Executables

This is a non-comprehensive list of executables available on CoCalc. The output of running the executable with --version or equivalent is shown below. This offers some information about the utility and version number.
To run the software executable, you need to either open a "Terminal" (create a file with the extension .term) or run it indirectly via an interactive worksheet.
On CoCalc, you can also install and/or compile your own executable binaries. You have a lot of control about your own project, which is essentially a containerized Linux environment.

4Ti2-Zsolve/usr/bin/4ti2-zsolve

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

7Z/usr/bin/7z

7-Zip [64] 16.02 : Copyright (c) 1999-2016 Igor Pavlov : 2016-05-21
p7zip Version 16.02 (locale=C.UTF-8,Utf16=on,HugeFiles=on,64 bits,8 CPUs Intel(R) Xeon(R) CPU @ 2.30GHz (306F0),ASM,AES-NI)

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

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

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

Advpng/usr/bin/advpng

advancecomp vnone by Andrea Mazzoleni, http://www.advancemame.it

Ansi2Html/cocalc/bin/ansi2html

ansi2html 1.5.2

Ant/usr/bin/ant

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/user/tmp/ -Xms64m
Apache Ant(TM) version 1.10.7 compiled on October 24 2019

Asciidoc/usr/bin/asciidoc

asciidoc 9.0.0rc1

Asciidoctor/usr/bin/asciidoctor

Asciidoctor 2.0.10 [https://asciidoctor.org]
Runtime Environment (ruby 2.7.0p0 (2019-12-25 revision 647ee6f091) [x86_64-linux-gnu]) (lc:UTF-8 fs:UTF-8 in:UTF-8 ex:UTF-8)

Aspell/usr/bin/aspell

@(#) International Ispell Version 3.1.20 (but really Aspell 0.60.8)

Asy/usr/bin/asy

Asymptote version 2.62 [(C) 2004 Andy Hammerlindl, John C. Bowman, Tom Prince]

ENABLED OPTIONS:
WebGL    3D HTML rendering
OpenGL   3D OpenGL rendering
GSL      GNU Scientific Library (special functions)
FFTW3    Fast Fourier transforms
XDR      external data representation (portable binary file format)
Readline interactive history and editing
Sigsegv  distinguish stack overflows from segmentation faults
GC       Boehm garbage collector

DISABLED OPTIONS:

Autoconf/usr/bin/autoconf

autoconf (GNU Autoconf) 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+/Autoconf: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>, <http://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.

Automake/usr/bin/automake

automake (GNU automake) 1.16.1
Copyright (C) 2018 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]>.

Autopep8/usr/local/bin/autopep8

autopep8 1.5.4 (pycodestyle: 2.6.0)

Bash/usr/bin/bash

GNU bash, version 5.0.17(1)-release (x86_64-pc-linux-gnu)
Copyright (C) 2019 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.

Bazel/usr/bin/bazel

Extracting Bazel installation...
WARNING: ignoring _JAVA_OPTIONS in environment.
Build label: 3.6.0
Build target: bazel-out/k8-opt/bin/src/main/java/com/google/devtools/build/lib/bazel/BazelServer_deploy.jar
Build time: Tue Oct 6 13:11:20 2020 (1601989880)
Build timestamp: 1601989880
Build timestamp as int: 1601989880

Bedtools/ext/bin/bedtools

bedtools v2.29.2

Biber/usr/bin/biber

biber version: 2.14 (beta)

Bibtex/usr/bin/bibtex

BibTeX 0.99d (TeX Live 2019/Debian)
kpathsea version 6.3.1
Copyright 2019 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.

Cabal/opt/ghc/bin/cabal

cabal-install version 3.2.0.0
compiled using version 3.2.0.0 of the Cabal library 

Cadabra2/usr/local/bin/cadabra2

Info at http://cadabra.science/
Available under the terms of the GNU General Public License v3

Cadabra 2.3.1 (build 1.a496d46 dated 2020-07-18)
Copyright (C) 2001-2020  Kasper Peeters <[email protected]>
Using SymPy version 1.6.2
> > 
now exiting Shell...

Cargo/ext/bin/cargo

cargo 1.47.0 (f3c7e066a 2020-08-28)

Cbc/usr/bin/cbc

Welcome to the CBC MILP Solver 
Version: 2.10.3 
Build Date: Mar 24 2020 

command line - cbc -help (default strategy 1)
Cbc version 2.10.3, build Mar 24 2020
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):       0.00   (Wallclock seconds):       0.00

Ccache/usr/bin/ccache

ccache version 3.7.7

Copyright (C) 2002-2007 Andrew Tridgell
Copyright (C) 2009-2020 Joel Rosdahl

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.

Cheetah3/usr/bin/cheetah3

3.2.4

Chromedriver/usr/bin/chromedriver

ChromeDriver 85.0.4183.87 (cd6713ebf92fa1cacc0f1a598df280093af0c5d7-refs/branch-heads/[email protected]{#1689})

Clang/usr/bin/clang

clang version 10.0.0-4ubuntu1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

Clang-Format/usr/bin/clang-format

clang-format version 10.0.0-4ubuntu1 

Clasp/usr/bin/clasp

clasp version 3.3.4
Address model: 64-bit
libclasp version 3.3.4 (libpotassco version 1.1.0)
Configuration: WITH_THREADS=1
Copyright (C) Benjamin Kaufmann
License: The MIT License <https://opensource.org/licenses/MIT>

Clojure/usr/bin/clojure

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/user/tmp/ -Xms64m
"1.10.1"

Clp/usr/bin/clp

Coin LP version 1.17.5, build Feb 17 2020
command line - clp -help 
No match for help - ? for list of commands
Clp takes input from arguments ( - switches to stdin)
Enter ? for list of commands or help
Clp:

Cmake/usr/bin/cmake

cmake version 3.18.4

CMake suite maintained and supported by Kitware (kitware.com/cmake).

Code/usr/bin/code

Visual Studio Code 1.50.0

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

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

Options
  -d --diff <file> <file>           Compare two files with each other.
  -a --add <folder>                 Add folder(s) to the last active window.
  -g --goto <file:line[:character]> Open a file at the path on the specified
                                    line and character position.
  -n --new-window                   Force to open a new window.
  -r --reuse-window                 Force to open a file or folder in an
                                    already opened window.
  --folder-uri <uri>                Opens a window with given folder uri(s)
  --file-uri <uri>                  Opens a window with given file uri(s)
  -w --wait                         Wait for the files to be closed before
                                    returning.
  --locale <locale>                 The locale to use (e.g. en-US or zh-TW).
  --user-data-dir <dir>             Specifies the directory that user data is
                                    kept in. Can be used to open multiple
                                    distinct instances of Code.
  -h --help                         Print usage.

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

Troubleshooting
  -v --version                       Print version.
  --verbose                          Print verbose output (implies --wait).
  --log <level>                      Log level to use. Default is 'info'.
                                     Allowed values are 'critical', 'error',
                                     'warn', 'info', 'debug', 'trace', 'off'.
  -s --status                        Print process usage and diagnostics
                                     information.
  --prof-startup                     Run CPU profiler during startup
  --disable-extensions               Disable all installed extensions.
  --disable-extension <extension-id> Disable an extension.
  --sync <on> <off>                  Turn sync on or off
  --inspect-extensions <port>        Allow debugging and profiling of
                                     extensions. Check the developer tools for
                                     the connection URI.
  --inspect-brk-extensions <port>    Allow debugging and profiling of
                                     extensions with the extension host being
                                     paused after start. Check the developer
                                     tools for the connection URI.
  --disable-gpu                      Disable GPU hardware acceleration.
  --max-memory                       Max memory size for a window (in Mbytes).
  --telemetry                        Shows all telemetry events which VS code
                                     collects.

Coffee/home/user/cocalc/src/node_modules/.bin/coffee

CoffeeScript version 2.5.1

Configurehomer.Pl/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
-	zebrafinch	v6.3	Taeniopygia guttata (zebrafinch) accession and ontology information
-	dicty	v6.3	Dictyostelium discoideum (dicty) accession and ontology information
-	bee	v6.3	Apis mellifera (bee) accession and ontology information
-	hydra	v6.3	Hydra vulgaris (hydra) accession and ontology information
-	patens	v6.3	Physcomitrella patens (patens) accession and ontology information
-	anemone	v6.3	Nematostella vectensis (anemone) accession and ontology information
-	chlamy	v6.3	Chlamydomonas reinhardtii (chlamy) accession and ontology information
-	volvox	v6.3	Volvox carteri (volvox) accession and ontology information
-	balbc_cocci	v5.2	Balbc/J mouse and Coccidioides genome combined
-	cow	v5.4	Bos taurus (cow) accession and ontology information
-	frog-o	v6.3	Xenopus tropicalis (frog) accession and ontology information
-	diatom	v6.3	Phaeodactylum tricornutum (diatom) accession and ontology information
-	arabidopsis-o	v6.3	Arabidopsis thaliana (arabidopsis) accession and ontology information
-	mosquito	v6.3	Anopheles gambiae (mosquito) accession and ontology information
-	ciona	v6.3	Ciona intestinalis (ciona) accession and ontology information
-	rat-o	v6.3	Rattus norvegicus (rat) accession and ontology information
-	laevis	v6.3	Xenopus laevis (laevis) accession and ontology information
-	zebrafish-o	v6.3	Danio rerio (zebrafish) accession and ontology information
-	rhesus	v6.3	Macaca mulatta (rhesus) accession and ontology information
-	urchin	v6.3	Strongylocentrotus purpuratus (urchin) accession and ontology information
-	rice	v6.3	Oryza sativa (rice) accession and ontology information
-	lamprey	v6.3	Petromyzon marinus (lamprey) accession and ontology information
-	seahare	v6.3	Aplysia californica (seahare) accession and ontology information
-	yeast-o	v6.3	Saccharomyces cerevisiae (yeast) accession and ontology information
-	selaginella	v6.3	Selaginella moellendorffii (selaginella) accession and ontology information
-	mushroom	v6.3	Agaricus bisporus (mushroom) accession and ontology information
-	ciliate	v6.3	Tetrahymena thermophila (ciliate) accession and ontology information
-	fugu	v6.3	Takifugu rubripes (fugu) accession and ontology information
-	chicken-o	v6.3	Gallus gallus (chicken) accession and ontology information
-	pseudonana	v6.3	Thalassiosira pseudonana (pseudonana) accession and ontology information
-	dog	v6.3	Canis lupus familiaris (dog) accession and ontology information
-	mouse-o	v6.3	Mus musculus (mouse) accession and ontology information
-	tomato	v6.3	Solanum lycopersicum (tomato) accession and ontology information
-	pombe	v6.3	Schizosaccharomyces pombe (pombe) accession and ontology information
-	worm-o	v6.3	Caenorhabditis elegans (worm) accession and ontology information
-	ascomycetes	v6.0	Neurospora crassa (ascomycetes) accession and ontology information
-	corn	v6.3	Zea mays (corn) accession and ontology information
-	ncrassa	v6.3	Neurospora crassa (ncrassa) accession and ontology information
-	fly-o	v6.3	Drosophila melanogaster (fly) accession and ontology information
-	pig	v6.3	Sus scrofa (pig) accession and ontology information
-	cocci	v6.3	Coccidioides immitis RS (cocci) accession and ontology information
PROMOTERS
-	frog-p	v5.5	frog promoters (frog)
-	arabidopsis-p	v6.3	arabidopsis promoters (arabidopsis)
-	yeast-p	v5.5	yeast promoters (yeast)
-	mouse-p	v5.5	mouse promoters (mouse)
-	rat-p	v5.5	rat promoters (rat)
-	worm-p	v5.5	worm promoters (worm)
-	human-p	v5.5	human promoters (human)
-	chicken-p	v5.5	chicken promoters (chicken)
-	fly-p	v5.5	fly promoters (fly)
-	zebrafish-p	v5.5	zebrafish promoters (zebrafish)
GENOMES
v5.10	hg18	v6.4	human genome and annotation for UCSC hg18
-	ci2	v6.4	ciona genome and annotation for UCSC ci2
-	ce10	v6.4	worm genome and annotation for UCSC ce10
-	danRer11	v6.4	zebrafish genome and annotation for UCSC danRer11
-	panPan1	v6.4	human genome and annotation for UCSC panPan1
-	rn5	v6.4	rat genome and annotation for UCSC rn5
-	xenTro7	v6.4	frog genome and annotation for UCSC xenTro7
-	panTro5	v6.4	human genome and annotation for UCSC panTro5
-	galGal5	v6.4	chicken genome and annotation for UCSC galGal5
-	hg19	v6.4	human genome and annotation for UCSC hg19
-	panTro3	v6.4	human genome and annotation for UCSC panTro3
-	xenTro2	v6.4	frog genome and annotation for UCSC xenTro2
-	rn6	v6.4	rat genome and annotation for UCSC rn6
-	danRer7	v6.4	zebrafish genome and annotation for UCSC danRer7
-	tetNig2	v6.4	fugu genome and annotation for UCSC tetNig2
-	mm9	v6.4	mouse genome and annotation for UCSC mm9
-	taeGut2	v6.4	zebrafinch genome and annotation for UCSC taeGut2
-	dm3	v6.0	fly genome and annotation for UCSC dm3
-	corn.AGPv3	v5.10	corn genome and annotation (corn.AGPv3)
-	ci3	v6.4	ciona genome and annotation for UCSC ci3
-	gorGor5	v6.4	human genome and annotation for UCSC gorGor5
-	dm6	v6.4	fly genome and annotation for UCSC dm6
-	gorGor3	v6.4	human genome and annotation for UCSC gorGor3
-	patens.ASM242v1	v5.10	patens genome and annotation (patens.ASM242v1)
-	rn4	v6.4	rat genome and annotation for UCSC rn4
-	strPur2	v6.0	urchin genome and annotation for UCSC strPur2
-	ce11	v6.4	worm genome and annotation for UCSC ce11
-	panTro6	v6.4	human genome and annotation for UCSC panTro6
-	galGal6	v6.4	chicken genome and annotation for UCSC galGal6
-	ce6	v6.4	worm genome and annotation for UCSC ce6
-	xenTro9	v6.4	frog genome and annotation for UCSC xenTro9
-	xenTro3	v6.4	frog genome and annotation for UCSC xenTro3
-	tair10	v6.0	arabidopsis genome and annotation (tair10)
-	panPan2	v6.4	human genome and annotation for UCSC panPan2
-	apiMel2	v6.4	bee genome and annotation for UCSC apiMel2
-	susScr3	v6.4	pig genome and annotation for UCSC susScr3
-	sacCer3	v6.4	yeast genome and annotation for UCSC sacCer3
-	aplCal1	v6.4	seahare genome and annotation for UCSC aplCal1
-	danRer10	v6.4	zebrafish genome and annotation for UCSC danRer10
-	petMar2	v6.4	lamprey genome and annotation for UCSC petMar2
-	hg17	v6.4	human genome and annotation for UCSC hg17
-	mm10	v6.4	mouse genome and annotation for UCSC mm10
-	rheMac8	v6.4	rhesus genome and annotation for UCSC rheMac8
-	fr3	v6.4	fugu genome and annotation for UCSC fr3
-	mm8	v6.4	mouse genome and annotation for UCSC mm8
-	hg38	v6.4	human genome and annotation for UCSC hg38
-	canFam3	v6.4	dog genome and annotation for UCSC canFam3
-	galGal4	v6.4	chicken genome and annotation for UCSC galGal4
-	rheMac2	v6.4	rhesus genome and annotation for UCSC rheMac2
-	panTro4	v6.4	human genome and annotation for UCSC panTro4
-	rice.IRGSP-1.0	v5.10	rice genome and annotation (rice.IRGSP-1.0)
-	papAnu2	v6.4	human genome and annotation for UCSC papAnu2
-	petMar3	v6.4	lamprey genome and annotation for UCSC petMar3
-	susScr11	v6.4	pig genome and annotation for UCSC susScr11
-	rheMac3	v6.4	rhesus genome and annotation for UCSC rheMac3
-	apiMel3	v6.4	bee genome and annotation for UCSC apiMel3
-	gorGor4	v6.4	human genome and annotation for UCSC gorGor4
-	sacCer2	v6.4	yeast genome and annotation for UCSC sacCer2
-	AGPv3	v5.10	corn genome and annotation (AGPv3)
-	anoGam1	v6.4	mosquito genome and annotation for UCSC anoGam1
SETTINGS

Convert/usr/bin/convert

Version: ImageMagick 6.9.10-23 Q16 x86_64 20190101 https://imagemagick.org
Copyright: © 1999-2019 ImageMagick Studio LLC
License: https://imagemagick.org/script/license.php
Features: Cipher DPC Modules OpenMP 
Delegates (built-in): bzlib djvu fftw fontconfig freetype jbig jng jpeg lcms lqr ltdl lzma openexr pangocairo png tiff webp wmf x xml zlib

Coqc/usr/bin/coqc

The Coq Proof Assistant, version 8.11.0 (March 2020)
compiled on Mar 5 2020 20:37:30 with OCaml 4.08.1

Cpp/usr/bin/cpp

cpp (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 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.

Csdp/usr/bin/csdp

CSDP 6.2.0
 
Usage: 

csdp <input problem> [<final solution>] [<initial solution>]

Cvs/usr/bin/cvs

Concurrent Versions System (CVS) 1.12.13-MirDebian-27 (client/server)

Copyright (C) 2005 Free Software Foundation, Inc.

Portions contributed by Thorsten Glaser for the MirOS Project and Debian.
Senior 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

Cython/usr/local/bin/cython

Cython version 0.29.21

Data/usr/bin/data

0.10.1

Dbar/usr/bin/dbar

usage: dbar [-w <characters>] [-s <symbol>] [-min <minvalue>] [-max <maxvalue>] [-l <string>] [-nonl]

Diff3/usr/bin/diff3

diff3 (GNU diffutils) 3.7
Copyright (C) 2018 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.

Docbook2Pdf/usr/bin/docbook2pdf

DocBook-utils version 0.6.14 (jw version 1.1)

Docx2Txt/usr/local/bin/docx2txt

usage: docx2txt [-h] [-i IMG_DIR] docx

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

positional arguments:
  docx                  path of the docx file

optional arguments:
  -h, --help            show this help message and exit
  -i IMG_DIR, --img_dir IMG_DIR
                        path of directory to extract images

Dot/usr/bin/dot

dot - graphviz version 2.43.0 (0)

Dotty/usr/bin/dotty

dotty version 96c (09-24-96)
Error: Can't open display: :0

Dvips/usr/bin/dvips

This is dvips(k) 5.999 Copyright 2019 Radical Eye Software
kpathsea version 6.3.1
Copyright 2019 Radical Eye Software.
There is NO warranty.  You may redistribute this software
under the terms of the GNU General Public License
and the Dvips copyright.
For more information about these matters, see the files
named COPYING and dvips.h.
Primary author of Dvips: T. Rokicki.

Ed/usr/bin/ed

GNU ed 1.16
Copyright (C) 1994 Andrew L. Moore.
Copyright (C) 2020 Antonio Diaz Diaz.
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.

Emacs/usr/bin/emacs

GNU Emacs 26.3
Copyright (C) 2019 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.

Encfs/usr/bin/encfs

encfs version 1.9.5

Erb/usr/bin/erb

erb.rb [2.2.0 $]

Erl/usr/bin/erl

Erlang (SMP,ASYNC_THREADS) (BEAM) emulator version 10.6.4

F2Py/usr/local/bin/f2py

2

F77/usr/bin/f77

GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 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.

F95/usr/bin/f95

GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 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.

Fenics-Version/usr/bin/fenics-version

2019.2.0.dev0

Feynmf/usr/bin/feynmf

This is feynmf: $Id: feynmf.pl,v 1.5 1996/12/02 01:38:45 ohl Exp $

Ffmpeg/usr/bin/ffmpeg

ffmpeg version 4.2.4-1ubuntu0.1 Copyright (c) 2000-2020 the FFmpeg developers
  built with gcc 9 (Ubuntu 9.3.0-10ubuntu2)
  configuration: --prefix=/usr --extra-version=1ubuntu0.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --enable-avresample --disable-filter=resample --enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-libpulse --enable-librsvg --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi --enable-lv2 --enable-omx --enable-openal --enable-opencl --enable-opengl --enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-nvenc --enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
  WARNING: library configuration mismatch
  avcodec     configuration: --prefix=/usr --extra-version=1ubuntu0.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --enable-avresample --disable-filter=resample --enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-libpulse --enable-librsvg --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi --enable-lv2 --enable-omx --enable-openal --enable-opencl --enable-opengl --enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-nvenc --enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared --enable-version3 --disable-doc --disable-programs --enable-libaribb24 --enable-liblensfun --enable-libopencore_amrnb --enable-libopencore_amrwb --enable-libtesseract --enable-libvo_amrwbenc
  libavutil      56. 31.100 / 56. 31.100
  libavcodec     58. 54.100 / 58. 54.100
  libavformat    58. 29.100 / 58. 29.100
  libavdevice    58.  8.100 / 58.  8.100
  libavfilter     7. 57.100 /  7. 57.100
  libavresample   4.  0.  0 /  4.  0.  0
  libswscale      5.  5.100 /  5.  5.100
  libswresample   3.  5.100 /  3.  5.100
  libpostproc    55.  5.100 / 55.  5.100
Unrecognized option '-version'.
Error splitting the argument list: Option not found

Firefox/usr/bin/firefox

Mozilla Firefox 81.0

Fish/usr/bin/fish

fish, version 3.1.0

Flex/usr/bin/flex

flex 2.6.4

Gap/ext/bin/gap

 ┌───────┐   GAP 4.11.0 of 29-Feb-2020
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv7
 Configuration:  gmp 6.2.0, GASMAN, readline
 Loading the library and packages ...

 Packages:   AClib 1.3.2, Alnuth 3.1.2, AtlasRep 2.1.0, AutoDoc 2019.09.04, 
             AutPGrp 1.10.2, Browse 1.8.8, CaratInterface 2.3.3, CRISP 1.4.5, 
             Cryst 4.1.23, CrystCat 1.1.9, CTblLib 1.2.2, FactInt 1.6.3, 
             FGA 1.4.0, Forms 1.2.5, GAPDoc 1.6.3, genss 1.6.6, IO 4.7.0, 
             IRREDSOL 1.4, LAGUNA 3.9.3, orb 4.8.3, Polenta 1.3.9, 
             Polycyclic 2.15.1, PrimGrp 3.4.0, RadiRoot 2.8, recog 1.3.2, 
             ResClasses 4.7.2, SmallGrp 1.4.1, Sophus 1.24, SpinSym 1.5.2, 
             TomLib 1.2.9, TransGrp 2.0.5, utils 0.69
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
gap> 

Gap-Sage/usr/local/bin/gap-sage

 ┌───────┐   GAP 4.10.2 of 19-Jun-2019
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv3
 Configuration:  gmp 6.2.0, readline
 Loading the library and packages ...
 Packages:   AClib 1.3.1, Alnuth 3.1.1, AtlasRep 2.1.0, AutoDoc 2019.05.20, 
             AutPGrp 1.10, CRISP 1.4.4, Cryst 4.1.19, CrystCat 1.1.9, 
             CTblLib 1.2.2, FactInt 1.6.2, FGA 1.4.0, GAPDoc 1.6.2, IO 4.6.0, 
             IRREDSOL 1.4, LAGUNA 3.9.3, Polenta 1.3.8, Polycyclic 2.14, 
             PrimGrp 3.3.2, RadiRoot 2.8, ResClasses 4.7.2, SmallGrp 1.3, 
             Sophus 1.24, TomLib 1.2.8, TransGrp 2.0.4, utils 0.63
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
gap> 

Gap3/ext/bin/gap3

             ########            Lehrstuhl D fuer Mathematik, RWTH Aachen
           ###    ####             #######            #########
          ##         ##           #      ##          ## #     ##
         ##          #           #       ##             #      ##
        ##           #           ##       #             #      ##
        ####        ##            #########             #######
         #####     ###  Version 3 Release 4.4 18 Apr 97 #
           ######### #                                  # Martin Schoenert
                    ##  Alice Niemeyer, Werner Nickel   # Erzsebet Horvath
                   ###  Bettina Eick,   Frank Celler,   # Udo Polis
                  ## #  Johannes Meier, Alex Wegner,    # Goetz Pfeiffer
                 ##  #  Juergen Mnich,  Thomas Breuer   # Heiko Theissen
                ##   #  Hans U. Besche, Volkmar Felsch  # Ansgar Kaup
               ##    #  Akos Seress,    Alexander Hulpke, Thomas Bischops
              ##    ##  
               ######   For help enter: ?<return>
 lib: 29 May 2017, src: 22 feb 2017, sys: linux gcc64
 for this GAP3 distribution see webusers.imj-prg.fr/~jmichel/gap3
--- Loading package arep -------- version 1.0 of 1998 Jul 22 ----------------
(C) Sebastian Egner, Markus Pueschel -- Abstract REPresentations
--- Loading package guava ------- version 1.3 -------------------------------
(C) Jasper Cramwinckel, Erik Roijackers, Reinald Baart, Eric Minkes
--- Loading package autag ------- version of 1997 Jan -----------------------
--- Loading package cryst ------- version of 1997 ---------------------------
--- Loading package dce --------- version of 1995 ---------------------------
--- Loading package gliss ------- version 1.0 of 1996 Sep 27 ----------------
(C) Christof Noebauer -- Glissando: small semigroups and near rings
--- Loading package grim -------- version 1.0 -------------------------------
(C) [email protected] -- Groups of Rational and Integer Matrices
--- Loading package matrix ------ version 1.0 -------------------------------
(C) Frank Celler, Derek Holt, Charles Leedham-Green, Alice Niemeyer
    Eamon O'Brien, Cheryl Praeger, Anthony Pye, Sarah Rees
--- Loading package monoid ------ version 2.2 -------------------------------
--- Loading package xmod -------- version 1.3.1 of 1997 Jan -----------------
(C) Chris Wensley, Murat Alp -- Crossed-modules, Cat1-groups
--- Loading package algebra ----- version of 2010 Oct -----------------------
(C) C'edric Bonnaf'e -- Finite dimensional algebras
--- Loading package specht ------ version 3.1 - unofficial (development) ----
    Decomposition numbers of Hecke algebras of type A and q-Schur algebras.
(C) Andrew Mathas  [email protected]     Sydney
--- Loading package chevie ------ version of 2017 Jun 30 --------------------
    If you use CHEVIE in your work please cite the authors as follows:
    [Jean Michel] The development version of the CHEVIE package of GAP3
     Journal of algebra 435 (2015) 308--336
    [Meinolf Geck, Gerhard Hiss, Frank Luebeck, Gunter Malle, Goetz Pfeiffer]
     CHEVIE -- a system for computing and processing generic character tables
     Applicable Algebra in Engineering Comm. and Computing 7 (1996) 175--210
--- Loading package vkcurve ----- version 1.2 of 2009 Mar -------------------
(C) David Bessis, Jean Michel -- compute Pi_1 of hypersurface complements
gap> 

Gcc/usr/bin/gcc

gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 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.

Geckodriver/usr/bin/geckodriver

geckodriver 0.27.0 (7b8c4f32cdde 2020-07-28 18:16 +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/.

Gfortran/usr/bin/gfortran

GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 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.

Ghc/opt/ghc/bin/ghc

The Glorious Glasgow Haskell Compilation System, version 8.10.2

Giac/ext/bin/giac

// Maximum number of parallel threads 8
// (c) 2001, 2018 B. Parisse & others
1.5.0

Git/usr/bin/git

git version 2.25.1

Git-Trac/usr/local/bin/git-trac

usage: git-trac [-h] [--debug] [--log LOG]
                {create,checkout,search,fetch,pull,push,get,depends,print,browse,review,find,try,log,config,cheat-sheet,help}
                ...

The trac command extension for git

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

optional arguments:
  -h                    show this help message and exit
  --debug               debug
  --log LOG             one of [DEBUG, INFO, ERROR, WARNING, CRITICAL]

Gnat/usr/bin/gnat

GNAT 9.3.0
Copyright (C) 1996-2019, 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.

Gnatmake/usr/bin/gnatmake

GNATMAKE 9.3.0
Copyright (C) 1995-2019, 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.

Google-Chrome/usr/bin/google-chrome

Google Chrome 86.0.4240.75 

Gp/usr/bin/gp

                                   GP/PARI CALCULATOR Version 2.11.2 (released)
                           amd64 running linux (x86-64/GMP-6.1.2 kernel) 64-bit version
                         compiled: Jul 12 2019, gcc version 9.1.0 (Ubuntu 9.1.0-8ubuntu1)
                                            threading engine: pthread
                                 (readline v8.0 disabled, extended help enabled)

Gradle/usr/bin/gradle

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/user/tmp/ -Xms64m

------------------------------------------------------------
Gradle 6.6.1
------------------------------------------------------------

Build time:   2020-08-25 16:29:12 UTC
Revision:     f2d1fb54a951d8b11d25748e4711bec8d128d7e3

Kotlin:       1.3.72
Groovy:       2.5.12
Ant:          Apache Ant(TM) version 1.10.8 compiled on May 10 2020
JVM:          11.0.8 (Ubuntu 11.0.8+10-post-Ubuntu-0ubuntu120.04)
OS:           Linux 5.3.0-1030-gcp amd64

Grass/usr/bin/grass

GRASS GIS 7.8.2

Geographic Resources Analysis Support System (GRASS) is Copyright,
1999-2019 by the GRASS Development Team, and licensed under terms of the
GNU General Public License (GPL) version >=2.
 
This GRASS GIS 7.8.2 release is coordinated and produced by
the GRASS Development Team with contributions from all over the world.

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

Grepcidr/usr/bin/grepcidr

grepcidr 2.0
Copyright (C) 2004 - 2014  Jem E. Berkes <[email protected]>

Gringo/usr/bin/gringo

gringo version 5.4.0
Address model: 64-bit

libgringo version 5.4.0
Configuration: with Python 3.8.2rc2, with Lua 5.3.3
License: The MIT License <https://opensource.org/licenses/MIT>

Gst/usr/bin/gst

GNU Smalltalk version 3.2.5
Copyright 2009 Free Software Foundation, Inc.
Written by Steve Byrne ([email protected]) and Paolo Bonzini ([email protected])

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

Using default kernel path: /usr/share/gnu-smalltalk/kernel
Using default image path: /usr/lib/gnu-smalltalk

Guile/usr/bin/guile

guile (GNU Guile) 2.2.7
Packaged by Debian (2.2.7-deb+1-4)
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.

Gyoto/usr/bin/gyoto

Gyoto 1.4.4
ABI compatibility version: 8
 Copyright (c) 2011-2019 Frédéric Vincent, Thibaut Paumard,
                         Odele Straub and Frédéric Lamy.
 GYOTO is distributed under the terms of the GPL v. 3 license.
 We request that use of Gyoto in scientific publications be  properly 
 acknowledged. Please cite:
  GYOTO: a new general relativistic ray-tracing code,
  F. H. Vincent, T. Paumard, E. Gourgoulhon & G. Perrin 2011,
  Classical and Quantum Gravity 28, 225011 (2011) [arXiv:1109.4769]

H5Dump/usr/bin/h5dump

h5dump: Version 1.10.4

H5Math/usr/bin/h5math

h5totxt 1.13.1 by Steven G. Johnson
Copyright (c) 1999-2017 Massachusetts Institute of Technology

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Haskell-Compiler/usr/bin/haskell-compiler

The Glorious Glasgow Haskell Compilation System, version 8.6.5

Head/usr/bin/head

mglconv convert mgl script to image file (default PNG).
Current version is 2.4.4

Heroku/usr/bin/heroku

 ›   Warning: Our terms of service have changed: 
 ›   https://dashboard.heroku.com/terms-of-service
heroku/7.45.0 linux-x64 node-v12.16.2

Hg/usr/bin/hg

Mercurial Distributed SCM (version 5.3.1)
(see https://mercurial-scm.org for more information)

Copyright (C) 2005-2020 Matt 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.

Htop/usr/bin/htop

htop 2.2.0 - (C) 2004-2019 Hisham Muhammad
Released under the GNU GPL.

Ijs/usr/bin/ijs

ijavascript 5.2.0
jmp 2.0.0
jp-kernel 2.0.0
nel 1.1.0
uuid 3.4.0
zeromq 5.2.0

Inkscape/usr/bin/inkscape

Inkscape 0.92.5 (2060ec1f9f, 2020-04-08)

Ipopt/ext/bin/ipopt

Ipopt 3.13.2 (Linux x86_64), ASL(20190605)

Ipython/ext/anaconda2020.02/bin/ipython

7.16.1

Ipython/usr/local/bin/ipython

7.18.1

Ipython2/usr/local/bin/ipython2

5.10.0

Ipython3/usr/local/bin/ipython3

7.18.1

Irssi/usr/bin/irssi

irssi 1.2.2-1ubuntu1.1 (20190829 0225)

Iverilog/usr/bin/iverilog

Icarus Verilog version 10.3 (stable) ()

Copyright 1998-2015 Stephen Williams

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

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

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

Icarus Verilog Preprocessor version 10.3 (stable) ()

Copyright (c) 1999-2011,2015 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 10.3 (stable) ()

Copyright (c) 1998-2017 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 10.3 (stable) ()

Copyright (c) 2001-2015 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.

Jags/usr/bin/jags

Welcome to JAGS 4.3.0 on Tue Oct 13 14:06:54 2020
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok

Java/usr/bin/java

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/user/tmp/ -Xms64m
openjdk version "11.0.8" 2020-07-14
OpenJDK Runtime Environment (build 11.0.8+10-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.8+10-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)

Javac/usr/bin/javac

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/user/tmp/ -Xms64m
javac 11.0.8

Julia/ext/bin/julia

julia version 1.5.2

Julia-1.5/ext/bin/julia-1.5

julia version 1.5.2

Jupyter/usr/local/bin/jupyter

6.0.7

Jupyter-Lab/usr/local/bin/jupyter-lab

2.2.8

Jupyter-Notebook/usr/local/bin/jupyter-notebook

6.1.4

Jupyterhub/usr/local/bin/jupyterhub

1.1.0

Jupytext/usr/local/bin/jupytext

usage: jupytext [-h] [--pre-commit] [--from INPUT_FORMAT] [--to OUTPUT_FORMAT]
                [-o OUTPUT] [--update] [--set-formats SET_FORMATS] [--sync]
                [--paired-paths] [--format-options FORMAT_OPTIONS]
                [--update-metadata UPDATE_METADATA] [--warn-only] [--test]
                [--test-strict] [--stop] [--pipe PIPE] [--check CHECK]
                [--pipe-fmt PIPE_FMT] [--set-kernel SET_KERNEL] [--execute]
                [--run-path RUN_PATH] [--quiet] [--version]
                [notebooks [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)

optional arguments:
  -h, --help            show this help message and exit
  --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)
  --from INPUT_FORMAT   Jupytext format for the input(s). Inferred from the
                        file extension and content when missing. (default:
                        None)
  --to OUTPUT_FORMAT    The destination format: 'ipynb', 'markdown' or
                        'script', or a file extension: 'md', 'Rmd', 'jl',
                        'py', 'R', ..., 'auto' (script extension matching the
                        notebook language), or a combination of an extension
                        and a format name, e.g. md:markdown, md:pandoc,
                        md:myst or py:hydrogen, py:percent, py:nomarker,
                        py:light, py:sphinx. The default format for scripts is
                        the 'light' format, which uses few cell markers (none
                        when possible). Alternatively, a format compatible
                        with many editors is the 'percent' format, which uses
                        '# %%' as cell markers. The main formats (markdown,
                        light, percent) preserve notebooks and text documents
                        in a roundtrip. Use the --test and and --test-strict
                        commands to test the roundtrip on your files. Read
                        more about the available formats at
                        https://jupytext.readthedocs.io/en/latest/formats.html
                        (default: None)
  -o OUTPUT, --output OUTPUT
                        Destination file. Defaults to the original file, with
                        prefix/suffix/extension changed according to the
                        destination format. Use '-' to print the notebook on
                        stdout. (default: None)
  --update              Preserve the output cells when the destination
                        notebook is an .ipynb file that already exists
                        (default: False)
  --set-formats SET_FORMATS
                        Turn the notebook or text document to one or more
                        alternative representations with e.g. '--set-formats
                        ipynb,py:light'. The --set-formats option also
                        triggers the creation/update of all paired files
                        (default: None)
  --sync, -s            Synchronize the content of the paired representations
                        of the given notebook. Input cells are taken from the
                        file that was last modified, and outputs are read from
                        the ipynb file, if present. (default: False)
  --paired-paths, -p    List the locations of the alternative representations
                        for this notebook. (default: False)
  --format-options FORMAT_OPTIONS, --opt FORMAT_OPTIONS
                        Set format options with e.g. '--opt
                        comment_magics=true' or '--opt
                        notebook_metadata_filter=-kernelspec'. (default: None)
  --update-metadata UPDATE_METADATA
                        Update the notebook metadata with the desired
                        dictionary. Argument must be given in JSON format. For
                        instance, if you want to activate a pairing in the
                        generated file, use e.g. --update-metadata
                        '{"jupytext":{"formats":"ipynb,py:light"}}' See also
                        the --opt and --set-formats options for other ways to
                        operate on the Jupytext metadata. (default: {})
  --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)
  --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 (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)
  --version, -v         Show jupytext's version number and exit (default:
                        False)

Latex/usr/bin/latex

pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian)
kpathsea version 6.3.1
Copyright 2019 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.37; using libpng 1.6.37
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 4.01

Latexmk/usr/bin/latexmk

Latexmk, John Collins, 26 Dec. 2019. Version 4.67

Lean/ext/bin/lean

Lean (version 3.11.0, commit fb3f3e88be8a, Release)

Libreoffice/usr/bin/libreoffice

LibreOffice 6.4.6.2 40(Build:2)

Lilypond/usr/bin/lilypond

GNU LilyPond 2.20.0

Copyright (c) 1996--2015 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.

Lneato/usr/bin/lneato

lneato version 95 (04-18-95)
Error: Can't open display: :0

Lrzip/usr/bin/lrzip

lrzip version 0.631

Lua/usr/bin/lua

Lua 5.2.4  Copyright (C) 1994-2015 Lua.org, PUC-Rio

Luatex/usr/bin/luatex

This is LuaTeX, Version 1.10.0 (TeX Live 2019/Debian)

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

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

LuaTeX is Copyright 2019 Taco Hoekwater and the LuaTeX Team.

Lzma/usr/bin/lzma

xz (XZ Utils) 5.2.4
liblzma 5.2.4

M2/usr/bin/M2

1.16

M4/usr/bin/m4

m4 (GNU M4) 1.4.18
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Rene' Seindal.

Make/usr/bin/make

GNU Make 4.2.1
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Markdown/usr/bin/markdown

This is Markdown, version 1.0.1.
Copyright 2004 John Gruber
http://daringfireball.net/projects/markdown/

Maxima/usr/bin/maxima

Maxima 5.43.2

Maxima-Sage/usr/local/bin/maxima-sage

;;; Loading #P"/ext/sage/sage-9.1/local/lib/ecl/sb-bsd-sockets.fas"
;;; Loading #P"/ext/sage/sage-9.1/local/lib/ecl/sockets.fas"
;;; Loading #P"/ext/sage/sage-9.1/local/lib/ecl/defsystem.fas"
;;; Loading #P"/ext/sage/sage-9.1/local/lib/ecl/cmp.fas"
Maxima 5.42.2

Mc/usr/bin/mc

GNU Midnight Commander 4.8.24
Built with GLib 2.63.3
Using the S-Lang library with terminfo database
With builtin Editor and Aspell support
With subshell support as default
With support for background operations
With mouse support on xterm and Linux console
With support for X11 events
With internationalization support
With multiple codepages support
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;

Meson/usr/local/bin/meson

0.55.0

Mongo/usr/bin/mongo

MongoDB shell version v4.2.10
git version: 88276238fa97b47c0ef14362b343c5317ecbd739
OpenSSL version: OpenSSL 1.1.1f  31 Mar 2020
allocator: tcmalloc
modules: none
build environment:
    distmod: ubuntu1804
    distarch: x86_64
    target_arch: x86_64

Mongod/usr/bin/mongod

db version v4.2.10
git version: 88276238fa97b47c0ef14362b343c5317ecbd739
OpenSSL version: OpenSSL 1.1.1f  31 Mar 2020
allocator: tcmalloc
modules: none
build environment:
    distmod: ubuntu1804
    distarch: x86_64
    target_arch: x86_64

Mono/usr/bin/mono

Mono JIT compiler version 6.8.0.105 (Debian 6.8.0.105+dfsg-2 Wed Feb 26 23:23:50 UTC 2020)
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)

Mpiexec/usr/bin/mpiexec

HYDRA build details:
    Version:                                 3.3.2
    Release Date:                            Tue Nov 12 21:23:16 CST 2019
    CC:                              gcc   -Wl,-Bsymbolic-functions -Wl,-z,relro 
    CXX:                             g++   -Wl,-Bsymbolic-functions -Wl,-z,relro 
    F77:                             f77  -Wl,-Bsymbolic-functions -Wl,-z,relro 
    F90:                             f95  -Wl,-Bsymbolic-functions -Wl,-z,relro 
    Configure options:                       '--disable-option-checking' '--prefix=/usr' '--build=x86_64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-libfabric' '--enable-shared' '--enable-fortran=all' '--disable-rpath' '--disable-wrapper-rpath' '--sysconfdir=/etc/mpich' '--libdir=/usr/lib/x86_64-linux-gnu' '--includedir=/usr/include/x86_64-linux-gnu/mpich' '--docdir=/usr/share/doc/mpich' 'CPPFLAGS= -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/mpich-VeuB8Z/mpich-3.3.2/src/mpl/include -I/build/mpich-VeuB8Z/mpich-3.3.2/src/mpl/include -I/build/mpich-VeuB8Z/mpich-3.3.2/src/openpa/src -I/build/mpich-VeuB8Z/mpich-3.3.2/src/openpa/src -D_REENTRANT -I/build/mpich-VeuB8Z/mpich-3.3.2/src/mpi/romio/include' 'CFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -O2' 'CXXFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -O2' 'FFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -O2' 'FCFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -cpp -O2' 'BASH_SHELL=/bin/bash' 'build_alias=x86_64-linux-gnu' 'MPICHLIB_CFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security' 'MPICHLIB_CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'MPICHLIB_CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security' 'MPICHLIB_FFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong' 'MPICHLIB_FCFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-VeuB8Z/mpich-3.3.2=. -fstack-protector-strong -cpp' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'FC=f95' 'F77=f77' 'MPILIBNAME=mpich' '--cache-file=/dev/null' '--srcdir=.' 'CC=gcc' 'LIBS=' 'MPLLIBNAME=mpl'
    Process Manager:                         pmi
    Launchers available:                     ssh rsh fork slurm ll lsf sge manual persist
    Topology libraries available:            hwloc
    Resource management kernels available:   user slurm ll lsf sge pbs cobalt
    Checkpointing libraries available:       
    Demux engines available:                 poll select

Nano/usr/bin/nano

 GNU nano, version 4.8
 (C) 1999-2011, 2013-2020 Free Software Foundation, Inc.
 (C) 2014-2020 the contributors to nano
 Email: [email protected]	Web: https://nano-editor.org/
 Compiled options: --disable-libmagic --enable-utf8

Nbgrader/usr/local/bin/nbgrader

Python version 3.8.5 (default, Jul 28 2020, 12:59:40) 
[GCC 9.3.0]
nbgrader version 0.6.1

Nettle-Hash/usr/bin/nettle-hash

nettle-hash (nettle 3.5.1)

Nim/usr/bin/nim

Nim Compiler Version 1.0.6 [Linux: amd64]
Compiled at 2020-02-27
Copyright (c) 2006-2019 by Andreas Rumpf

active boot switches: -d:release

Ninja/usr/bin/ninja

1.10.0

Node/usr/bin/node

v12.19.0

Nosetests3/usr/bin/nosetests3

nosetests3 version 1.3.7

Notedown/usr/local/bin/notedown

1.5.1

Npm/usr/bin/npm

6.14.8

Nvim/usr/bin/nvim

NVIM v0.4.3
Build type: Release
LuaJIT 2.1.0-beta3
Compilation: /usr/bin/cc -g -O2 -fdebug-prefix-map=/build/neovim-gOb7vg/neovim-0.4.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=1 -DDISABLE_LOG -Wdate-time -D_FORTIFY_SOURCE=1 -O2 -DNDEBUG -DMIN_LOG_LEVEL=3 -Wall -Wextra -pedantic -Wno-unused-parameter -Wstrict-prototypes -std=gnu99 -Wshadow -Wconversion -Wmissing-prototypes -Wimplicit-fallthrough -Wvla -fstack-protector-strong -fdiagnostics-color=always -DINCLUDE_GENERATED_DECLARATIONS -D_GNU_SOURCE -DNVIM_MSGPACK_HAS_FLOAT32 -DNVIM_UNIBI_HAS_VAR_FROM -I/build/neovim-gOb7vg/neovim-0.4.3/build/config -I/build/neovim-gOb7vg/neovim-0.4.3/src -I/usr/include -I/usr/include/lua5.1 -I/build/neovim-gOb7vg/neovim-0.4.3/build/src/nvim/auto -I/build/neovim-gOb7vg/neovim-0.4.3/build/include
Compiled by [email protected]

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

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

Run :checkhealth for more info

Ocaml/usr/bin/ocaml

The OCaml toplevel, version 4.08.1

Octave/usr/local/bin/octave

GNU Octave, version 5.2.0
Copyright (C) 2020 John W. Eaton and others.
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.

Octave-Cli/usr/local/bin/octave-cli

GNU Octave, version 5.2.0
Copyright (C) 2020 John W. Eaton and others.
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.

Oligotm/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 0mM

-n  dNTP_conc       - concentration of deoxynycleotide triphosphate in mM, by default 0mM

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

-tp [0|1]     - Specifies the table of thermodynamic parameters and
                the method of melting temperature calculation:
                 0  Breslauer et al., 1986 and Rychlik et al., 1990
                    (used by primer3 up to and including release 1.1.0).
                    This is the default, but _not_ the recommended value.
                 1  Use nearest neighbor parameters from SantaLucia 1998
                    *THIS IS THE 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.
                     This is the default but _not_ the recommended value.
                  1  SantaLucia 1998
                     *THIS IS THE RECOMMENDED VAULE*
                  2  Owczarzy et al., 2004



Prints oligo's melting temperature on stdout.

Opam/usr/bin/opam

2.0.5

Openscad/usr/bin/openscad

OpenSCAD version 2019.05

Pandoc/usr/bin/pandoc

pandoc 2.10.1
Compiled with pandoc-types 1.21, texmath 0.12.0.2, skylighting 0.8.5
Default user data directory: /home/user/.local/share/pandoc or /home/user/.pandoc
Copyright (C) 2006-2020 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.

Pdflatex/usr/bin/pdflatex

pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian)
kpathsea version 6.3.1
Copyright 2019 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.37; using libpng 1.6.37
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 4.01

Pdftotext/usr/bin/pdftotext

pdftotext version 0.86.1
Copyright 2005-2020 The Poppler Developers - http://poppler.freedesktop.org
Copyright 1996-2011 Glyph & Cog, LLC

Perl/usr/bin/perl

This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi
(with 46 registered patches, see perl -V for more detail)

Copyright 1987-2019, Larry Wall

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

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

Php/usr/bin/php

PHP 7.4.3 (cli) (built: May 26 2020 12:24:22) ( NTS )
Copyright (c) The PHP Group
Zend Engine v3.4.0, Copyright (c) Zend Technologies
    with Zend OPcache v7.4.3, Copyright (c), by Zend Technologies

Phylip/ext/bin/phylip

Starting main
running main
['/ext/bin/phylip', 'test']
/ext/anaconda2020.02/share/phylip-3.697-0/exe
testing dnapars...
passed; cleaning up
testing dnaml...
passed; cleaning up
testing dnadist...
passed; cleaning up
testing dnapenny...
passed; cleaning up
testing dnacomp...
passed; cleaning up
testing dnamlk...
passed; cleaning up
testing protpars...
passed; cleaning up
testing protdist...
passed; cleaning up
testing proml...
passed; cleaning up
testing promlk...
passed; cleaning up
testing pars...
passed; cleaning up
testing penny...
passed; cleaning up
testing dollop...
passed; cleaning up
testing dolpenny...
passed; cleaning up
testing clique...
passed; cleaning up
testing mix...
passed; cleaning up
testing restml...
passed; cleaning up
testing restdist...
passed; cleaning up
testing fitch...
passed; cleaning up
testing kitsch...
passed; cleaning up
testing neighbor...
passed; cleaning up
testing drawtree...
passed; cleaning up
testing drawgram...
passed; cleaning up

Pip/usr/local/bin/pip

pip 20.2.3 from /usr/local/lib/python3.8/dist-packages/pip (python 3.8)

Pip-Upgrade/usr/local/bin/pip-upgrade

1.4.15

Pip2/usr/local/bin/pip2

pip 20.2 from /usr/local/lib/python2.7/dist-packages/pip (python 2.7)

Pip3/usr/local/bin/pip3

pip 20.2.3 from /usr/local/lib/python3.8/dist-packages/pip (python 3.8)

Pipenv/usr/local/bin/pipenv

pipenv, version 2020.8.13

Plink/ext/bin/plink

@[email protected]
|        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/        |
@[email protected]

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Tue Oct 13 14:07:53 2020

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

Pm2/usr/bin/pm2

pm2 launched in no-daemon mode (you can add DEBUG="*" env variable to get more messages)
2020-10-13T14:07:54: PM2 log: Launching in no daemon mode
4.4.1

Polymake/usr/bin/polymake

polymake version 4.0
Copyright (c) 1997-2020
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.

Postgres/usr/lib/postgresql/10/bin/postgres

postgres (PostgreSQL) 10.14 (Ubuntu 10.14-1.pgdg20.04+1)

Prettier/home/user/cocalc/src/node_modules/.bin/prettier

2.1.1

Primer3_Core/usr/bin/primer3_core

Copyright (c) 1996-2017
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 2.4.0)
Input can also be provided on standard input.
For example:
$ primer3_core < my_input_file

Primesieve/usr/bin/primesieve

primesieve 7.5, <https://github.com/kimwalisch/primesieve>
Copyright (C) 2010 - 2019 Kim Walisch
BSD 2-Clause License <https://opensource.org/licenses/BSD-2-Clause>

Prolog/usr/bin/prolog

SWI-Prolog version 7.6.4 for amd64

Py.Test/usr/local/bin/py.test

pytest 6.0.1

Pyls/usr/local/bin/pyls

usage: pyls [-h] [--tcp] [--host HOST] [--port PORT] [--check-parent-process]
            [--log-config LOG_CONFIG | --log-file LOG_FILE] [-v]

Python Language Server

optional arguments:
  -h, --help            show this help message and exit
  --tcp                 Use TCP server instead of stdio
  --host HOST           Bind to this address
  --port PORT           Bind to this port
  --check-parent-process
                        Check whether parent process is still alive using
                        os.kill(ppid, 0) and auto shut down language server
                        process when parent process is not alive.Note that
                        this may not work on a Windows machine.
  --log-config LOG_CONFIG
                        Path to a JSON file containing Python logging config.
  --log-file LOG_FILE   Redirect logs to the given file instead of writing to
                        stderr.Has no effect if used with --log-config.
  -v, --verbose         Increase verbosity of log output, overrides log config
                        file

Pypy3/usr/bin/pypy3

Python 3.6.9 (7.3.2+dfsg-2~ppa1~ubuntu20.04, Sep 26 2020, 22:37:47)
[PyPy 7.3.2 with GCC 9.3.0]

Pytest/usr/local/bin/pytest

pytest 6.0.1

Python/ext/anaconda2020.02/bin/python

Python 3.7.8

Python2/usr/bin/python2

Python 2.7.18

Python3/usr/bin/python3

Python 3.8.5

Pythontex/usr/bin/pythontex

PythonTeX 0.17

Pythontex3/usr/bin/pythontex3

PythonTeX 0.17

Qgis/usr/bin/qgis

QGIS 3.14.16-Pi 'Pi' (a235a149f0)

R/usr/bin/R

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

R-Sage/usr/local/bin/R-sage

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

Racket/usr/bin/racket

Welcome to Racket v7.7.

Rclone/usr/bin/rclone

rclone v1.52.2
- os/arch: linux/amd64
- go version: go1.14.4

Reveal-Md/usr/bin/reveal-md

4.1.6

Ros/usr/bin/ros

roswell 20.06.14.107(NO-GIT-REVISION)

Rscript/usr/bin/Rscript

R scripting front-end version 4.0.3 (2020-10-10)

Rstudio/ext/bin/rstudio

RStudio is a trademarks of RStudio, Inc.

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

Launching RStudio...
1.3.1056

Rsync/usr/bin/rsync

rsync  version 3.1.3  protocol version 31
Copyright (C) 1996-2018 by Andrew Tridgell, Wayne Davison, and others.
Web site: http://rsync.samba.org/
Capabilities:
    64-bit files, 64-bit inums, 64-bit timestamps, 64-bit long ints,
    socketpairs, hardlinks, symlinks, IPv6, batchfiles, inplace,
    append, ACLs, xattrs, iconv, symtimes, prealloc

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.

Ruby/usr/bin/ruby

ruby 2.7.0p0 (2019-12-25 revision 647ee6f091) [x86_64-linux-gnu]

Run-One/usr/bin/run-one

Rustc/ext/bin/rustc

rustc 1.47.0 (18bf6b4f0 2020-10-07)

Rustfmt/ext/bin/rustfmt

rustfmt 1.4.20-stable (48f6c32 2020-08-09)

Rustup/ext/bin/rustup

rustup 1.22.1 (b01adbbc3 2020-07-08)

Sage/ext/bin/sage

SageMath version 9.1, Release Date: 2020-05-20

Sage-9.1/ext/bin/sage-9.1

SageMath version 9.1, Release Date: 2020-05-20

Samtools/ext/bin/samtools

samtools 1.10
Using htslib 1.10.2
Copyright (C) 2019 Genome Research Ltd.

Sass/usr/bin/sass

Ruby Sass 3.7.4

Sbcl/usr/bin/sbcl

SBCL 2.0.1.debian

Scala/usr/bin/scala

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/user/tmp/ -Xms64m
Welcome to Scala 2.11.12 (OpenJDK 64-Bit Server VM, Java 11.0.8).
Type in expressions for evaluation. Or try :help.

scala> :quit

Scheme/usr/bin/scheme

MIT/GNU Scheme microcode 15.3
Copyright (C) 2019 Massachusetts Institute of Technology
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Image saved on Thursday September 5, 2019 at 11:51:46 AM
  Release 10.1.10   || Microcode 15.3 || Runtime 15.7 || SF 4.41
  LIAR/x86-64 4.118
..#]^@^@^@ NO CARRIER

Scons/usr/bin/scons

SCons by Steven Knight et al.:
	script: v3.1.2.bee7caf9defd6e108fc2998a2520ddb36a967691, 2019-12-17 02:07:09, by bdeegan on octodog
	engine: v3.1.2.bee7caf9defd6e108fc2998a2520ddb36a967691, 2019-12-17 02:07:09, by bdeegan on octodog
	engine path: ['/usr/lib/scons/SCons']
Copyright (c) 2001 - 2019 The SCons Foundation

Sed/usr/bin/sed

sed (GNU sed) 4.7
Packaged by Debian
Copyright (C) 2018 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.
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]>.

Sha1Sum/usr/bin/sha1sum

sha1sum (GNU coreutils) 8.30
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Ulrich Drepper, Scott Miller, and David Madore.

Sha256Sum/usr/bin/sha256sum

sha256sum (GNU coreutils) 8.30
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Ulrich Drepper, Scott Miller, and David Madore.

Singular/usr/bin/Singular

Singular for x86_64-Linux version 4.1.1 (4112, 64 bit) Mar 24 2020 14:10:46 #debian-1:4.1.1-p2+ds-4build2
with
	GMP(6.2.0),NTL(11.4.3),FLINT(2.5.2),factory(4.1.0),
	omalloc,static readline(8),Plural,DBM,
	dynamic modules,dynamic p_Procs,OM_NDEBUG,SING_NDEBUG,
	CC:OPTIMIZE,GenericAdd,GenericMult,no invTable,
	eigenvalues,Gauss-Manin system,random=1602597922
built-in modules: {}
AC_CONFIGURE_ARGS =  '--build=x86_64-linux-gnu' '--prefix=/usr' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--libexecdir=${prefix}/lib/x86_64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=x86_64-linux-gnu' 'CFLAGS=-g -O2 -fdebug-prefix-map=/build/singular-hTIl2W/singular-4.1.1-p2+ds=. -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/singular-hTIl2W/singular-4.1.1-p2+ds=. -fstack-protector-strong -Wformat -Werror=format-security' --enable-omalloc  OMALLOC_LIBS='/build/singular-hTIl2W/singular-4.1.1-p2+ds/omalloc/libsingular-omalloc.la' OMALLOC_INCLUDES='-I/build/singular-hTIl2W/singular-4.1.1-p2+ds' --with-Singular RESOURCES_LIBS='/build/singular-hTIl2W/singular-4.1.1-p2+ds/resources/libsingular-resources.la' RESOURCES_INCLUDES='-I/build/singular-hTIl2W/singular-4.1.1-p2+ds ' FACTORY_LIBS='/build/singular-hTIl2W/singular-4.1.1-p2+ds/factory/libsingular-factory.la' FACTORY_INCLUDES='-I/build/singular-hTIl2W/singular-4.1.1-p2+ds -I/build/singular-hTIl2W/singular-4.1.1-p2+ds/factory/include',
CC = gcc,FLAGS : -g -O2 -fdebug-prefix-map=/build/singular-hTIl2W/singular-4.1.1-p2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -fno-common -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -fno-delete-null-pointer-checks -pthread,
CXX = g++,FLAGS : -g -O2 -fdebug-prefix-map=/build/singular-hTIl2W/singular-4.1.1-p2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -fno-common -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -fno-delete-null-pointer-checks -fno-rtti,
DEFS : ,CPPFLAGS : -Wdate-time -D_FORTIFY_SOURCE=2,
LDFLAGS : -Wl,-Bsymbolic-functions -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 -fno-delete-null-pointer-checks  -rdynamic -Wl,-undefined,dynamic_lookup,LIBS : -lreadline -lncurses -lmpfr -lrt -lpthread  (ver: 9.3.0)
argv[0]   :	Singular
SearchPath:	/usr/bin/../share/singular/LIB:/usr/bin/../share/singular/factory:/usr/lib/x86_64-linux-gnu/singular/MOD:/usr/bin
Singular  :	/usr/bin/Singular
BinDir    :	/usr/bin
ProcDir   :	/usr/lib/x86_64-linux-gnu/singular/MOD
RootDir   :	/usr/bin/..
DataDir   :	/usr/bin/../share
DefaultDir:	/usr
InfoFile  :	
IdxFile   :	
HtmlDir   :	
ManualUrl :	http://www.singular.uni-kl.de/Manual/
ExDir     :	
Path      :	/usr/bin:/usr/lib/x86_64-linux-gnu/singular/MOD:/home/user/cocalc/src:/home/user/cocalc/src/smc-hub/scripts:/home/user/cocalc/src/scripts/storage:/home/user/cocalc/src/scripts/gce:/home/user/cocalc/src/scripts/hub:/home/user/cocalc/src/node_modules/.bin:/home/user/cocalc/src/scripts:/home/user/bin:/home/user/.local/bin:/cocalc/bin:/cocalc/src/smc-project/bin:/ext/bin:/usr/lib/xpra:/opt/ghc/bin:/usr/local/bin:/bin:/ext/data/homer/bin:/ext/data/weblogo:/usr/lib/postgresql/10/bin:/home/user/.gem/ruby/2.3.0/bin
emacs     :	/usr/bin/emacs
xemacs    :	
SingularEmacs:	/usr/bin/Singular
EmacsLoad :	
EmacsDir  :	
SingularXterm:	/usr/bin/Singular
xterm     :	/usr/bin/xterm
EmacsDir  :	
Available HelpBrowsers: firefox-www, lynx-www, dummy, emacs, 
Current HelpBrowser: firefox-www 
                     SINGULAR                                 /  Development
 A Computer Algebra System for Polynomial Computations       /   version 4.1.1
                                                           0<
 by: W. Decker, G.-M. Greuel, G. Pfister, H. Schoenemann     \   Feb 2018
FB Mathematik der Universitaet, D-67653 Kaiserslautern        \  Debian 1:4.1.1-p2+ds-4build2
// ** Can not open /dev/null
Auf Wiedersehen.

Singular-Sage/usr/local/bin/Singular-sage

Singular for x86_64-Linux version 4.1.1 (4112, 64 bit) Jun  1 2020 15:00:48 #UNKNOWN_GIT_VERSION
with
	GMP(6.2.0),NTL(11.4.3),FLINT(2.5.2),factory(4.1.0),
	omalloc,static readline(8),Plural,DBM,
	dynamic modules,dynamic p_Procs,OM_NDEBUG,SING_NDEBUG,
	CC:OPTIMIZE,GenericAdd,GenericMult,no invTable,
	eigenvalues,Gauss-Manin system,random=1602597922
built-in modules: {}
AC_CONFIGURE_ARGS =  '--prefix=/ext/sage/sage-9.1/local' '--libdir=/ext/sage/sage-9.1/local/lib' '--disable-maintainer-mode' '--disable-dependency-tracking' '--exec-prefix=/ext/sage/sage-9.1/local' '--bindir=/ext/sage/sage-9.1/local/bin' '--with-ntl=/ext/sage/sage-9.1/local' '--with-flint=/ext/sage/sage-9.1/local' '--enable-gfanlib' '--enable-Singular' '--enable-factory' '--disable-doc' '--disable-polymake' '--with-python=sage-python23' 'CC=gcc' 'CFLAGS=-O2 -g ' 'LDFLAGS=-Wl,-rpath-link,/ext/sage/sage-9.1/local/lib -L/ext/sage/sage-9.1/local/lib -Wl,-rpath,/ext/sage/sage-9.1/local/lib ' 'CXX=g++ -std=gnu++11' 'CXXFLAGS=-O2 -g ' --enable-omalloc  OMALLOC_LIBS='/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src/omalloc/libomalloc.la' OMALLOC_INCLUDES='-I/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src' --with-Singular RESOURCES_LIBS='/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src/resources/libsingular_resources.la' RESOURCES_INCLUDES='-I/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src ' FACTORY_LIBS='/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src/factory/libfactory.la' FACTORY_INCLUDES='-I/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src -I/ext/sage/sage-9.1/local/var/tmp/sage/build/singular-4.1.1p2.p0/src/factory/include',
CC = gcc,FLAGS : -O2 -g  -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 -fno-delete-null-pointer-checks -pthread,
CXX = g++ -std=gnu++11,FLAGS : -O2 -g  -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-delete-null-pointer-checks -fno-rtti,
DEFS : ,CPPFLAGS : ,
LDFLAGS : -Wl,-rpath-link,/ext/sage/sage-9.1/local/lib -L/ext/sage/sage-9.1/local/lib -Wl,-rpath,/ext/sage/sage-9.1/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 -fno-delete-null-pointer-checks  -rdynamic -Wl,-undefined,dynamic_lookup,LIBS : -lreadline -lncurses -lmpfr -lrt -lpthread  (ver: 9.3.0)
argv[0]   :	Singular
SearchPath:	/ext/sage/sage-9.1/local/share/singular:/ext/sage/sage-9.1/local/bin/../share/singular/LIB:/ext/sage/sage-9.1/local/bin/../share/factory:/ext/sage/sage-9.1/local/bin/../libexec/singular/MOD:/ext/sage/sage-9.1/local/libexec/singular/MOD:/ext/sage/sage-9.1/local/bin
Singular  :	/ext/sage/sage-9.1/local/bin/Singular
BinDir    :	/ext/sage/sage-9.1/local/bin
ProcDir   :	/ext/sage/sage-9.1/local/bin/../libexec/singular/MOD:/ext/sage/sage-9.1/local/libexec/singular/MOD
RootDir   :	/ext/sage/sage-9.1/local/bin/..
DataDir   :	/ext/sage/sage-9.1/local/bin/../share
DefaultDir:	/ext/sage/sage-9.1/local
InfoFile  :	/ext/sage/sage-9.1/local/bin/../share/info/singular.hlp
IdxFile   :	
HtmlDir   :	/ext/sage/sage-9.1/local/bin/../share/singular/html
ManualUrl :	http://www.singular.uni-kl.de/Manual/
ExDir     :	/ext/sage/sage-9.1/local/bin/../examples
Path      :	/ext/sage/sage-9.1/local/bin:/ext/sage/sage-9.1/local/bin/../libexec/singular/MOD:/ext/sage/sage-9.1/local/libexec/singular/MOD:/ext/sage/sage-9.1/build/bin:/ext/sage/sage-9.1/src/bin:/home/user/cocalc/src:/home/user/cocalc/src/smc-hub/scripts:/home/user/cocalc/src/scripts/storage:/home/user/cocalc/src/scripts/gce:/home/user/cocalc/src/scripts/hub:/home/user/cocalc/src/node_modules/.bin:/home/user/cocalc/src/scripts:/home/user/bin:/home/user/.local/bin:/cocalc/bin:/cocalc/src/smc-project/bin:/ext/bin:/usr/lib/xpra:/opt/ghc/bin:/usr/local/bin:/usr/bin:/bin:/ext/data/homer/bin:/ext/data/weblogo:/usr/lib/postgresql/10/bin:/home/user/.gem/ruby/2.3.0/bin
emacs     :	/usr/bin/emacs-gtk
xemacs    :	
SingularEmacs:	/ext/sage/sage-9.1/local/bin/Singular
EmacsLoad :	/ext/sage/sage-9.1/local/bin/../share/singular/emacs/.emacs-singular
EmacsDir  :	/ext/sage/sage-9.1/local/bin/../share/singular/emacs
SingularXterm:	/ext/sage/sage-9.1/local/bin/Singular
xterm     :	/usr/bin/xterm
EmacsDir  :	/ext/sage/sage-9.1/local/bin/../share/singular/emacs
Available HelpBrowsers: firefox-www, lynx-www, builtin, dummy, emacs, 
Current HelpBrowser: firefox-www 
                     SINGULAR                                 /  Development
 A Computer Algebra System for Polynomial Computations       /   version 4.1.1
                                                           0<
 by: W. Decker, G.-M. Greuel, G. Pfister, H. Schoenemann     \   Feb 2018
FB Mathematik der Universitaet, D-67653 Kaiserslautern        \
// ** Can not open /dev/null
Auf Wiedersehen.

Sml/usr/bin/sml

sml 110.79

Sqlite/usr/bin/sqlite

2.8.17

Sqlite3/usr/bin/sqlite3

3.31.1 2020-01-27 19:55:54 3bfa9cc97da10598521b342961df8f5f68c7388fa117345eeb516eaa837balt1

Sqlline/usr/bin/sqlline

[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: -Djava.io.tmpdir=/home/user/tmp/ -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

Ssh/usr/bin/ssh

OpenSSH_8.2p1 Ubuntu-4ubuntu0.1, OpenSSL 1.1.1f  31 Mar 2020

Stack/usr/local/bin/stack

Version 2.3.1, Git revision de2a7b694f07de7e6cf17f8c92338c16286b2878 (8103 commits) x86_64 hpack-0.33.0

Stapler/usr/local/bin/stapler

usage: usage: stapler [options] mode (input.pdf|input handle) ... [output.pdf]

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

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

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

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

positional arguments:
  mode                  requested stapler mode

optional arguments:
  -h, --help            show this help message and exit
  -o OWNERPW, --ownerpw OWNERPW
                        Set owner password to encrypt output file with
  -u USERPW, --userpw USERPW
                        Set user password to encrypt output file with
  -v, --verbose
  -f, --force           Overwrite output file if it exists
  -d DESTDIR, --destdir DESTDIR
                        directory where to store output file

Sumo/usr/bin/sumo

Eclipse SUMO sumo Version 1.7.0
 Build features: Linux-4.15.0-117-generic x86_64 GNU 9.3.0 Release Proj GUI SWIG GDAL GL2PS
 Copyright (C) 2001-2020 German Aerospace Center (DLR) and others; https://sumo.dlr.de

Eclipse SUMO sumo Version 1.7.0 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
SPDX-License-Identifier: EPL-2.0

Symphony/usr/bin/symphony

==  Welcome to the SYMPHONY MILP Solver 
==  Copyright 2000-2015 Ted Ralphs and others 
==  All Rights Reserved. 
==  Distributed under the Eclipse Public License 1.0 
==  Version: 5.6.16 
==  Build Date: Mar 24 2020 

Synctex/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.

T1Asm/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.

Tidy/usr/bin/tidy

HTML Tidy for Linux version 5.6.0

Tmux/usr/bin/tmux

tmux 3.0a

Tmuxp/usr/local/bin/tmuxp

tmuxp 1.5.4

Tsc/home/user/cocalc/src/node_modules/.bin/tsc

Version 4.0.2

Vim/usr/bin/vim

VIM - Vi IMproved 8.1 (2018 May 18, compiled Apr 15 2020 06:40:31)
Included patches: 1-2269
Modified by [email protected]
Compiled by [email protected]
Huge version with GTK3 GUI.  Features included (+) or not (-):
+acl               -farsi             -mouse_sysmouse    -tag_any_white
+arabic            +file_in_path      +mouse_urxvt       +tcl
+autocmd           +find_in_path      +mouse_xterm       +termguicolors
+autochdir         +float             +multi_byte        +terminal
-autoservername    +folding           +multi_lang        +terminfo
+balloon_eval      -footer            -mzscheme          +termresponse
+balloon_eval_term +fork()            +netbeans_intg     +textobjects
+browse            +gettext           +num64             +textprop
++builtin_terms    -hangul_input      +packages          +timers
+byte_offset       +iconv             +path_extra        +title
+channel           +insert_expand     +perl              +toolbar
+cindent           +job               +persistent_undo   +user_commands
+clientserver      +jumplist          +postscript        +vartabs
+clipboard         +keymap            +printer           +vertsplit
+cmdline_compl     +lambda            +profile           +virtualedit
+cmdline_hist      +langmap           -python            +visual
+cmdline_info      +libcall           +python3           +visualextra
+comments          +linebreak         +quickfix          +viminfo
+conceal           +lispindent        +reltime           +vreplace
+cryptv            +listcmds          +rightleft         +wildignore
+cscope            +localmap          -ruby              +wildmenu
+cursorbind        +lua               +scrollbind        +windows
+cursorshape       +menu              +signs             +writebackup
+dialog_con_gui    +mksession         +smartindent       +X11
+diff              +modify_fname      +sound             -xfontset
+digraphs          +mouse             +spell             +xim
+dnd               +mouseshape        +startuptime       +xpm
-ebcdic            +mouse_dec         +statusline        +xsmp_interact
+emacs_tags        +mouse_gpm         -sun_workshop      +xterm_clipboard
+eval              -mouse_jsbterm     +syntax            -xterm_save
+ex_extra          +mouse_netterm     +tag_binary        
+extra_search      +mouse_sgr         -tag_old_static    
   system vimrc file: "$VIM/vimrc"
     user vimrc file: "$HOME/.vimrc"
 2nd user vimrc file: "~/.vim/vimrc"
      user exrc file: "$HOME/.exrc"
  system gvimrc file: "$VIM/gvimrc"
    user gvimrc file: "$HOME/.gvimrc"
2nd user gvimrc file: "~/.vim/gvimrc"
       defaults file: "$VIMRUNTIME/defaults.vim"
    system menu file: "$VIMRUNTIME/menu.vim"
  fall-back for $VIM: "/usr/share/vim"
Compilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -DFEAT_GUI_GTK  -pthread -I/usr/include/gtk-3.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib/x86_64-linux-gnu/dbus-1.0/include -I/usr/include/gtk-3.0 -I/usr/include/gio-unix-2.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Wdate-time  -g -O2 -fdebug-prefix-map=/build/vim-iU6mZD/vim-8.1.2269=. -fstack-protector-strong -Wformat -Werror=format-security -D_REENTRANT -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1       
Linking: gcc   -Wl,-E  -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vim   -lgtk-3 -lgdk-3 -lpangocairo-1.0 -lpango-1.0 -lharfbuzz -latk-1.0 -lcairo-gobject -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lSM -lICE -lXpm -lXt -lX11 -lXdmcp -lSM -lICE  -lm -ltinfo -lnsl  -lselinux  -lcanberra -lacl -lattr -lgpm -ldl  -L/usr/lib -llua5.2 -Wl,-E  -fstack-protector-strong -L/usr/local/lib  -L/usr/lib/x86_64-linux-gnu/perl/5.30/CORE -lperl -ldl -lm -lpthread -lcrypt  -L/usr/lib/python3.8/config-3.8-x86_64-linux-gnu -lpython3.8 -lcrypt -lpthread -ldl -lutil -lm -lm -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm     

Wdiff/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]>.

Weasyprint/usr/local/bin/weasyprint

WeasyPrint version 51

Which/home/user/cocalc/src/node_modules/.bin/which

/usr/bin/rpcinfo

Xclip/usr/bin/xclip

xclip version 0.13
Copyright (C) 2001-2008 Kim Saunders et al.
Distributed under the terms of the GNU GPL

Xdotool/usr/bin/xdotool

xdotool version 3.20160805.1

Xelatex/usr/bin/xelatex

XeTeX 3.14159265-2.6-0.999991 (TeX Live 2019/Debian)
kpathsea version 6.3.1
Copyright 2019 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 66.1; using 66.1
Compiled with zlib version 1.2.11; using 1.2.11
Compiled with FreeType2 version 2.10.1; using 2.10.1
Compiled with Graphite2 version 1.3.13; using 1.3.13
Compiled with HarfBuzz version 2.6.4; using 2.6.4
Compiled with libpng version 1.6.37; using 1.6.37
Compiled with poppler version 0.68.0
Compiled with fontconfig version 2.13.1; using 2.13.1

Xindy/usr/bin/xindy

xindy release: unknown
xindy script version: 1.18
xindy kernel version: 3.0
CLISP version 2.49.92 (2018-02-18) (built on lcy01-amd64-025.buildd [127.0.1.1])
    architecture: X86_64

Xpra/usr/bin/xpra

xpra v4.0.4-r27557

Xsel/usr/bin/xsel

xsel version 1.2.0 by Conrad Parker <[email protected]>

Xz/usr/bin/xz

xz (XZ Utils) 5.2.4
liblzma 5.2.4

Yacc/usr/bin/yacc

bison (GNU Bison) 3.5.1
Written by Robert Corbett and Richard Stallman.

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.

Yapf/usr/local/bin/yapf

yapf 0.30.0

Z3/usr/bin/z3

Z3 version 4.8.7 - 64 bit

Zsh/usr/bin/zsh

zsh 5.8 (x86_64-ubuntu-linux-gnu)