.8.3.0 - byteorder-1.0.4 - bytestring-0.11.5.2 - casa-client-0.0.2 - casa-types-0.0.2 - case-insensitive-1.2.1.0 - cereal-0.5.8.3 - clock-0.8.4 - colour-2.3.6 - comonad-5.0.8 - conduit-1.3.5 - conduit-extra-1.3.6 - connection-0.3.1 - containers-0.6.7 - contravariant-1.5.5 - cookie-0.4.6 - cryptohash-sha256-0.11.102.1 - crypton-0.33 - cryptonite-0.30 - cryptonite-conduit-0.2.2 - data-default-class-0.1.2.0 - data-fix-0.3.2 - deepseq-1.4.8.0 - digest-0.0.1.7 - directory-1.3.7.1 - distributive-0.6.2.1 - dlist-1.0 - easy-file-0.2.5 - echo-0.1.4 - ed25519-0.0.5.0 - exceptions-0.10.5 - extra-1.7.14 - fast-logger-3.2.2 - file-embed-0.0.15.0 - filelock-0.1.1.7 - filepath-1.4.2.2 - foldable1-classes-compat-0.1 - fsnotify-0.4.1.0 - generic-deriving-1.14.5 - ghc-bignum-1.3 - ghc-boot-th-9.4.7 - ghc-prim-0.9.1 - hackage-security-0.6.2.3 - hashable-1.4.3.0 - hi-file-parser-0.1.5.0 - hinotify-0.4.1 - hourglass-0.2.12 - hpack-0.35.2 - hpc-0.6.1.0 - http-api-data-0.5 - http-client-0.7.14 - http-client-tls-0.3.6.1 - http-conduit-2.3.8.1 - http-download-0.2.0.0 - http-types-0.12.3 - indexed-traversable-0.1.3 - indexed-traversable-instances-0.1.1.2 - infer-license-0.2.0 - integer-gmp-1.1 - integer-logarithms-1.0.3.1 - iproute-1.7.12 - libyaml-0.1.2 - lift-type-0.1.1.1 - lifted-base-0.2.3.12 - megaparsec-9.3.1 - memory-0.18.0 - microlens-0.4.13.1 - microlens-mtl-0.2.0.3 - microlens-th-0.4.3.14 - mime-types-0.1.1.0 - monad-control-1.0.3.1 - monad-logger-0.3.40 - monad-loops-0.4.3 - mono-traversable-1.0.15.3 - mtl-2.2.2 - mustache-2.4.2 - neat-interpolation-0.5.1.4 - network-3.1.4.0 - network-uri-2.6.4.2 - old-locale-1.0.0.7 - old-time-1.1.0.3 - open-browser-0.2.1.0 - optparse-applicative-0.17.1.0 - pantry-0.8.3 - parsec-3.1.16.1 - parser-combinators-1.3.0 - path-0.9.2 - path-io-1.8.1 - path-pieces-0.2.1 - pem-0.2.4 - persistent-2.14.6.0 - persistent-sqlite-2.13.2.0 - persistent-template-2.12.0.0 - pretty-1.1.3.6 - primitive-0.8.0.0 - process-1.6.17.0 - project-template-0.2.1.0 - random-1.2.1.1 - resource-pool-0.4.0.0 - resourcet-1.2.6 - retry-0.9.3.1 - rio-0.1.22.0 - rio-orphans-0.1.2.0 - rio-prettyprint-0.1.7.0 - rts-1.0.2 - safe-0.3.19 - safe-exceptions-0.1.7.4 - scientific-0.3.7.0 - semialign-1.3 - semigroupoids-5.3.7 - semigroups-0.20 - silently-1.2.5.3 - socks-0.6.1 - split-0.2.3.5 - splitmix-0.1.0.5 - stm-2.5.1.0 - stm-chans-3.0.0.9 - streaming-commons-0.2.2.6 - strict-0.5 - syb-0.7.2.4 - tagged-0.8.7 - tar-0.5.1.1 - tar-conduit-0.3.2.1 - template-haskell-2.19.0.0 - temporary-1.3 - text-2.0.2 - text-metrics-0.3.2 - text-short-0.1.5 - th-abstraction-0.4.5.0 - th-compat-0.1.4 - th-expand-syns-0.4.11.0 - th-lift-0.8.4 - th-lift-instances-0.1.20 - th-reify-many-0.1.10 - these-1.2 - time-1.12.2 - time-compat-1.9.6.1 - tls-1.6.0 - transformers-0.5.6.2 - transformers-base-0.4.6 - transformers-compat-0.7.2 - typed-process-0.2.11.1 - unicode-data-0.4.0.1 - unicode-transforms-0.4.0.1 - unix-2.7.3 - unix-compat-0.7 - unix-time-0.4.11 - unliftio-0.2.25.0 - unliftio-core-0.2.1.0 - unordered-containers-0.2.19.1 - uuid-types-1.0.5.1 - vault-0.3.1.5 - vector-0.13.1.0 - vector-algorithms-0.9.0.1 - vector-stream-0.1.0.0 - witherable-0.4.2 - x509-1.7.7 - x509-store-1.6.9 - x509-system-1.6.7 - x509-validation-1.6.12 - yaml-0.11.11.2 - zip-archive-0.4.3 - zlib-0.6.3.0 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'.
`/ext/venvs/cocalc/bin/streamlit`	Streamlit, version 1.45.1
`/usr/bin/sumo`	Eclipse SUMO sumo Version 1.18.0 Build features: Linux-5.4.0-173-generic x86_64 GNU 13.2.0 None FMI Proj GUI Intl SWIG GDAL FFmpeg OSG GL2PS Eigen Copyright (C) 2001-2023 German Aerospace Center (DLR) and others; https://sumo.dlr.de Eclipse SUMO sumo Version 1.18.0 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
`/ext/texlive/2025/bin/x86_64-linux/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.
`/ext/texlive/2025/bin/x86_64-linux/t1asm`	t1asm (LCDF t1utils) 1.42 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.
`/ext/venvs/cocalc/bin/tclsh`	8.6
`/ext/venvs/cocalc/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 3.4
`/usr/bin/tmuxp`	tmuxp 1.38.0, libtmux 0.30.2
`/usr/bin/toilet`	TOIlet Copyright 2006 Sam Hocevar Internet: <[email protected]> Version: 0.3, date: TOIlet, along with the various TOIlet fonts and documentation, may be freely copied and distributed. If you use TOIlet, please send an e-mail message to <[email protected]>. The latest version of TOIlet is available from the web site, http://libcaca.zoy.org/toilet.html Usage: toilet [ -hkostvSW ] [ -d fontdirectory ] [ -f fontfile ] [ -F filter ] [ -w outputwidth ] [ -I infocode ] [ -E format ] [ message ]
`/usr/bin/tsc`	Version 5.8.3
`/ext/bin/ty`	ty 0.0.0-alpha.8
`/ext/bin/uv`	uv 0.7.3
`/usr/bin/valgrind`	valgrind-3.22.0
`/usr/bin/vim`	VIM - Vi IMproved 9.1 (2024 Jan 02, compiled Apr 01 2025 20:12:31) Included patches: 1-16, 647, 678, 697 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 +xattr +dnd +mouseshape +spell -xfontset -ebcdic +mouse_dec +startuptime +xim +emacs_tags +mouse_gpm +statusline -xpm +eval -mouse_jsbterm -sun_workshop +xsmp_interact +ex_extra +mouse_netterm +syntax +xterm_clipboard +extra_search +mouse_sgr +tag_binary -xterm_save -farsi -mouse_sysmouse -tag_old_static system vimrc file: "/etc/vim/vimrc" user vimrc file: "$HOME/.vimrc" 2nd user vimrc file: "~/.vim/vimrc" user exrc file: "$HOME/.exrc" system gvimrc file: "/etc/vim/gvimrc" user gvimrc file: "$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 -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I/usr/include/gio-unix-2.0 -I/usr/include/atk-1.0 -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 -pthread -Wdate-time -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/vim-AkQQan/vim-9.1.0016=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/vim-AkQQan/vim-9.1.0016=/usr/src/vim-2:9.1.0016-1ubuntu7.8 -DSYS_VIMRC_FILE=\"/etc/vim/vimrc\" -DSYS_GVIMRC_FILE=\"/etc/vim/gvimrc\" -D_REENTRANT -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 Linking: gcc -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vim -lgtk-3 -lgdk-3 -lz -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 -lXt -lX11 -lXdmcp -lSM -lICE -lm -ltinfo -lselinux -lcanberra -lsodium -lacl -lattr -lgpm -L/usr/lib -llua5.1 -Wl,-E -fstack-protector-strong -L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/perl/5.38/CORE -lperl -ldl -lm -lpthread -lcrypt -L/usr/lib/python3.12/config-3.12-x86_64-linux-gnu -lpython3.12 -ldl -lm -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -lruby-3.2 -lm -lpthread -L/usr/lib
`/usr/bin/vis`	vis 0.8 +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/bin/weasyprint`	WeasyPrint version 61.1
`/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
`/ext/texlive/2025/bin/x86_64-linux/xelatex`	XeTeX 3.141592653-2.6-0.999997 (TeX Live 2025) kpathsea version 6.4.1 Copyright 2025 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 76.1; using 76.1 Compiled with zlib version 1.3.1; using 1.3.1 Compiled with FreeType2 version 2.13.3; using 2.13.3 Compiled with Graphite2 version 1.3.14; using 1.3.14 Compiled with HarfBuzz version 10.2.0; using 10.2.0 Compiled with libpng version 1.6.46; using 1.6.46 Compiled with pplib version v2.2 Compiled with fontconfig version 2.13.1; using 2.15.0
`/ext/texlive/2025/bin/x86_64-linux/xindy`	xindy release: 2.5.1 xindy script version: 1.18.TL59893 xindy kernel version: 3.0 CLISP version 2.49.92 (2018-02-18) (built on bulldog [127.0.0.1]) architecture: X86_64
`/usr/bin/xpra`	xpra v3.1.5
`/usr/bin/xsel`	xsel version 1.2.1 by Conrad Parker <[email protected]>
`/usr/bin/xz`	xz (XZ Utils) 5.4.5 liblzma 5.4.5
`/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.
`/ext/venvs/cocalc/bin/yapf`	yapf 0.43.0
`/usr/bin/z3`	Z3 version 4.8.12 - 64 bit
`/ext/bin/zig`	0.14.0-dev.2441+3670910f2
`/ext/bin/zimpl`	3.6.2
`/usr/bin/zotero`	Zotero Zotero 115.14.0esr, Copyright (c) 2006-2022 Contributors
`/usr/bin/zsh`	zsh 5.9 (x86_64-ubuntu-linux-gnu)

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