[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 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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