Executables in CoCalc (Ubuntu 24.04)
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 239 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 2.7.14 (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 2.7.14 (amd64)
Usage: apt-get [options] command
apt-get [options] install|remove pkg1 [pkg2 ...]
apt-get [options] source pkg1 [pkg2 ...]
apt-get is a command line interface for retrieval of packages
and information about them from authenticated sources and
for installation, upgrade and removal of packages together
with their dependencies.
Most used commands:
update - Retrieve new lists of packages
upgrade - Perform an upgrade
install - Install new packages (pkg is libc6 not libc6.deb)
reinstall - Reinstall packages (pkg is libc6 not libc6.deb)
remove - Remove packages
purge - Remove packages and config files
autoremove - Remove automatically all unused packages
dist-upgrade - Distribution upgrade, see apt-get(8)
dselect-upgrade - Follow dselect selections
build-dep - Configure build-dependencies for source packages
satisfy - Satisfy dependency strings
clean - Erase downloaded archive files
autoclean - Erase old downloaded archive files
check - Verify that there are no broken dependencies
source - Download source archives
download - Download the binary package into the current directory
changelog - Download and display the changelog for the given package
See apt-get(8) for more information about the available commands.
Configuration options and syntax is detailed in apt.conf(5).
Information about how to configure sources can be found in sources.list(5).
Package and version choices can be expressed via apt_preferences(5).
Security details are available in apt-secure(8).
This APT has Super Cow Powers. |
/usr/bin/aspell | @(#) International Ispell Version 3.1.20 (but really Aspell 0.60.8.1) |
/usr/bin/asy | Asymptote version 2.87 [(C) 2004 Andy Hammerlindl, John C. Bowman, Tom Prince] ENABLED OPTIONS: V3D 3D vector graphics output WebGL 3D HTML rendering OpenGL 3D OpenGL rendering SSBO GLSL shader storage buffer objects GSL GNU Scientific Library (special functions) FFTW3 Fast Fourier transforms Eigen Eigenvalue library XDR External Data Representation (portable binary file format for V3D) CURL URL support LSP Language Server Protocol Readline Interactive history and editing Sigsegv Distinguish stack overflows from segmentation faults GC Boehm garbage collector threads Render OpenGL in separate thread DISABLED OPTIONS: |
/usr/bin/autoconf | autoconf (GNU Autoconf) 2.71 Copyright (C) 2021 Free Software Foundation, Inc. License GPLv3+/Autoconf: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>, <https://gnu.org/licenses/exceptions.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by David J. MacKenzie and Akim Demaille. |
/usr/bin/automake | automake (GNU automake) 1.16.5 Copyright (C) 2021 Free Software Foundation, Inc. License GPLv2+: GNU GPL version 2 or later <https://gnu.org/licenses/gpl-2.0.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by Tom Tromey <[email protected]> and Alexandre Duret-Lutz <[email protected]>. |
/usr/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 |
/usr/bin/biber | biber version: 2.19 |
/usr/bin/bibtex | BibTeX 0.99d (TeX Live 2023/Debian) kpathsea version 6.3.5 Copyright 2023 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, 24.10.0 (compiled: yes) Python (CPython) 3.12.3 |
/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 | 1.1.36 |
/usr/bin/bup | 0.33.3 |
/usr/bin/cal | December 2024
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/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): 0.04 |
/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. |
/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/miniforge2024/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/miniforge2024=/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/miniforge2024/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/miniforge2024=/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/miniforge2024/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/miniforge2024=/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/8.11.1(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 : 2.39.0
NetCDF library version : 4.9.2 of Jun 6 2024 10:56:48 $
exse library version : 2.0.0
FILE library version : 1.9.1
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/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. |
/usr/bin/chromedriver | ChromeDriver 131.0.6778.85 (3d81e41b6f3ac8bcae63b32e8145c9eb0cd60a2d-refs/branch-heads/6778@{#2285}) |
/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/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 3.31.2 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 | 4.95.3 b0c935a6e0742adde9f7a5f6e5816553ee0e7ffb with Code 1.95.3 |
/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 - chlamy v6.3 Chlamydomonas reinhardtii (chlamy) accession and ontology information - patens v6.3 Physcomitrella patens (patens) 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 - fly-o v6.3 Drosophila melanogaster (fly) accession and ontology information - bee v6.3 Apis mellifera (bee) accession and ontology information - cow v5.4 Bos taurus (cow) accession and ontology information - dicty v6.3 Dictyostelium discoideum (dicty) accession and ontology information - chicken-o v6.3 Gallus gallus (chicken) accession and ontology information - corn v6.3 Zea mays (corn) accession and ontology information - mosquito v6.3 Anopheles gambiae (mosquito) accession and ontology information - urchin v6.3 Strongylocentrotus purpuratus (urchin) accession and ontology information - mushroom v6.3 Agaricus bisporus (mushroom) accession and ontology information - pseudonana v6.3 Thalassiosira pseudonana (pseudonana) accession and ontology information - worm-o v6.3 Caenorhabditis elegans (worm) accession and ontology information - tomato v6.3 Solanum lycopersicum (tomato) accession and ontology information - hydra v6.3 Hydra vulgaris (hydra) accession and ontology information - balbc_cocci v5.2 Balbc/J mouse and Coccidioides genome combined - zebrafish-o v6.3 Danio rerio (zebrafish) accession and ontology information - zebrafinch v6.3 Taeniopygia guttata (zebrafinch) accession and ontology information - ciliate v6.3 Tetrahymena thermophila (ciliate) accession and ontology information - seahare v6.3 Aplysia californica (seahare) accession and ontology information - rat-o v6.3 Rattus norvegicus (rat) accession and ontology information - ciona v6.3 Ciona intestinalis (ciona) accession and ontology information - pombe v6.3 Schizosaccharomyces pombe (pombe) accession and ontology information - diatom v6.3 Phaeodactylum tricornutum (diatom) accession and ontology information - volvox v6.3 Volvox carteri (volvox) accession and ontology information - pig v6.3 Sus scrofa (pig) accession and ontology information - ncrassa v6.3 Neurospora crassa (ncrassa) accession and ontology information - fugu v6.3 Takifugu rubripes (fugu) accession and ontology information - arabidopsis-o v6.3 Arabidopsis thaliana (arabidopsis) accession and ontology information - ascomycetes v6.0 Neurospora crassa (ascomycetes) accession and ontology information - yeast-o v6.3 Saccharomyces cerevisiae (yeast) accession and ontology information - laevis v6.3 Xenopus laevis (laevis) accession and ontology information - mouse-o v6.3 Mus musculus (mouse) accession and ontology information - frog-o v6.3 Xenopus tropicalis (frog) accession and ontology information - rice v6.3 Oryza sativa (rice) accession and ontology information - rhesus v6.3 Macaca mulatta (rhesus) accession and ontology information - selaginella v6.3 Selaginella moellendorffii (selaginella) accession and ontology information - anemone v6.3 Nematostella vectensis (anemone) accession and ontology information PROMOTERS - worm-p v5.5 worm promoters (worm) - rat-p v5.5 rat promoters (rat) - chicken-p v5.5 chicken promoters (chicken) - frog-p v5.5 frog promoters (frog) - human-p v5.5 human promoters (human) - mouse-p v5.5 mouse promoters (mouse) - zebrafish-p v5.5 zebrafish promoters (zebrafish) - arabidopsis-p v6.3 arabidopsis promoters (arabidopsis) - fly-p v5.5 fly promoters (fly) - yeast-p v5.5 yeast promoters (yeast) GENOMES v5.10 hg18 v6.4 human genome and annotation for UCSC hg18 - dm3 v6.0 fly genome and annotation for UCSC dm3 - hg38 v6.4 human genome and annotation for UCSC hg38 - xenTro7 v6.4 frog genome and annotation for UCSC xenTro7 - tair10 v6.0 arabidopsis genome and annotation (tair10) - ce6 v6.4 worm genome and annotation for UCSC ce6 - tetNig2 v6.4 fugu genome and annotation for UCSC tetNig2 - petMar2 v6.4 lamprey genome and annotation for UCSC petMar2 - danRer10 v6.4 zebrafish genome and annotation for UCSC danRer10 - panTro4 v6.4 human genome and annotation for UCSC panTro4 - rheMac3 v6.4 rhesus genome and annotation for UCSC rheMac3 - danRer7 v6.4 zebrafish genome and annotation for UCSC danRer7 - hg19 v6.4 human genome and annotation for UCSC hg19 - rheMac8 v6.4 rhesus genome and annotation for UCSC rheMac8 - AGPv3 v5.10 corn genome and annotation (AGPv3) - danRer11 v6.4 zebrafish genome and annotation for UCSC danRer11 - xenTro3 v6.4 frog genome and annotation for UCSC xenTro3 - susScr11 v6.4 pig genome and annotation for UCSC susScr11 - fr3 v6.4 fugu genome and annotation for UCSC fr3 - apiMel2 v6.4 bee genome and annotation for UCSC apiMel2 - mm9 v6.4 mouse genome and annotation for UCSC mm9 - ce10 v6.4 worm genome and annotation for UCSC ce10 - panTro5 v6.4 human genome and annotation for UCSC panTro5 - susScr3 v6.4 pig genome and annotation for UCSC susScr3 - sacCer3 v6.4 yeast genome and annotation for UCSC sacCer3 - ce11 v6.4 worm genome and annotation for UCSC ce11 - galGal6 v6.4 chicken genome and annotation for UCSC galGal6 - panTro3 v6.4 human genome and annotation for UCSC panTro3 - rice.IRGSP-1.0 v5.10 rice genome and annotation (rice.IRGSP-1.0) - anoGam1 v6.4 mosquito genome and annotation for UCSC anoGam1 - panPan2 v6.4 human genome and annotation for UCSC panPan2 - aplCal1 v6.4 seahare genome and annotation for UCSC aplCal1 - apiMel3 v6.4 bee genome and annotation for UCSC apiMel3 - panTro6 v6.4 human genome and annotation for UCSC panTro6 - taeGut2 v6.4 zebrafinch genome and annotation for UCSC taeGut2 - xenTro2 v6.4 frog genome and annotation for UCSC xenTro2 - ci2 v6.4 ciona genome and annotation for UCSC ci2 - hg17 v6.4 human genome and annotation for UCSC hg17 - corn.AGPv3 v5.10 corn genome and annotation (corn.AGPv3) - panPan1 v6.4 human genome and annotation for UCSC panPan1 - galGal5 v6.4 chicken genome and annotation for UCSC galGal5 - mm10 v6.4 mouse genome and annotation for UCSC mm10 - rn6 v6.4 rat genome and annotation for UCSC rn6 - dm6 v6.4 fly genome and annotation for UCSC dm6 - ci3 v6.4 ciona genome and annotation for UCSC ci3 - mm8 v6.4 mouse genome and annotation for UCSC mm8 - sacCer2 v6.4 yeast genome and annotation for UCSC sacCer2 - gorGor4 v6.4 human genome and annotation for UCSC gorGor4 - gorGor5 v6.4 human genome and annotation for UCSC gorGor5 - strPur2 v6.0 urchin genome and annotation for UCSC strPur2 - petMar3 v6.4 lamprey genome and annotation for UCSC petMar3 - papAnu2 v6.4 human genome and annotation for UCSC papAnu2 - xenTro9 v6.4 frog genome and annotation for UCSC xenTro9 - gorGor3 v6.4 human genome and annotation for UCSC gorGor3 - rn4 v6.4 rat genome and annotation for UCSC rn4 - galGal4 v6.4 chicken genome and annotation for UCSC galGal4 - rn5 v6.4 rat genome and annotation for UCSC rn5 - canFam3 v6.4 dog genome and annotation for UCSC canFam3 - patens.ASM242v1 v5.10 patens genome and annotation (patens.ASM242v1) - rheMac2 v6.4 rhesus genome and annotation for UCSC rheMac2 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/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/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 3.0.11 |
/usr/bin/data | 0.10.1 |
/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/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/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 1.1.1 |
/usr/bin/dvips | This is dvips(k) 2023.1 (TeX Live 2023) Copyright 2023 Radical Eye Software kpathsea version 6.3.5 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 | 2.0.2 |
/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/feynmf | This is feynmf: $Id: feynmf.pl,v 1.5 1996/12/02 01:38:45 ohl Exp $ |
/usr/bin/fish | fish, version 3.7.0 |
/usr/bin/flex | flex 2.6.4 |
/ext/bin/fscip | syntax: fscip fscip_param_file problem_file_name [-l <logfile>] [-q] [-sl <settings>] [-s <settings>] [-sr <root_settings>] [-w <prefix_warm>] [-sth <number>] [-fsol <solution_file>] [-isol <initial solution file] -l <logfile> : copy output into log file -q : suppress screen messages -sl <settings> : load parameter settings (.set) file for LC presolving -s <settings> : load parameter settings (.set) file for solvers -sr <root_settings> : load parameter settings (.set) file for root -w <prefix_warm> : warm start file prefix ( prefix_warm_nodes.gz and prefix_warm_solution.txt are read ) -sth <number> : the number of solver threads used -fsol <solution file> : specify output solution file -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. |
/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/geckodriver | geckodriver 0.35.0 (9f0a0036bea4 2024-08-03 07:11 +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 2.63.2 (2024-12-05) https://github.com/cli/cli/releases/tag/v2.63.2 |
/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 131.0.6778.139 |
/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 "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Ubuntu-1ubuntu124.04) OpenJDK 64-Bit Server VM (build 21.0.5+11-Ubuntu-1ubuntu124.04, 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: 21.0.5 (Ubuntu 21.0.5+11-Ubuntu-1ubuntu124.04) OS: Linux 5.15.0-1046-gcp amd64 |
/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/h5dump | h5dump: Version 1.10.10 |
/usr/bin/hardlink | hardlink from util-linux 2.39.3 (features: reflink, cryptoapi) |
/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 6.9) (see https://mercurial-scm.org for more information) Copyright (C) 2005-2024 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 3.14.16 (Linux x86_64), ASL(20231111) |
/ext/miniforge2024/bin/ipython | 8.30.0 |
/ext/venvs/cocalc/bin/ipython | 8.30.0 |
/ext/venvs/cocalc/bin/ipython3 | 8.30.0 |
/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 Dec 18 18:13:43 2024 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod: ok Loading module: bugs: ok |
/usr/bin/java | Picked up _JAVA_OPTIONS: -Xms64m openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Ubuntu-1ubuntu124.04) OpenJDK 64-Bit Server VM (build 21.0.5+11-Ubuntu-1ubuntu124.04, mixed mode, sharing) |
/usr/bin/javac | Picked up _JAVA_OPTIONS: -Xms64m javac 21.0.5 |
/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 : 1.0.3 External ToC : 1.0.1 MyST-Parser : 2.0.0 MyST-NB : 1.1.2 Sphinx Book Theme : 1.1.3 Jupyter-Cache : 1.0.1 NbClient : 0.10.1 |
/ext/venvs/cocalc/bin/jupyter-nbconvert | 7.16.4 |
/ext/venvs/cocalc/bin/jupyter-notebook | 7.3.1 |
/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:markdown, md:myst,
md:pandoc or py:nomarker, py:light, py:hydrogen,
py:sphinx, py:percent. The default format for scripts
is the 'light' format, which uses few cell markers
(none when possible). Alternatively, a format
compatible with many editors is the 'percent' format,
which uses '# %%' as cell markers. The main formats
(markdown, light, percent) preserve notebooks and text
documents in a roundtrip. Use the --test and and
--test-strict commands to test the roundtrip on your
files. Read more about the available formats at
https://jupytext.readthedocs.io/en/latest/formats.html
(default: None)
-o OUTPUT, --output OUTPUT
Destination file. Defaults to the original file, with
prefix/suffix/extension changed according to the
destination format. Use '-' to print the notebook on
stdout. (default: None)
--update Preserve the output cells when the destination
notebook is an .ipynb file that already exists
(default: False)
--set-formats SET_FORMATS
Turn the notebook or text document to one or more
alternative representations with e.g. '--set-formats
ipynb,py:light'. The --set-formats option also
triggers the creation/update of all paired files
(default: None)
--sync, -s Synchronize the content of the paired representations
of the given notebook. Input cells are taken from the
file that was last modified, and outputs are read from
the ipynb file, if present. (default: False)
--paired-paths, -p List the locations of the alternative representations
for this notebook. (default: False)
--format-options FORMAT_OPTIONS, --opt FORMAT_OPTIONS
Set format options with e.g. '--opt
comment_magics=true' or '--opt
notebook_metadata_filter=-kernelspec'. (default: None)
--update-metadata UPDATE_METADATA
Update the notebook metadata with the desired
dictionary. Argument must be given in JSON format. For
instance, if you want to activate a pairing in the
generated file, use e.g. --update-metadata
'{"jupytext":{"formats":"ipynb,py:light"}}' See also
the --opt and --set-formats options for other ways to
operate on the Jupytext metadata. (default: {})
--use-source-timestamp
Set the modification timestamp of the output file(s)
equalto that of the source file, and keep the source
file and its timestamp unchanged. (default: False)
--warn-only, -w Only issue a warning and continue processing other
notebooks when the conversion of a given notebook
fails (default: False)
--test Test that the notebook is stable under a round trip
conversion, up to the expected changes (default:
False)
--test-strict Test that the notebook is strictly stable under a
round trip conversion (default: False)
--stop, -x In --test mode, stop on first round trip conversion
error, and report stack traceback (default: False)
--pipe PIPE Pipe the text representation (in format --pipe-fmt) of
the notebook into another program, and read the
notebook back. For instance, reformat your notebook
with: 'jupytext notebook.ipynb --pipe black' If you
want to reformat it and sync the paired
representation, execute: 'jupytext notebook.ipynb
--sync --pipe black' In case the program that you want
to execute does not accept pipes, use {} as a
placeholder for a temporary file name into which
jupytext will write the text representation of the
notebook, e.g.: jupytext notebook.ipynb --pipe 'black
{}' (default: None)
--diff, -d Show the differences between (the inputs) of two
notebooks (default: False)
--diff-format DIFF_FORMAT
The text format used to show differences in --diff
(default: None)
--check CHECK Pipe the text representation (in format --pipe-fmt) of
the notebook into another program, and test that the
returned value is non zero. For instance, test that
your notebook is pep8 compliant with: 'jupytext
notebook.ipynb --check flake8' or run pytest on your
notebook with: 'jupytext notebook.ipynb --check
pytest' In case the program that you want to execute
does not accept pipes, use {} as a placeholder for a
temporary file name into which jupytext will write the
text representation of the notebook, e.g.: jupytext
notebook.ipynb --check 'pytest {}' (default: None)
--pipe-fmt PIPE_FMT The format in which the notebook should be piped to
other programs, when using the --pipe and/or --check
commands. (default: auto:percent)
--set-kernel SET_KERNEL, -k SET_KERNEL
Set the kernel with the given name on the notebook.
Use '--set-kernel -' to set a kernel matching the
current environment on Python notebooks, and matching
the notebook language otherwise (get the list of
available kernels with 'jupyter kernelspec list')
(default: None)
--execute Execute the notebook with the given kernel. In the
--pre-commit-mode, the notebook is executed only if a
code cell changed, or if some execution outputs are
missing or not ordered. (default: False)
--run-path RUN_PATH Execute the notebook at the given path (defaults to
the notebook parent directory) (default: None)
--quiet, -q Quiet mode: do not comment about files being updated
or created (default: False)
--show-changes Display the diff for each output file (default: False)
--version, -v Show jupytext's version number and exit (default:
False)
--pre-commit Ignore the notebook argument, and instead apply
Jupytext on the notebooks found in the git index,
which have an extension that matches the (optional)
--from argument. (default: False)
--pre-commit-mode This is a mode that is compatible with the pre-commit
framework. In this mode, --sync won't use timestamp
but instead will determines the source notebook as the
element of the pair that is added to the git index. An
alert is raised if multiple inconsistent
representations are in the index. It also raises an
alert after updating the paired files or outputs if
those files need to be added to the index. Finally,
filepaths that aren't in the source format you are
trying to convert from are ignored. (default: False) |
/usr/bin/latex | pdfTeX 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) kpathsea version 6.3.5 Copyright 2023 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 1.6.43; using libpng 1.6.43 Compiled with zlib 1.3; using zlib 1.3 Compiled with xpdf version 4.04 |
/usr/bin/latexmk | Latexmk, John Collins, 31 Jan. 2024. Version 4.83 |
/ext/bin/lean | Lean (version 3.11.0, commit fb3f3e88be8a, Release) |
/usr/bin/lfm | usage: lfm [-h] [-d] [-w] [--restore-config] [--restore-keys]
[--restore-theme] [--delete-history]
[path1] [path2]
lfm v3.0 - (C) 2001-17, by Iñigo Serna <[email protected]>
positional arguments:
path1 Path to show in left pane (default: ".")
path2 Path to show in right pane (default: ".")
options:
-h, --help show this help message and exit
-d, --debug Enable debug level in log file
-w, --use-wide-chars Enable support for wide chars
--restore-config Restore default configuration
--restore-keys Restore default key bindings
--restore-theme Restore default theme
--delete-history Delete history
'Last File Manager' is a powerful file manager for UNIX console.
It has a curses interface and it's written in Python version 3.4+.
Released under GNU Public License, read COPYING file for more details. |
/usr/bin/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 | 24.04 |
/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 |
/usr/bin/luatex | This is LuaTeX, Version 1.17.0 (TeX Live 2023/Debian) Development id: 7581 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 2022 Taco Hoekwater and the LuaTeX Team. |
/usr/bin/lzma | xz (XZ Utils) 5.4.5 liblzma 5.4.5 |
/usr/bin/M2 | 1.24.11 |
/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. |
/ext/bin/mageck | 0.5.9.5 |
/usr/bin/make | GNU Make 4.3 Built for x86_64-pc-linux-gnu Copyright (C) 1988-2020 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. |
/usr/bin/markdown | This is Markdown, version 1.0.1. Copyright 2004 John Gruber http://daringfireball.net/projects/markdown/ |
/usr/bin/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/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/ninja | 1.11.1 |
/usr/bin/nnn | 4.9 |
/ext/venvs/cocalc/bin/nosetests | nosetests version 1.5.3 |
/ext/venvs/cocalc/bin/notedown | 1.5.1 |
/usr/bin/npm | 10.9.2 |
/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 9.2.0 Copyright (C) 1993-2024 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-9.2.0 | GNU Octave, version 9.2.0 Copyright (C) 1993-2024 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 9.2.0 Copyright (C) 1993-2024 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-9.2.0 | GNU Octave, version 9.2.0 Copyright (C) 1993-2024 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. |
/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 3.5 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 (3.12.3) |
/usr/bin/pdflatex | pdfTeX 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) kpathsea version 6.3.5 Copyright 2023 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 1.6.43; using libpng 1.6.43 Compiled with zlib 1.3; using zlib 1.3 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 44 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: Dec 2 2024 12:36:18) (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/venvs/cocalc/bin/pip | pip 24.3.1 from /ext/venvs/cocalc/lib/python3.12/site-packages/pip (python 3.12) |
/ext/venvs/cocalc/bin/pipenv | pipenv, version 2024.4.0 |
/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 Dec 18 18:14:25 2024 Options in effect: --noweb Before frequency and genotyping pruning, there are 0 SNPs 0 founders and 0 non-founders found 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 0 SNPs ERROR: Stopping as there are no SNPs left for analysis |
/usr/bin/pm2 | pm2 launched in no-daemon mode (you can add DEBUG="*" env variable to get more messages) 2024-12-18T18:14:26: PM2 log: Launching in no daemon mode 5.4.3 |
/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 | 9.15.0 |
/ext/venvs/cocalc/bin/poetry | Poetry (version 1.8.5) |
/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. |
/ext/venvs/cocalc/bin/pretext | 2.10.1 |
/usr/bin/prettier | 3.4.2 |
/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/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 8.3.4 |
/ext/venvs/cocalc/bin/pytest | pytest 8.3.4 |
/ext/miniforge2024/bin/python | Python 3.12.8 |
/ext/miniforge2024/bin/python3 | Python 3.12.8 |
/ext/venvs/cocalc/bin/python3 | Python 3.12.3 |
/usr/bin/pythontex | /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 |
/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 |
/usr/bin/qgis | QGIS 3.40.1-Bratislava 'Bratislava' (989853a7a31) |
/usr/local/bin/quarto | 1.6.37 |
/usr/bin/R | R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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/bin/racket | Welcome to Racket v8.10 [cs]. |
/usr/bin/ranger | ranger version: ranger 1.9.3 Python version: 3.12.3 (main, Nov 6 2024, 18:32:19) [GCC 13.2.0] Locale: C.UTF-8 |
/usr/bin/rclone | rclone v1.68.2 - os/version: ubuntu 24.04 (64 bit) - os/kernel: 5.15.0-1046-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/ros | roswell 24.10.115(NO-GIT-REVISION) |
/usr/bin/Rscript | Rscript (R) version 4.4.2 (2024-10-31) |
/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/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 Nov 06 2024 19:04:03) 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-jS9mzH/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-jS9mzH/vim-9.1.0016=/usr/src/vim-2:9.1.0016-1ubuntu7.5 -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 10.5, Release Date: 2024-12-04 |
/ext/bin/sage-10.5 | SageMath version 10.5, Release Date: 2024-12-04 |
/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_1726175734089/_build_env/bin/x86_64-conda-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /ext/miniforge2024/include
CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2024/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1726175734089/work=/usr/local/src/conda/samtools-1.21 -fdebug-prefix-map=/ext/miniforge2024=/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/miniforge2024/lib -Wl,-rpath-link,/ext/miniforge2024/lib -L/ext/miniforge2024/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/miniforge2024/libexec/htslib htscodecs=1.6.1
CC: /opt/conda/conda-bld/htslib_1726172129301/_build_env/bin/x86_64-conda-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /ext/miniforge2024/include
CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /ext/miniforge2024/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1726172129301/work=/usr/local/src/conda/htslib-1.21 -fdebug-prefix-map=/ext/miniforge2024=/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/miniforge2024/lib -Wl,-rpath-link,/ext/miniforge2024/lib -L/ext/miniforge2024/lib -fvisibility=hidden -rdynamic
HTSlib URL scheme handlers present:
built-in: file, preload, data
S3 Multipart Upload: s3w+https, s3w+http, s3w
Amazon S3: s3+https, s3, s3+http
libcurl: gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet
Google Cloud Storage: gs+http, gs+https, gs
crypt4gh-needed: crypt4gh
mem: mem |
/usr/bin/sbcl | SBCL 2.2.9.debian |
/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]>. |
/ext/venvs/cocalc/bin/shiny | shiny, version 1.2.1 |
/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=1734545549
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/bin/nosudo:/ext/bin:/usr/lib/xpra:/usr/local/sbin:/usr/local/bin:/usr/sbin:/sbin:/bin:/ext/data/homer/bin:/ext/data/weblogo
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=1734545551
built-in modules: {}
AC_CONFIGURE_ARGS = '--prefix=/ext/sage/10.5/local' '--libdir=/ext/sage/10.5/local/lib' '--disable-maintainer-mode' '--disable-dependency-tracking' '--exec-prefix=/ext/sage/10.5/local' '--bindir=/ext/sage/10.5/local/bin' '--with-ntl=/ext/sage/10.5/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/10.5/local/lib -L/ext/sage/10.5/local/lib -Wl,-rpath,/ext/sage/10.5/local/lib -Wl,-rpath-link,/ext/sage/10.5/local/lib -L/ext/sage/10.5/local/lib -Wl,-rpath,/ext/sage/10.5/local/lib ' 'CXX=g++ -std=gnu++11' 'CXXFLAGS=-g -O2' --enable-omalloc OMALLOC_LIBS='/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src/omalloc/libomalloc.la' OMALLOC_INCLUDES='-I/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src' --htmldir=${prefix}/share/doc/singular --with-Singular RESOURCES_LIBS='/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src/resources/libsingular_resources.la' RESOURCES_INCLUDES='-I/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src ' FACTORY_LIBS='/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src/factory/libfactory.la' FACTORY_INCLUDES='-I/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src -I/ext/sage/10.5/local/var/tmp/sage/build/singular-4.4.0/src/factory -I/ext/sage/10.5/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/10.5/local/lib -L/ext/sage/10.5/local/lib -Wl,-rpath,/ext/sage/10.5/local/lib -Wl,-rpath-link,/ext/sage/10.5/local/lib -L/ext/sage/10.5/local/lib -Wl,-rpath,/ext/sage/10.5/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: 13.2.0)
argv[0] : Singular
SearchPath: /ext/sage/10.5/local/bin/../share/singular/LIB:/ext/sage/10.5/local/bin/../share/factory:/ext/sage/10.5/local/bin/../libexec/singular/MOD:/ext/sage/10.5/local/libexec/singular/MOD:/ext/sage/10.5/local/bin:/ext/sage/10.5/local/bin/..
Singular : /ext/sage/10.5/local/bin/Singular
BinDir : /ext/sage/10.5/local/bin
ProcDir : /ext/sage/10.5/local/bin/..:/ext/sage/10.5/local/bin/../libexec/singular/MOD:/ext/sage/10.5/local/libexec/singular/MOD
RootDir : /ext/sage/10.5/local/bin/..
DataDir : /ext/sage/10.5/local/bin/../share
DefaultDir: /ext/sage/10.5/local
InfoFile : /ext/sage/10.5/local/bin/../share/info/singular.info
IdxFile : /ext/sage/10.5/local/bin/../share/singular/singular.idx
HtmlDir : /ext/sage/10.5/local/bin/../share/doc/singular
ManualUrl : https://www.singular.uni-kl.de/Manual/
ExDir :
Path : /ext/sage/10.5/local/bin:/ext/sage/10.5/local/bin/..:/ext/sage/10.5/local/bin/../libexec/singular/MOD:/ext/sage/10.5/local/libexec/singular/MOD:/ext/sage/10.5/src/bin:/ext/sage/10.5/local/libexec/ccache:/ext/sage/10.5/build/bin:/ext/sage/10.5/local/var/lib/sage/venv-python3.12.5/bin:/cocalc/bin:/ext/venvs/cocalc/bin:/ext/bin/nosudo:/ext/bin:/usr/lib/xpra:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/ext/data/homer/bin:/ext/data/weblogo
emacs : /usr/bin/emacs-gtk
xemacs :
SingularEmacs: /ext/sage/10.5/local/bin/Singular
EmacsLoad : /ext/sage/10.5/local/bin/../share/singular/emacs/.emacs-singular
EmacsDir : /ext/sage/10.5/local/bin/../share/singular/emacs
SingularXterm: /ext/sage/10.5/local/bin/Singular
xterm : /usr/bin/xterm
EmacsDir : /ext/sage/10.5/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
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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
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/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 |
/ext/venvs/cocalc/bin/streamlit | Streamlit, version 1.41.1 |
/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 |
/usr/bin/synctex | This is SyncTeX command line utility, version 1.5 usage: synctex <subcommand> [options] [args] Synchronize TeXnology command-line client, version 1.21 The Synchronization TeXnology by Jérôme Laurens is a rather new feature of recent TeX engines. It allows to synchronize between input and output, which means to navigate from the source document to the typeset material and vice versa. Available subcommands: view to perform forwards synchronization edit to perform backwards synchronization update to update a synctex file after a dvi/xdv to pdf filter help this help Type 'synctex help <subcommand>' for help on a specific subcommand. There is also an undocumented test subcommand. |
/usr/bin/t1asm | t1asm (LCDF t1utils) 1.41 Copyright (C) 1992-2017 I. Lee Hetherington, Eddie Kohler et al. This is free software; see the source for copying conditions. There is NO warranty, not even for merchantability or fitness for a particular purpose. |
/usr/bin/tclsh | 8.6 |
/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/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 5.7.2 |
/usr/bin/valgrind | valgrind-3.22.0 |
/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/which | /usr/sbin/rpcinfo |
/usr/bin/wordmatch | EMBOSS:6.6.0.0 |
/usr/bin/xclip | xclip version 0.13 Copyright (C) 2001-2008 Kim Saunders et al. Distributed under the terms of the GNU GPL |
/usr/bin/xdotool | xdotool version 3.20160805.1 |
/usr/bin/xelatex | XeTeX 3.141592653-2.6-0.999995 (TeX Live 2023/Debian) kpathsea version 6.3.5 Copyright 2023 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 74.2; using 74.2 Compiled with zlib version 1.3; using 1.3 Compiled with FreeType2 version 2.13.2; using 2.13.2 Compiled with Graphite2 version 1.3.14; using 1.3.14 Compiled with HarfBuzz version 8.3.0; using 8.3.0 Compiled with libpng version 1.6.43; using 1.6.43 Compiled with pplib version v2.05 less toxic i hope Compiled with fontconfig version 2.15.0; using 2.15.0 |
/usr/bin/xindy | xindy release: unknown
xindy script version: 1.18
xindy kernel version: 3.0
CLISP version 2.49.93+ (2018-02-18) (built on lcy02-amd64-013.buildd [127.0.1.1])
architecture: X86_64 |
/usr/bin/xpra | xpra v3.1.5 |
/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/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) |
This information was collected at 20241218-1811.