[Debichem-devel] problem with python3-rdkit in Debian Sid

Francois Berenger beren314 at bio.kyutech.ac.jp
Fri Nov 29 03:42:50 GMT 2019


Hello,

This small pyhon3 code fragment does not work:

---
import rdkit
from rdkit import Chem
---

Log file, test script and all installed packages on the system are attached.

What needs to be fixed?

Can I help testing a fix?

Do you need more info in order to fix this?

Thanks a lot,
F.
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ii  adduser                             3.118                          all          add and remove users and groups
ii  apparmor                            2.13.3-7                       amd64        user-space parser utility for AppArmor
ii  apt                                 1.8.4                          amd64        commandline package manager
ii  apt-listchanges                     3.21                           all          package change history notification tool
ii  apt-utils                           1.8.4                          amd64        package management related utility programs
ii  aptitude                            0.8.12-1                       amd64        terminal-based package manager
ii  aptitude-common                     0.8.12-1                       all          architecture independent files for the aptitude package manager
ii  base-files                          11                             amd64        Debian base system miscellaneous files
ii  base-passwd                         3.5.46                         amd64        Debian base system master password and group files
ii  bash                                5.0-5                          amd64        GNU Bourne Again SHell
ii  bash-completion                     1:2.9-1                        all          programmable completion for the bash shell
ii  bind9-host                          1:9.11.5.P4+dfsg-5.1+b1        amd64        DNS lookup utility (deprecated)
ii  binutils                            2.33.1-4                       amd64        GNU assembler, linker and binary utilities
ii  binutils-common:amd64               2.33.1-4                       amd64        Common files for the GNU assembler, linker and binary utilities
ii  binutils-x86-64-linux-gnu           2.33.1-4                       amd64        GNU binary utilities, for x86-64-linux-gnu target
ii  bsdmainutils                        11.1.2+b1                      amd64        collection of more utilities from FreeBSD
ii  bsdutils                            1:2.34-0.1                     amd64        basic utilities from 4.4BSD-Lite
ii  bubblewrap                          0.4.0-1                        amd64        setuid wrapper for unprivileged chroot and namespace manipulation
ii  build-essential                     12.8                           amd64        Informational list of build-essential packages
ii  busybox                             1:1.30.1-4                     amd64        Tiny utilities for small and embedded systems
ii  bzip2                               1.0.8-2                        amd64        high-quality block-sorting file compressor - utilities
ii  ca-certificates                     20190110                       all          Common CA certificates
ii  console-setup                       1.194                          all          console font and keymap setup program
ii  console-setup-linux                 1.194                          all          Linux specific part of console-setup
ii  coreutils                           8.30-3+b1                      amd64        GNU core utilities
ii  cpio                                2.13+dfsg-1                    amd64        GNU cpio -- a program to manage archives of files
ii  cpp                                 4:9.2.1-3.1                    amd64        GNU C preprocessor (cpp)
ii  cpp-9                               9.2.1-20                       amd64        GNU C preprocessor
ii  cron                                3.0pl1-135                     amd64        process scheduling daemon
ii  darcs                               2.14.2-2                       amd64        distributed, interactive, smart revision control system
ii  dash                                0.5.10.2-6                     amd64        POSIX-compliant shell
ii  dbus                                1.12.16-2                      amd64        simple interprocess messaging system (daemon and utilities)
ii  debconf                             1.5.73                         all          Debian configuration management system
ii  debconf-i18n                        1.5.73                         all          full internationalization support for debconf
ii  debian-archive-keyring              2019.1                         all          GnuPG archive keys of the Debian archive
ii  debian-faq                          10.1                           all          Debian Frequently Asked Questions
ii  debianutils                         4.9                            amd64        Miscellaneous utilities specific to Debian
ii  dictionaries-common                 1.28.1                         all          spelling dictionaries - common utilities
ii  diffutils                           1:3.7-3                        amd64        File comparison utilities
ii  dirmngr                             2.2.17-3                       amd64        GNU privacy guard - network certificate management service
ii  discover                            2.1.2-8                        amd64        hardware identification system
ii  discover-data                       2.2013.01.11                   all          Data lists for Discover hardware detection system
ii  distro-info-data                    0.43                           all          information about the distributions' releases (data files)
ii  dmidecode                           3.2-2                          amd64        SMBIOS/DMI table decoder
ii  dmsetup                             2:1.02.155-3                   amd64        Linux Kernel Device Mapper userspace library
ii  doc-debian                          6.4                            all          Debian Project documentation and other documents
ii  dpkg                                1.19.7                         amd64        Debian package management system
ii  dpkg-dev                            1.19.7                         all          Debian package development tools
ii  e2fsprogs                           1.45.4-1                       amd64        ext2/ext3/ext4 file system utilities
ii  eject                               2.1.5+deb1+cvs20081104-14+b1   amd64        ejects CDs and operates CD-Changers under Linux
ii  emacsen-common                      3.0.4                          all          Common facilities for all emacsen
ii  fakeroot                            1.24-1                         amd64        tool for simulating superuser privileges
ii  fdisk                               2.34-0.1                       amd64        collection of partitioning utilities
ii  file                                1:5.37-6                       amd64        Recognize the type of data in a file using "magic" numbers
ii  findutils                           4.7.0-1                        amd64        utilities for finding files--find, xargs
ii  firmware-linux-free                 3.4                            all          Binary firmware for various drivers in the Linux kernel
ii  fonts-freefont-ttf                  20120503-9                     all          Freefont Serif, Sans and Mono Truetype fonts
ii  g++                                 4:9.2.1-3.1                    amd64        GNU C++ compiler
ii  g++-9                               9.2.1-20                       amd64        GNU C++ compiler
ii  gcc                                 4:9.2.1-3.1                    amd64        GNU C compiler
ii  gcc-8-base:amd64                    8.3.0-25                       amd64        GCC, the GNU Compiler Collection (base package)
ii  gcc-9                               9.2.1-20                       amd64        GNU C compiler
ii  gcc-9-base:amd64                    9.2.1-20                       amd64        GCC, the GNU Compiler Collection (base package)
ii  gdbm-l10n                           1.18.1-5                       all          GNU dbm database routines (translation files) 
ii  geoip-database                      20191108-1                     all          IP lookup command line tools that use the GeoIP library (country database)
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ii  git                                 1:2.24.0-1                     amd64        fast, scalable, distributed revision control system
ii  git-man                             1:2.24.0-1                     all          fast, scalable, distributed revision control system (manual pages)
ii  gnupg                               2.2.17-3                       all          GNU privacy guard - a free PGP replacement
ii  gnupg-l10n                          2.2.17-3                       all          GNU privacy guard - localization files
ii  gnupg-utils                         2.2.17-3                       amd64        GNU privacy guard - utility programs
ii  gpg                                 2.2.17-3                       amd64        GNU Privacy Guard -- minimalist public key operations
ii  gpg-agent                           2.2.17-3                       amd64        GNU privacy guard - cryptographic agent
ii  gpg-wks-client                      2.2.17-3                       amd64        GNU privacy guard - Web Key Service client
ii  gpg-wks-server                      2.2.17-3                       amd64        GNU privacy guard - Web Key Service server
ii  gpgconf                             2.2.17-3                       amd64        GNU privacy guard - core configuration utilities
ii  gpgsm                               2.2.17-3                       amd64        GNU privacy guard - S/MIME version
ii  gpgv                                2.2.17-3                       amd64        GNU privacy guard - signature verification tool
ii  gpm                                 1.20.7-5+b1                    amd64        General Purpose Mouse interface
ii  grep                                3.3-1                          amd64        GNU grep, egrep and fgrep
ii  groff-base                          1.22.4-3                       amd64        GNU troff text-formatting system (base system components)
ii  grub-common                         2.04-4                         amd64        GRand Unified Bootloader (common files)
ii  grub-pc                             2.04-4                         amd64        GRand Unified Bootloader, version 2 (PC/BIOS version)
ii  grub-pc-bin                         2.04-4                         amd64        GRand Unified Bootloader, version 2 (PC/BIOS modules)
ii  grub2-common                        2.04-4                         amd64        GRand Unified Bootloader (common files for version 2)
ii  gzip                                1.9-3+b1                       amd64        GNU compression utilities
ii  hdparm                              9.58+ds-4                      amd64        tune hard disk parameters for high performance
ii  hostname                            3.23                           amd64        utility to set/show the host name or domain name
ii  iamerican                           3.4.00-8                       all          American English dictionary for ispell (standard version)
ii  ibritish                            3.4.00-8                       all          British English dictionary for ispell (standard version)
ii  ienglish-common                     3.4.00-8                       all          Common files for British and American ispell dictionaries
ii  ifupdown                            0.8.35+b1                      amd64        high level tools to configure network interfaces
ii  init                                1.57                           amd64        metapackage ensuring an init system is installed
ii  init-system-helpers                 1.57                           all          helper tools for all init systems
ii  initramfs-tools                     0.135                          all          generic modular initramfs generator (automation)
ii  initramfs-tools-core                0.135                          all          generic modular initramfs generator (core tools)
ii  installation-report                 2.72                           all          system installation report
ii  iproute2                            5.4.0-1                        amd64        networking and traffic control tools
ii  iptables                            1.8.3-2                        amd64        administration tools for packet filtering and NAT
ii  iputils-ping                        3:20190709-2                   amd64        Tools to test the reachability of network hosts
ii  isc-dhcp-client                     4.4.1-2                        amd64        DHCP client for automatically obtaining an IP address
ii  isc-dhcp-common                     4.4.1-2                        amd64        common manpages relevant to all of the isc-dhcp packages
ii  iso-codes                           4.4-1                          all          ISO language, territory, currency, script codes and their translations
ii  ispell                              3.4.00-8                       amd64        International Ispell (an interactive spelling corrector)
ii  kbd                                 2.0.4-4                        amd64        Linux console font and keytable utilities
ii  keyboard-configuration              1.194                          all          system-wide keyboard preferences
ii  klibc-utils                         2.0.7-1                        amd64        small utilities built with klibc for early boot
ii  kmod                                26-3                           amd64        tools for managing Linux kernel modules
ii  krb5-locales                        1.17-6                         all          internationalization support for MIT Kerberos
ii  laptop-detect                       0.16                           all          system chassis type checker
ii  ledit                               2.04-4                         all          line editor for interactive programs
ii  less                                551-1                          amd64        pager program similar to more
ii  libacl1:amd64                       2.2.53-5                       amd64        access control list - shared library
ii  libalgorithm-diff-perl              1.19.03-2                      all          module to find differences between files
ii  libalgorithm-diff-xs-perl           0.04-6                         amd64        module to find differences between files (XS accelerated)
ii  libalgorithm-merge-perl             0.08-3                         all          Perl module for three-way merge of textual data
ii  libamd2:amd64                       1:5.6.0+dfsg-2                 amd64        approximate minimum degree ordering library for sparse matrices
ii  libapparmor1:amd64                  2.13.3-7                       amd64        changehat AppArmor library
ii  libapt-inst2.0:amd64                1.8.4                          amd64        deb package format runtime library
ii  libapt-pkg5.0:amd64                 1.8.4                          amd64        package management runtime library
ii  libargon2-1:amd64                   0~20171227-0.2                 amd64        memory-hard hashing function - runtime library
ii  libasan5:amd64                      9.2.1-20                       amd64        AddressSanitizer -- a fast memory error detector
ii  libassuan0:amd64                    2.5.3-7                        amd64        IPC library for the GnuPG components
ii  libatomic1:amd64                    9.2.1-20                       amd64        support library providing __atomic built-in functions
ii  libattr1:amd64                      1:2.4.48-5                     amd64        extended attribute handling - shared library
ii  libaudit-common                     1:2.8.5-2                      all          Dynamic library for security auditing - common files
ii  libaudit1:amd64                     1:2.8.5-2+b1                   amd64        Dynamic library for security auditing
ii  libbind9-161:amd64                  1:9.11.5.P4+dfsg-5.1+b1        amd64        BIND9 Shared Library used by BIND
ii  libbinutils:amd64                   2.33.1-4                       amd64        GNU binary utilities (private shared library)
ii  libblas3:amd64                      3.9.0-1                        amd64        Basic Linear Algebra Reference implementations, shared library
ii  libblkid1:amd64                     2.34-0.1                       amd64        block device ID library
ii  libboost-iostreams1.67.0:amd64      1.67.0-14                      amd64        Boost.Iostreams Library
ii  libboost-python1.67.0               1.67.0-14                      amd64        Boost.Python Library
ii  libboost-serialization1.67.0:amd64  1.67.0-14                      amd64        serialization library for C++
ii  libbrotli1:amd64                    1.0.7-5+b1                     amd64        library implementing brotli encoder and decoder (shared libraries)
ii  libbsd0:amd64                       0.10.0-1                       amd64        utility functions from BSD systems - shared library
ii  libbz2-1.0:amd64                    1.0.8-2                        amd64        high-quality block-sorting file compressor library - runtime
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ii  libc-dev-bin                        2.29-3                         amd64        GNU C Library: Development binaries
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ii  libc6:amd64                         2.29-3                         amd64        GNU C Library: Shared libraries
ii  libc6-dev:amd64                     2.29-3                         amd64        GNU C Library: Development Libraries and Header Files
ii  libcap-ng0:amd64                    0.7.9-2.1+b1                   amd64        An alternate POSIX capabilities library
ii  libcap2:amd64                       1:2.27-1                       amd64        POSIX 1003.1e capabilities (library)
ii  libcap2-bin                         1:2.27-1                       amd64        POSIX 1003.1e capabilities (utilities)
ii  libcc1-0:amd64                      9.2.1-20                       amd64        GCC cc1 plugin for GDB
ii  libcgi-fast-perl                    1:2.15-1                       all          CGI subclass for work with FCGI
ii  libcgi-pm-perl                      4.44-1                         all          module for Common Gateway Interface applications
ii  libclass-accessor-perl              0.51-1                         all          Perl module that automatically generates accessors
ii  libcolamd2:amd64                    1:5.6.0+dfsg-2                 amd64        column approximate minimum degree ordering library for sparse matrices
ii  libcom-err2:amd64                   1.45.4-1                       amd64        common error description library
ii  libcryptsetup12:amd64               2:2.2.2-1                      amd64        disk encryption support - shared library
ii  libcurl3-gnutls:amd64               7.66.0-1+b1                    amd64        easy-to-use client-side URL transfer library (GnuTLS flavour)
ii  libcwidget4:amd64                   0.5.18-5                       amd64        high-level terminal interface library for C++ (runtime files)
ii  libdb5.3:amd64                      5.3.28+dfsg1-0.6               amd64        Berkeley v5.3 Database Libraries [runtime]
ii  libdbus-1-3:amd64                   1.12.16-2                      amd64        simple interprocess messaging system (library)
ii  libdebconfclient0:amd64             0.250                          amd64        Debian Configuration Management System (C-implementation library)
ii  libdevmapper1.02.1:amd64            2:1.02.155-3                   amd64        Linux Kernel Device Mapper userspace library
ii  libdiscover2                        2.1.2-8                        amd64        hardware identification library
ii  libdns-export1104                   1:9.11.5.P4+dfsg-5.1+b1        amd64        Exported DNS Shared Library
ii  libdns1104:amd64                    1:9.11.5.P4+dfsg-5.1+b1        amd64        DNS Shared Library used by BIND
ii  libdpkg-perl                        1.19.7                         all          Dpkg perl modules
ii  libedit2:amd64                      3.1-20191025-1                 amd64        BSD editline and history libraries
ii  libefiboot1:amd64                   37-2                           amd64        Library to manage UEFI variables
ii  libefivar1:amd64                    37-2                           amd64        Library to manage UEFI variables
ii  libelf1:amd64                       0.176-1.1                      amd64        library to read and write ELF files
ii  libencode-locale-perl               1.05-1                         all          utility to determine the locale encoding
ii  liberror-perl                       0.17028-1                      all          Perl module for error/exception handling in an OO-ish way
ii  libestr0:amd64                      0.1.10-2.1+b1                  amd64        Helper functions for handling strings (lib)
ii  libexpat1:amd64                     2.2.9-1                        amd64        XML parsing C library - runtime library
ii  libext2fs2:amd64                    1.45.4-1                       amd64        ext2/ext3/ext4 file system libraries
ii  libfakeroot:amd64                   1.24-1                         amd64        tool for simulating superuser privileges - shared libraries
ii  libfastjson4:amd64                  0.99.8-2                       amd64        fast json library for C
ii  libfcgi-perl                        0.78-2+b4                      amd64        helper module for FastCGI
ii  libfdisk1:amd64                     2.34-0.1                       amd64        fdisk partitioning library
ii  libffi6:amd64                       3.2.1-9                        amd64        Foreign Function Interface library runtime
ii  libfile-fcntllock-perl              0.22-3+b6                      amd64        Perl module for file locking with fcntl(2)
ii  libfreetype6:amd64                  2.10.1-2                       amd64        FreeType 2 font engine, shared library files
ii  libfstrm0:amd64                     0.6.0-1+b1                     amd64        Frame Streams (fstrm) library
ii  libfuse2:amd64                      2.9.9-2                        amd64        Filesystem in Userspace (library)
ii  libgcc-9-dev:amd64                  9.2.1-20                       amd64        GCC support library (development files)
ii  libgcc1:amd64                       1:9.2.1-20                     amd64        GCC support library
ii  libgcrypt20:amd64                   1.8.5-3                        amd64        LGPL Crypto library - runtime library
ii  libgdbm-compat4:amd64               1.18.1-5                       amd64        GNU dbm database routines (legacy support runtime version) 
ii  libgdbm6:amd64                      1.18.1-5                       amd64        GNU dbm database routines (runtime version) 
ii  libgeoip1:amd64                     1.6.12-5                       amd64        non-DNS IP-to-country resolver library
ii  libgfortran5:amd64                  9.2.1-20                       amd64        Runtime library for GNU Fortran applications
ii  libglpk40:amd64                     4.65-2                         amd64        linear programming kit with integer (MIP) support
ii  libgmp10:amd64                      2:6.1.2+dfsg-4                 amd64        Multiprecision arithmetic library
ii  libgnutls30:amd64                   3.6.10-5                       amd64        GNU TLS library - main runtime library
ii  libgomp1:amd64                      9.2.1-20                       amd64        GCC OpenMP (GOMP) support library
ii  libgpg-error0:amd64                 1.36-7                         amd64        GnuPG development runtime library
ii  libgpm2:amd64                       1.20.7-5+b1                    amd64        General Purpose Mouse - shared library
ii  libgssapi-krb5-2:amd64              1.17-6                         amd64        MIT Kerberos runtime libraries - krb5 GSS-API Mechanism
ii  libhogweed4:amd64                   3.5.1+really3.4.1-1            amd64        low level cryptographic library (public-key cryptos)
ii  libhogweed5:amd64                   3.5.1+really3.5.1-2            amd64        low level cryptographic library (public-key cryptos)
ii  libhtml-parser-perl                 3.72-3+b4                      amd64        collection of modules that parse HTML text documents
ii  libhtml-tagset-perl                 3.20-4                         all          data tables pertaining to HTML
ii  libhttp-date-perl                   6.05-1                         all          module of date conversion routines
ii  libhttp-message-perl                6.18-1                         all          perl interface to HTTP style messages
ii  libicu63:amd64                      63.2-2                         amd64        International Components for Unicode
ii  libidn11:amd64                      1.33-2.2                       amd64        GNU Libidn library, implementation of IETF IDN specifications
ii  libidn2-0:amd64                     2.2.0-2                        amd64        Internationalized domain names (IDNA2008/TR46) library
ii  libio-html-perl                     1.001-1                        all          open an HTML file with automatic charset detection
ii  libio-string-perl                   1.08-3                         all          Emulate IO::File interface for in-core strings
ii  libip4tc0:amd64                     1.8.2-4                        amd64        netfilter libip4tc library
ii  libip4tc2:amd64                     1.8.3-2                        amd64        netfilter libip4tc library
ii  libip6tc0:amd64                     1.8.2-4                        amd64        netfilter libip6tc library
ii  libip6tc2:amd64                     1.8.3-2                        amd64        netfilter libip6tc library
ii  libiptc0:amd64                      1.8.3-2                        amd64        netfilter libiptc library
ii  libisc-export1100:amd64             1:9.11.5.P4+dfsg-5.1+b1        amd64        Exported ISC Shared Library
ii  libisc1100:amd64                    1:9.11.5.P4+dfsg-5.1+b1        amd64        ISC Shared Library used by BIND
ii  libisccc161:amd64                   1:9.11.5.P4+dfsg-5.1+b1        amd64        Command Channel Library used by BIND
ii  libisccfg163:amd64                  1:9.11.5.P4+dfsg-5.1+b1        amd64        Config File Handling Library used by BIND
ii  libisl21:amd64                      0.21-2                         amd64        manipulating sets and relations of integer points bounded by linear constraints
ii  libitm1:amd64                       9.2.1-20                       amd64        GNU Transactional Memory Library
ii  libjson-c3:amd64                    0.12.1+ds-2                    amd64        JSON manipulation library - shared library
ii  libjson-c4:amd64                    0.13.1+dfsg-6                  amd64        JSON manipulation library - shared library
ii  libk5crypto3:amd64                  1.17-6                         amd64        MIT Kerberos runtime libraries - Crypto Library
ii  libkeyutils1:amd64                  1.6-6                          amd64        Linux Key Management Utilities (library)
ii  libklibc:amd64                      2.0.7-1                        amd64        minimal libc subset for use with initramfs
ii  libkmod2:amd64                      26-3                           amd64        libkmod shared library
ii  libkrb5-3:amd64                     1.17-6                         amd64        MIT Kerberos runtime libraries
ii  libkrb5support0:amd64               1.17-6                         amd64        MIT Kerberos runtime libraries - Support library
ii  libksba8:amd64                      1.3.5-2                        amd64        X.509 and CMS support library
ii  liblapack3:amd64                    3.9.0-1                        amd64        Library of linear algebra routines 3 - shared version
ii  libldap-2.4-2:amd64                 2.4.48+dfsg-1+b2               amd64        OpenLDAP libraries
ii  libldap-common                      2.4.48+dfsg-1                  all          OpenLDAP common files for libraries
ii  liblmdb0:amd64                      0.9.22-1                       amd64        Lightning Memory-Mapped Database shared library
ii  liblocale-gettext-perl              1.07-4                         amd64        module using libc functions for internationalization in Perl
ii  liblockfile-bin                     1.16-1.1                       amd64        support binaries for and cli utilities based on liblockfile
ii  liblognorm5:amd64                   2.0.5-1+b1                     amd64        log normalizing library
ii  liblsan0:amd64                      9.2.1-20                       amd64        LeakSanitizer -- a memory leak detector (runtime)
ii  libltdl7:amd64                      2.4.6-11                       amd64        System independent dlopen wrapper for GNU libtool
ii  liblwp-mediatypes-perl              6.04-1                         all          module to guess media type for a file or a URL
ii  liblwres161:amd64                   1:9.11.5.P4+dfsg-5.1+b1        amd64        Lightweight Resolver Library used by BIND
ii  liblz4-1:amd64                      1.9.2-2                        amd64        Fast LZ compression algorithm library - runtime
ii  liblzma5:amd64                      5.2.4-1+b1                     amd64        XZ-format compression library
ii  libmagic-mgc                        1:5.37-6                       amd64        File type determination library using "magic" numbers (compiled magic file)
ii  libmagic1:amd64                     1:5.37-6                       amd64        Recognize the type of data in a file using "magic" numbers - library
ii  libmnl0:amd64                       1.0.4-2+b1                     amd64        minimalistic Netlink communication library
ii  libmount1:amd64                     2.34-0.1                       amd64        device mounting library
ii  libmpc3:amd64                       1.1.0-1                        amd64        multiple precision complex floating-point library
ii  libmpdec2:amd64                     2.4.2-2                        amd64        library for decimal floating point arithmetic (runtime library)
ii  libmpfr6:amd64                      4.0.2-1                        amd64        multiple precision floating-point computation
ii  libncurses-dev:amd64                6.1+20191019-1                 amd64        developer's libraries for ncurses
ii  libncurses5-dev:amd64               6.1+20191019-1                 amd64        transitional package for libncurses-dev
ii  libncurses6:amd64                   6.1+20191019-1                 amd64        shared libraries for terminal handling
ii  libncursesw6:amd64                  6.1+20191019-1                 amd64        shared libraries for terminal handling (wide character support)
ii  libnetfilter-conntrack3:amd64       1.0.7-2                        amd64        Netfilter netlink-conntrack library
ii  libnettle6:amd64                    3.5.1+really3.4.1-1            amd64        low level cryptographic library (symmetric and one-way cryptos)
ii  libnettle7:amd64                    3.5.1+really3.5.1-2            amd64        low level cryptographic library (symmetric and one-way cryptos)
ii  libnewt0.52:amd64                   0.52.21-3+b1                   amd64        Not Erik's Windowing Toolkit - text mode windowing with slang
ii  libnfnetlink0:amd64                 1.0.1-3+b1                     amd64        Netfilter netlink library
ii  libnftnl11:amd64                    1.1.4-1                        amd64        Netfilter nftables userspace API library
ii  libnghttp2-14:amd64                 1.40.0-1                       amd64        library implementing HTTP/2 protocol (shared library)
ii  libnpth0:amd64                      1.6-1                          amd64        replacement for GNU Pth using system threads
ii  libnss-systemd:amd64                243-8                          amd64        nss module providing dynamic user and group name resolution
ii  libp11-kit0:amd64                   0.23.18.1-2                    amd64        library for loading and coordinating access to PKCS#11 modules - runtime
ii  libpam-modules:amd64                1.3.1-5                        amd64        Pluggable Authentication Modules for PAM
ii  libpam-modules-bin                  1.3.1-5                        amd64        Pluggable Authentication Modules for PAM - helper binaries
ii  libpam-runtime                      1.3.1-5                        all          Runtime support for the PAM library
ii  libpam-systemd:amd64                243-8                          amd64        system and service manager - PAM module
ii  libpam0g:amd64                      1.3.1-5                        amd64        Pluggable Authentication Modules library
ii  libparse-debianchangelog-perl       1.2.0-13                       all          parse Debian changelogs and output them in other formats
ii  libpci3:amd64                       1:3.6.2-5                      amd64        PCI utilities (shared library)
ii  libpcre2-8-0:amd64                  10.34-1                        amd64        New Perl Compatible Regular Expression Library- 8 bit runtime files
ii  libpcre3:amd64                      2:8.39-12+b1                   amd64        Old Perl 5 Compatible Regular Expression Library - runtime files
ii  libperl5.28:amd64                   5.28.1-6                       amd64        shared Perl library
ii  libperl5.30:amd64                   5.30.0-9                       amd64        shared Perl library
ii  libpipeline1:amd64                  1.5.1-2                        amd64        pipeline manipulation library
ii  libpng16-16:amd64                   1.6.37-1                       amd64        PNG library - runtime (version 1.6)
ii  libpopt0:amd64                      1.16-14                        amd64        lib for parsing cmdline parameters
ii  libprocps7:amd64                    2:3.3.15-2+b1                  amd64        library for accessing process information from /proc
ii  libprotobuf-c1:amd64                1.3.2-1+b1                     amd64        Protocol Buffers C shared library (protobuf-c)
ii  libpsl5:amd64                       0.20.2-2                       amd64        Library for Public Suffix List (shared libraries)
ii  libpthread-stubs0-dev:amd64         0.4-1                          amd64        pthread stubs not provided by native libc, development files
ii  libpython-stdlib:amd64              2.7.17-2                       amd64        interactive high-level object-oriented language (Python2)
ii  libpython2-stdlib:amd64             2.7.17-2                       amd64        interactive high-level object-oriented language (Python2)
ii  libpython2.7-minimal:amd64          2.7.17-1                       amd64        Minimal subset of the Python language (version 2.7)
ii  libpython2.7-stdlib:amd64           2.7.17-1                       amd64        Interactive high-level object-oriented language (standard library, version 2.7)
ii  libpython3-stdlib:amd64             3.7.5-3                        amd64        interactive high-level object-oriented language (default python3 version)
ii  libpython3.7:amd64                  3.7.5-2                        amd64        Shared Python runtime library (version 3.7)
ii  libpython3.7-minimal:amd64          3.7.5-2                        amd64        Minimal subset of the Python language (version 3.7)
ii  libpython3.7-stdlib:amd64           3.7.5-2                        amd64        Interactive high-level object-oriented language (standard library, version 3.7)
ii  libpython3.8-minimal:amd64          3.8.0-5                        amd64        Minimal subset of the Python language (version 3.8)
ii  libpython3.8-stdlib:amd64           3.8.0-5                        amd64        Interactive high-level object-oriented language (standard library, version 3.8)
ii  libquadmath0:amd64                  9.2.1-20                       amd64        GCC Quad-Precision Math Library
ii  librdkit1                           201903.1-2                     amd64        Collection of cheminformatics and machine-learning software (shared libraries)
ii  libreadline7:amd64                  7.0-5                          amd64        GNU readline and history libraries, run-time libraries
ii  libreadline8:amd64                  8.0-3                          amd64        GNU readline and history libraries, run-time libraries
ii  librtmp1:amd64                      2.4+20151223.gitfa8646d.1-2+b1 amd64        toolkit for RTMP streams (shared library)
ii  libsasl2-2:amd64                    2.1.27+dfsg-1                  amd64        Cyrus SASL - authentication abstraction library
ii  libsasl2-modules:amd64              2.1.27+dfsg-1                  amd64        Cyrus SASL - pluggable authentication modules
ii  libsasl2-modules-db:amd64           2.1.27+dfsg-1                  amd64        Cyrus SASL - pluggable authentication modules (DB)
ii  libschroedinger-coordgenlibs1:amd64 1.3-1                          amd64        2D coordinate generation for chemical compounds
ii  libschroedinger-maeparser1:amd64    1.2.2-1                        amd64        parser for Schrödinger Maestro files
ii  libseccomp2:amd64                   2.4.2-2                        amd64        high level interface to Linux seccomp filter
ii  libselinux1:amd64                   2.9-3+b1                       amd64        SELinux runtime shared libraries
ii  libsemanage-common                  2.9-3                          all          Common files for SELinux policy management libraries
ii  libsemanage1:amd64                  2.9-3+b1                       amd64        SELinux policy management library
ii  libsepol1:amd64                     2.9-2+b2                       amd64        SELinux library for manipulating binary security policies
ii  libsigc++-2.0-0v5:amd64             2.10.2-1                       amd64        type-safe Signal Framework for C++ - runtime
ii  libsigsegv2:amd64                   2.12-2                         amd64        Library for handling page faults in a portable way
ii  libslang2:amd64                     2.3.2-4                        amd64        S-Lang programming library - runtime version
ii  libsmartcols1:amd64                 2.34-0.1                       amd64        smart column output alignment library
ii  libsqlite3-0:amd64                  3.30.1-1                       amd64        SQLite 3 shared library
ii  libss2:amd64                        1.45.4-1                       amd64        command-line interface parsing library
ii  libssh2-1:amd64                     1.8.0-2.1                      amd64        SSH2 client-side library
ii  libssl1.1:amd64                     1.1.1d-2                       amd64        Secure Sockets Layer toolkit - shared libraries
ii  libstdc++-9-dev:amd64               9.2.1-20                       amd64        GNU Standard C++ Library v3 (development files)
ii  libstdc++6:amd64                    9.2.1-20                       amd64        GNU Standard C++ Library v3
ii  libsub-name-perl                    0.26-1                         amd64        module for assigning a new name to referenced sub
ii  libsuitesparseconfig5:amd64         1:5.6.0+dfsg-2                 amd64        configuration routines for all SuiteSparse modules
ii  libsystemd0:amd64                   243-8                          amd64        systemd utility library
ii  libtasn1-6:amd64                    4.14-3                         amd64        Manage ASN.1 structures (runtime)
ii  libtext-charwidth-perl              0.04-10                        amd64        get display widths of characters on the terminal
ii  libtext-iconv-perl                  1.7-7                          amd64        module to convert between character sets in Perl
ii  libtext-wrapi18n-perl               0.06-9                         all          internationalized substitute of Text::Wrap
ii  libtimedate-perl                    2.3000-2                       all          collection of modules to manipulate date/time information
ii  libtinfo6:amd64                     6.1+20191019-1                 amd64        shared low-level terminfo library for terminal handling
ii  libtsan0:amd64                      9.2.1-20                       amd64        ThreadSanitizer -- a Valgrind-based detector of data races (runtime)
ii  libubsan1:amd64                     9.2.1-20                       amd64        UBSan -- undefined behaviour sanitizer (runtime)
ii  libuchardet0:amd64                  0.0.6-3                        amd64        universal charset detection library - shared library
ii  libudev1:amd64                      243-8                          amd64        libudev shared library
ii  libunistring2:amd64                 0.9.10-2                       amd64        Unicode string library for C
ii  liburi-perl                         1.76-1                         all          module to manipulate and access URI strings
ii  libusb-0.1-4:amd64                  2:0.1.12-32                    amd64        userspace USB programming library
ii  libusb-1.0-0:amd64                  2:1.0.23-1                     amd64        userspace USB programming library
ii  libuuid1:amd64                      2.34-0.1                       amd64        Universally Unique ID library
ii  libx11-6:amd64                      2:1.6.8-1                      amd64        X11 client-side library
ii  libx11-data                         2:1.6.8-1                      all          X11 client-side library
ii  libx11-dev:amd64                    2:1.6.8-1                      amd64        X11 client-side library (development headers)
ii  libxapian30:amd64                   1.4.12-1                       amd64        Search engine library
ii  libxau-dev:amd64                    1:1.0.8-1+b2                   amd64        X11 authorisation library (development headers)
ii  libxau6:amd64                       1:1.0.8-1+b2                   amd64        X11 authorisation library
ii  libxcb1:amd64                       1.13.1-2                       amd64        X C Binding
ii  libxcb1-dev:amd64                   1.13.1-2                       amd64        X C Binding, development files
ii  libxdmcp-dev:amd64                  1:1.1.2-3                      amd64        X11 authorisation library (development headers)
ii  libxdmcp6:amd64                     1:1.1.2-3                      amd64        X11 Display Manager Control Protocol library
ii  libxext6:amd64                      2:1.3.3-1+b2                   amd64        X11 miscellaneous extension library
ii  libxml2:amd64                       2.9.4+dfsg1-8                  amd64        GNOME XML library
ii  libxmuu1:amd64                      2:1.1.2-2+b3                   amd64        X11 miscellaneous micro-utility library
ii  libxtables12:amd64                  1.8.3-2                        amd64        netfilter xtables library
ii  libzstd1:amd64                      1.4.4+dfsg-1                   amd64        fast lossless compression algorithm
ii  linux-base                          4.6                            all          Linux image base package
ii  linux-image-4.19.0-6-amd64          4.19.67-2+deb10u2              amd64        Linux 4.19 for 64-bit PCs (signed)
ii  linux-image-5.3.0-2-amd64           5.3.9-3                        amd64        Linux 5.3 for 64-bit PCs (signed)
ii  linux-image-amd64                   5.3.9-3                        amd64        Linux for 64-bit PCs (meta-package)
ii  linux-libc-dev:amd64                5.3.9-3                        amd64        Linux support headers for userspace development
ii  locales                             2.29-3                         all          GNU C Library: National Language (locale) data [support]
ii  login                               1:4.7-2                        amd64        system login tools
ii  logrotate                           3.15.1-2                       amd64        Log rotation utility
ii  logsave                             1.45.4-1                       amd64        save the output of a command in a log file
ii  lsb-base                            11.1.0                         all          Linux Standard Base init script functionality
ii  lsb-release                         11.1.0                         all          Linux Standard Base version reporting utility
ii  lsof                                4.93.2+dfsg-1                  amd64        utility to list open files
ii  m4                                  1.4.18-4                       amd64        macro processing language
ii  make                                4.2.1-1.2                      amd64        utility for directing compilation
ii  man-db                              2.9.0-1                        amd64        tools for reading manual pages
ii  manpages                            5.04-1                         all          Manual pages about using a GNU/Linux system
ii  manpages-dev                        5.04-1                         all          Manual pages about using GNU/Linux for development
ii  mawk                                1.3.3-17+b3                    amd64        a pattern scanning and text processing language
ii  mercurial                           5.2-1                          amd64        easy-to-use, scalable distributed version control system
ii  mercurial-common                    5.2-1                          all          easy-to-use, scalable distributed version control system (common files)
ii  mg                                  20180927-1                     amd64        microscopic GNU Emacs-style editor
ii  mime-support                        3.64                           all          MIME files 'mime.types' & 'mailcap', and support programs
ii  mount                               2.34-0.1                       amd64        tools for mounting and manipulating filesystems
ii  nano                                4.5-1                          amd64        small, friendly text editor inspired by Pico
ii  ncurses-base                        6.1+20191019-1                 all          basic terminal type definitions
ii  ncurses-bin                         6.1+20191019-1                 amd64        terminal-related programs and man pages
ii  ncurses-term                        6.1+20191019-1                 all          additional terminal type definitions
ii  netbase                             5.7                            all          Basic TCP/IP networking system
ii  netcat-traditional                  1.10-41.1+b1                   amd64        TCP/IP swiss army knife
ii  ocaml                               4.08.1-4                       amd64        ML language implementation with a class-based object system
ii  ocaml-base                          4.08.1-4                       amd64        Runtime system for OCaml bytecode executables
ii  ocaml-base-nox                      4.08.1-4                       amd64        Runtime system for OCaml bytecode executables (no X)
ii  ocaml-compiler-libs                 4.08.1-4                       amd64        OCaml interpreter and standard libraries
ii  ocaml-interp                        4.08.1-4                       amd64        OCaml interactive interpreter and standard libraries
ii  ocaml-man                           4.08.1-4                       all          OCaml interpreter and standard libraries (lib manpages)
ii  ocaml-nox                           4.08.1-4                       amd64        ML implementation with a class-based object system (no X)
ii  opam                                2.0.5-1                        amd64        package manager for OCaml
ii  opam-doc                            2.0.5-1                        all          package manager for OCaml (documentation)
ii  opam-installer                      2.0.5-1                        amd64        Utility handling (un)installation of Opam .install files
ii  openssh-client                      1:8.1p1-1                      amd64        secure shell (SSH) client, for secure access to remote machines
ii  openssl                             1.1.1d-2                       amd64        Secure Sockets Layer toolkit - cryptographic utility
ii  os-prober                           1.77                           amd64        utility to detect other OSes on a set of drives
ii  passwd                              1:4.7-2                        amd64        change and administer password and group data
ii  patch                               2.7.6-6                        amd64        Apply a diff file to an original
ii  pci.ids                             0.0~2019.11.10-2               all          PCI ID Repository
ii  pciutils                            1:3.6.2-5                      amd64        PCI utilities
ii  perl                                5.30.0-9                       amd64        Larry Wall's Practical Extraction and Report Language
ii  perl-base                           5.30.0-9                       amd64        minimal Perl system
ii  perl-modules-5.28                   5.28.1-6                       all          Core Perl modules
ii  perl-modules-5.30                   5.30.0-9                       all          Core Perl modules
ii  pinentry-curses                     1.1.0-3                        amd64        curses-based PIN or pass-phrase entry dialog for GnuPG
ii  powermgmt-base                      1.36                           all          common utils for power management
ii  procps                              2:3.3.15-2+b1                  amd64        /proc file system utilities
ii  publicsuffix                        20191120.1745-1                all          accurate, machine-readable list of domain name suffixes
ii  python                              2.7.17-2                       amd64        interactive high-level object-oriented language (Python2 version)
ii  python-apt-common                   1.8.4                          all          Python interface to libapt-pkg (locales)
ii  python-minimal                      2.7.17-2                       amd64        minimal subset of the Python2 language
ii  python2                             2.7.17-2                       amd64        interactive high-level object-oriented language (Python2 version)
ii  python2-minimal                     2.7.17-2                       amd64        minimal subset of the Python2 language
ii  python2.7                           2.7.17-1                       amd64        Interactive high-level object-oriented language (version 2.7)
ii  python2.7-minimal                   2.7.17-1                       amd64        Minimal subset of the Python language (version 2.7)
ii  python3                             3.7.5-3                        amd64        interactive high-level object-oriented language (default python3 version)
ii  python3-apt                         1.8.4+b1                       amd64        Python 3 interface to libapt-pkg
ii  python3-certifi                     2018.8.24-1                    all          root certificates for validating SSL certs and verifying TLS hosts (python3)
ii  python3-chardet                     3.0.4-4                        all          universal character encoding detector for Python3
ii  python3-debconf                     1.5.73                         all          interact with debconf from Python 3
ii  python3-debian                      0.1.36                         all          Python 3 modules to work with Debian-related data formats
ii  python3-debianbts                   3.0.2                          all          Python interface to Debian's Bug Tracking System
ii  python3-httplib2                    0.11.3-2                       all          comprehensive HTTP client library written for Python3
ii  python3-idna                        2.6-2                          all          Python IDNA2008 (RFC 5891) handling (Python 3)
ii  python3-minimal                     3.7.5-3                        amd64        minimal subset of the Python language (default python3 version)
ii  python3-numpy                       1:1.17.4-3                     amd64        Fast array facility to the Python 3 language
ii  python3-pkg-resources               41.4.0-1                       all          Package Discovery and Resource Access using pkg_resources
ii  python3-pycurl                      7.43.0.2-0.1+b2                amd64        Python bindings to libcurl (Python 3)
ii  python3-pysimplesoap                1.16.2-2                       all          simple and lightweight SOAP Library (Python 3)
ii  python3-rdkit                       201903.1-2                     amd64        Collection of cheminformatics and machine-learning software
ii  python3-reportbug                   7.5.3                          all          Python modules for interacting with bug tracking systems
ii  python3-requests                    2.21.0-1                       all          elegant and simple HTTP library for Python3, built for human beings
ii  python3-six                         1.13.0-1                       all          Python 2 and 3 compatibility library (Python 3 interface)
ii  python3-urllib3                     1.24.1-1                       all          HTTP library with thread-safe connection pooling for Python3
ii  python3.7                           3.7.5-2                        amd64        Interactive high-level object-oriented language (version 3.7)
ii  python3.7-minimal                   3.7.5-2                        amd64        Minimal subset of the Python language (version 3.7)
ii  python3.8                           3.8.0-5                        amd64        Interactive high-level object-oriented language (version 3.8)
ii  python3.8-minimal                   3.8.0-5                        amd64        Minimal subset of the Python language (version 3.8)
ii  rdkit-data                          201903.1-2                     all          Collection of cheminformatics and machine-learning software (data files)
ii  readline-common                     8.0-3                          all          GNU readline and history libraries, common files
ii  reportbug                           7.5.3                          all          reports bugs in the Debian distribution
ii  rsync                               3.1.3-8                        amd64        fast, versatile, remote (and local) file-copying tool
ii  rsyslog                             8.1911.0-1                     amd64        reliable system and kernel logging daemon
ii  sed                                 4.7-1                          amd64        GNU stream editor for filtering/transforming text
ii  sensible-utils                      0.0.12+nmu1                    all          Utilities for sensible alternative selection
ii  systemd                             243-8                          amd64        system and service manager
ii  systemd-sysv                        243-8                          amd64        system and service manager - SysV links
ii  sysvinit-utils                      2.96-1                         amd64        System-V-like utilities
ii  tar                                 1.30+dfsg-6+b1                 amd64        GNU version of the tar archiving utility
ii  task-english                        3.56                           all          General English environment
ii  tasksel                             3.56                           all          tool for selecting tasks for installation on Debian systems
ii  tasksel-data                        3.56                           all          official tasks used for installation of Debian systems
ii  telnet                              0.17-41.2                      amd64        basic telnet client
ii  traceroute                          1:2.1.0-2+b1                   amd64        Traces the route taken by packets over an IPv4/IPv6 network
ii  tzdata                              2019c-3                        all          time zone and daylight-saving time data
ii  ucf                                 3.0038+nmu1                    all          Update Configuration File(s): preserve user changes to config files
ii  udev                                243-8                          amd64        /dev/ and hotplug management daemon
ii  unzip                               6.0-25                         amd64        De-archiver for .zip files
ii  usb.ids                             2019.10.25-1                   all          USB ID Repository
ii  usbutils                            1:012-2                        amd64        Linux USB utilities
ii  util-linux                          2.34-0.1                       amd64        miscellaneous system utilities
ii  util-linux-locales                  2.34-0.1                       all          locales files for util-linux
ii  vim-common                          2:8.1.2269-1                   all          Vi IMproved - Common files
ii  vim-tiny                            2:8.1.2269-1                   amd64        Vi IMproved - enhanced vi editor - compact version
ii  wamerican                           2018.04.16-1                   all          American English dictionary words for /usr/share/dict
ii  wget                                1.20.3-1+b2                    amd64        retrieves files from the web
ii  whiptail                            0.52.21-3+b1                   amd64        Displays user-friendly dialog boxes from shell scripts
ii  x11proto-core-dev                   2018.4-4                       all          transitional dummy package
ii  x11proto-dev                        2018.4-4                       all          X11 extension protocols and auxiliary headers
ii  xauth                               1:1.0.10-1                     amd64        X authentication utility
ii  xkb-data                            2.26-2                         all          X Keyboard Extension (XKB) configuration data
ii  xorg-sgml-doctools                  1:1.11-1                       all          Common tools for building X.Org SGML documentation
ii  xtrans-dev                          1.3.5-1                        all          X transport library (development files)
ii  xxd                                 2:8.1.2269-1                   amd64        tool to make (or reverse) a hex dump
ii  xz-utils                            5.2.4-1+b1                     amd64        XZ-format compression utilities
ii  zlib1g:amd64                        1:1.2.11.dfsg-1+b1             amd64        compression library - runtime
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