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Created January 24, 2018 18:40
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log of beakerx installing with conda on ubuntu on docker
$ docker run -v `pwd`:/mnt/host -it ubuntu:16.04 /mnt/host/install_test
+ apt-get update
Get:1 http://archive.ubuntu.com/ubuntu xenial InRelease [247 kB]
Get:2 http://security.ubuntu.com/ubuntu xenial-security InRelease [102 kB]
Get:3 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB]
Get:4 http://security.ubuntu.com/ubuntu xenial-security/universe Sources [57.4 kB]
Get:5 http://archive.ubuntu.com/ubuntu xenial-backports InRelease [102 kB]
Get:6 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [547 kB]
Get:7 http://security.ubuntu.com/ubuntu xenial-security/restricted amd64 Packages [12.7 kB]
Get:8 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 Packages [250 kB]
Get:9 http://security.ubuntu.com/ubuntu xenial-security/multiverse amd64 Packages [3492 B]
Get:10 http://archive.ubuntu.com/ubuntu xenial/universe Sources [9802 kB]
Get:11 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages [1558 kB]
Get:12 http://archive.ubuntu.com/ubuntu xenial/restricted amd64 Packages [14.1 kB]
Get:13 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages [9827 kB]
Get:13 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages [9827 kB]
Get:14 http://archive.ubuntu.com/ubuntu xenial/multiverse amd64 Packages [176 kB]
Get:15 http://archive.ubuntu.com/ubuntu xenial-updates/universe Sources [237 kB]
Get:16 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [912 kB]
Get:17 http://archive.ubuntu.com/ubuntu xenial-updates/restricted amd64 Packages [13.1 kB]
Get:18 http://archive.ubuntu.com/ubuntu xenial-updates/universe amd64 Packages [741 kB]
Get:19 http://archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 Packages [18.5 kB]
Get:20 http://archive.ubuntu.com/ubuntu xenial-backports/main amd64 Packages [5162 B]
Get:21 http://archive.ubuntu.com/ubuntu xenial-backports/universe amd64 Packages [7146 B]
Fetched 15.5 MB in 1min 29s (173 kB/s)
Reading package lists... Done
+ apt-get install -y --no-install-recommends apt-utils sudo curl unzip software-properties-common apt-transport-https git bzip2 wget
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
ca-certificates dh-python distro-info-data gir1.2-glib-2.0 git-man iso-codes libapt-inst2.0 libasn1-8-heimdal
libcurl3-gnutls libdbus-1-3 libdbus-glib-1-2 liberror-perl libexpat1 libffi6 libgdbm3 libgirepository-1.0-1
libglib2.0-0 libgmp10 libgnutls30 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3
libkrb5support0 libldap-2.4-2 libmpdec2 libnettle6 libp11-kit0 libperl5.22 libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssl1.0.0 libtasn1-6
libwind0-heimdal lsb-release mime-support openssl perl perl-modules-5.22 python-apt-common python3 python3-apt
python3-dbus python3-gi python3-minimal python3-pycurl python3-software-properties python3.5 python3.5-minimal
Suggested packages:
bzip2-doc libdpkg-perl gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-el git-email git-gui gitk gitweb
git-arch git-cvs git-mediawiki git-svn isoquery gnutls-bin krb5-doc krb5-user lsb perl-doc libterm-readline-gnu-perl
| libterm-readline-perl-perl make python3-doc python3-tk python3-venv python3-apt-dbg python-apt-doc python-dbus-doc
python3-dbus-dbg libcurl4-gnutls-dev python-pycurl-doc python3-pycurl-dbg python3.5-venv python3.5-doc binutils
binfmt-support zip
Recommended packages:
patch less rsync ssh-client dbus libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libsasl2-modules file
netbase rename unattended-upgrades
The following NEW packages will be installed:
apt-transport-https apt-utils bzip2 ca-certificates curl dh-python distro-info-data gir1.2-glib-2.0 git git-man
iso-codes libapt-inst2.0 libasn1-8-heimdal libcurl3-gnutls libdbus-1-3 libdbus-glib-1-2 liberror-perl libexpat1 libffi6
libgdbm3 libgirepository-1.0-1 libglib2.0-0 libgmp10 libgnutls30 libgssapi-krb5-2 libgssapi3-heimdal
libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libk5crypto3
libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libmpdec2 libnettle6 libp11-kit0 libperl5.22
libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db
libsqlite3-0 libssl1.0.0 libtasn1-6 libwind0-heimdal lsb-release mime-support openssl perl perl-modules-5.22
python-apt-common python3 python3-apt python3-dbus python3-gi python3-minimal python3-pycurl
python3-software-properties python3.5 python3.5-minimal software-properties-common sudo unzip wget
0 upgraded, 72 newly installed, 0 to remove and 6 not upgraded.
Need to get 25.6 MB of archives.
After this operation, 134 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu4.10 [1083 kB]
Get:2 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython3.5-minimal amd64 3.5.2-2ubuntu0~16.04.4 [523 kB]
Get:3 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libexpat1 amd64 2.1.0-7ubuntu0.16.04.3 [71.2 kB]
Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python3.5-minimal amd64 3.5.2-2ubuntu0~16.04.4 [1597 kB]
Get:5 http://archive.ubuntu.com/ubuntu xenial/main amd64 python3-minimal amd64 3.5.1-3 [23.3 kB]
Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 mime-support all 3.59ubuntu1 [31.0 kB]
Get:7 http://archive.ubuntu.com/ubuntu xenial/main amd64 libmpdec2 amd64 2.4.2-1 [82.6 kB]
Get:8 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsqlite3-0 amd64 3.11.0-1ubuntu1 [396 kB]
Get:9 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython3.5-stdlib amd64 3.5.2-2ubuntu0~16.04.4 [2132 kB]
Get:10 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python3.5 amd64 3.5.2-2ubuntu0~16.04.4 [165 kB]
Get:11 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpython3-stdlib amd64 3.5.1-3 [6818 B]
Get:12 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 dh-python all 2.20151103ubuntu1.1 [74.1 kB]
Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 python3 amd64 3.5.1-3 [8710 B]
Get:14 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgdbm3 amd64 1.8.3-13.1 [16.9 kB]
Get:15 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 perl-modules-5.22 all 5.22.1-9ubuntu0.2 [2661 kB]
Get:16 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libperl5.22 amd64 5.22.1-9ubuntu0.2 [3391 kB]
Get:17 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 perl amd64 5.22.1-9ubuntu0.2 [237 kB]
Get:18 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapt-inst2.0 amd64 1.2.24 [55.4 kB]
Get:19 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 apt-utils amd64 1.2.24 [197 kB]
Get:20 http://archive.ubuntu.com/ubuntu xenial/main amd64 bzip2 amd64 1.0.6-8 [32.7 kB]
Get:21 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 distro-info-data all 0.28ubuntu0.7 [4334 B]
Get:22 http://archive.ubuntu.com/ubuntu xenial/main amd64 libffi6 amd64 3.2.1-4 [17.8 kB]
Get:23 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgmp10 amd64 2:6.1.0+dfsg-2 [240 kB]
Get:24 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libnettle6 amd64 3.2-1ubuntu0.16.04.1 [93.5 kB]
Get:25 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhogweed4 amd64 3.2-1ubuntu0.16.04.1 [136 kB]
Get:26 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.2 [46.5 kB]
Get:27 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libp11-kit0 amd64 0.23.2-5~ubuntu16.04.1 [105 kB]
Get:28 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtasn1-6 amd64 4.7-3ubuntu0.16.04.2 [43.3 kB]
Get:29 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgnutls30 amd64 3.4.10-4ubuntu1.4 [548 kB]
Get:30 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 lsb-release all 9.20160110ubuntu0.2 [11.8 kB]
Get:31 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 sudo amd64 1.8.16-0ubuntu1.5 [390 kB]
Get:32 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5support0 amd64 1.13.2+dfsg-5ubuntu2 [30.8 kB]
Get:33 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libk5crypto3 amd64 1.13.2+dfsg-5ubuntu2 [81.2 kB]
Get:34 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkeyutils1 amd64 1.5.9-8ubuntu1 [9904 B]
Get:35 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5-3 amd64 1.13.2+dfsg-5ubuntu2 [273 kB]
Get:36 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgssapi-krb5-2 amd64 1.13.2+dfsg-5ubuntu2 [120 kB]
Get:37 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libroken18-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [41.4 kB]
Get:38 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libasn1-8-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [174 kB]
Get:39 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhcrypto4-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [85.0 kB]
Get:40 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libheimbase1-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [29.3 kB]
Get:41 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwind0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [47.8 kB]
Get:42 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhx509-5-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [107 kB]
Get:43 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5-26-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [202 kB]
Get:44 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libheimntlm0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [15.1 kB]
Get:45 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgssapi3-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [96.1 kB]
Get:46 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-14build1 [14.5 kB]
Get:47 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-14build1 [48.7 kB]
Get:48 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2ubuntu3.2 [160 kB]
Get:49 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d-1ubuntu0.1 [54.4 kB]
Get:50 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcurl3-gnutls amd64 7.47.0-1ubuntu2.5 [184 kB]
Get:51 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 apt-transport-https amd64 1.2.24 [26.1 kB]
Get:52 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 openssl amd64 1.0.2g-1ubuntu4.10 [492 kB]
Get:53 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 ca-certificates all 20170717~16.04.1 [168 kB]
Get:54 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libglib2.0-0 amd64 2.48.2-0ubuntu1 [1119 kB]
Get:55 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgirepository-1.0-1 amd64 1.46.0-3ubuntu1 [88.3 kB]
Get:56 http://archive.ubuntu.com/ubuntu xenial/main amd64 gir1.2-glib-2.0 amd64 1.46.0-3ubuntu1 [127 kB]
Get:57 http://archive.ubuntu.com/ubuntu xenial/main amd64 iso-codes all 3.65-1 [2268 kB]
Get:58 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdbus-1-3 amd64 1.10.6-1ubuntu3.3 [161 kB]
Get:59 http://archive.ubuntu.com/ubuntu xenial/main amd64 libdbus-glib-1-2 amd64 0.106-1 [67.1 kB]
Get:60 http://archive.ubuntu.com/ubuntu xenial/main amd64 python-apt-common all 1.1.0~beta1build1 [17.3 kB]
Get:61 http://archive.ubuntu.com/ubuntu xenial/main amd64 python3-apt amd64 1.1.0~beta1build1 [137 kB]
Get:62 http://archive.ubuntu.com/ubuntu xenial/main amd64 python3-dbus amd64 1.2.0-3 [83.1 kB]
Get:63 http://archive.ubuntu.com/ubuntu xenial/main amd64 python3-gi amd64 3.20.0-0ubuntu1 [153 kB]
Get:64 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 wget amd64 1.17.1-1ubuntu1.3 [299 kB]
Get:65 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 curl amd64 7.47.0-1ubuntu2.5 [138 kB]
Get:66 http://archive.ubuntu.com/ubuntu xenial/main amd64 liberror-perl all 0.17-1.2 [19.6 kB]
Get:67 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 git-man all 1:2.7.4-0ubuntu1.3 [736 kB]
Get:68 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 git amd64 1:2.7.4-0ubuntu1.3 [3102 kB]
Get:69 http://archive.ubuntu.com/ubuntu xenial/main amd64 python3-pycurl amd64 7.43.0-1ubuntu1 [42.3 kB]
Get:70 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python3-software-properties all 0.96.20.7 [20.3 kB]
Get:71 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 software-properties-common all 0.96.20.7 [9452 B]
Get:72 http://archive.ubuntu.com/ubuntu xenial/main amd64 unzip amd64 6.0-20ubuntu1 [158 kB]
Fetched 25.6 MB in 19s (1321 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libssl1.0.0:amd64.
(Reading database ... 4768 files and directories currently installed.)
Preparing to unpack .../libssl1.0.0_1.0.2g-1ubuntu4.10_amd64.deb ...
Unpacking libssl1.0.0:amd64 (1.0.2g-1ubuntu4.10) ...
Selecting previously unselected package libpython3.5-minimal:amd64.
Preparing to unpack .../libpython3.5-minimal_3.5.2-2ubuntu0~16.04.4_amd64.deb ...
Unpacking libpython3.5-minimal:amd64 (3.5.2-2ubuntu0~16.04.4) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.1.0-7ubuntu0.16.04.3_amd64.deb ...
Unpacking libexpat1:amd64 (2.1.0-7ubuntu0.16.04.3) ...
Selecting previously unselected package python3.5-minimal.
Preparing to unpack .../python3.5-minimal_3.5.2-2ubuntu0~16.04.4_amd64.deb ...
Unpacking python3.5-minimal (3.5.2-2ubuntu0~16.04.4) ...
Selecting previously unselected package python3-minimal.
Preparing to unpack .../python3-minimal_3.5.1-3_amd64.deb ...
Unpacking python3-minimal (3.5.1-3) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../mime-support_3.59ubuntu1_all.deb ...
Unpacking mime-support (3.59ubuntu1) ...
Selecting previously unselected package libmpdec2:amd64.
Preparing to unpack .../libmpdec2_2.4.2-1_amd64.deb ...
Unpacking libmpdec2:amd64 (2.4.2-1) ...
Selecting previously unselected package libsqlite3-0:amd64.
Preparing to unpack .../libsqlite3-0_3.11.0-1ubuntu1_amd64.deb ...
Unpacking libsqlite3-0:amd64 (3.11.0-1ubuntu1) ...
Selecting previously unselected package libpython3.5-stdlib:amd64.
Preparing to unpack .../libpython3.5-stdlib_3.5.2-2ubuntu0~16.04.4_amd64.deb ...
Unpacking libpython3.5-stdlib:amd64 (3.5.2-2ubuntu0~16.04.4) ...
Selecting previously unselected package python3.5.
Preparing to unpack .../python3.5_3.5.2-2ubuntu0~16.04.4_amd64.deb ...
Unpacking python3.5 (3.5.2-2ubuntu0~16.04.4) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../libpython3-stdlib_3.5.1-3_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.5.1-3) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../dh-python_2.20151103ubuntu1.1_all.deb ...
Unpacking dh-python (2.20151103ubuntu1.1) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Setting up libssl1.0.0:amd64 (1.0.2g-1ubuntu4.10) ...
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (Can't locate Term/ReadLine.pm in @INC (you may need to install the Term::ReadLine module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/perl5/Debconf/FrontEnd/Readline.pm line 7.)
debconf: falling back to frontend: Teletype
Setting up libpython3.5-minimal:amd64 (3.5.2-2ubuntu0~16.04.4) ...
Setting up libexpat1:amd64 (2.1.0-7ubuntu0.16.04.3) ...
Setting up python3.5-minimal (3.5.2-2ubuntu0~16.04.4) ...
Setting up python3-minimal (3.5.1-3) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Selecting previously unselected package python3.
(Reading database ... 5744 files and directories currently installed.)
Preparing to unpack .../python3_3.5.1-3_amd64.deb ...
Unpacking python3 (3.5.1-3) ...
Selecting previously unselected package libgdbm3:amd64.
Preparing to unpack .../libgdbm3_1.8.3-13.1_amd64.deb ...
Unpacking libgdbm3:amd64 (1.8.3-13.1) ...
Selecting previously unselected package perl-modules-5.22.
Preparing to unpack .../perl-modules-5.22_5.22.1-9ubuntu0.2_all.deb ...
Unpacking perl-modules-5.22 (5.22.1-9ubuntu0.2) ...
Selecting previously unselected package libperl5.22:amd64.
Preparing to unpack .../libperl5.22_5.22.1-9ubuntu0.2_amd64.deb ...
Unpacking libperl5.22:amd64 (5.22.1-9ubuntu0.2) ...
Selecting previously unselected package perl.
Preparing to unpack .../perl_5.22.1-9ubuntu0.2_amd64.deb ...
Unpacking perl (5.22.1-9ubuntu0.2) ...
Selecting previously unselected package libapt-inst2.0:amd64.
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Unpacking libapt-inst2.0:amd64 (1.2.24) ...
Selecting previously unselected package apt-utils.
Preparing to unpack .../apt-utils_1.2.24_amd64.deb ...
Unpacking apt-utils (1.2.24) ...
Selecting previously unselected package bzip2.
Preparing to unpack .../bzip2_1.0.6-8_amd64.deb ...
Unpacking bzip2 (1.0.6-8) ...
Selecting previously unselected package distro-info-data.
Preparing to unpack .../distro-info-data_0.28ubuntu0.7_all.deb ...
Unpacking distro-info-data (0.28ubuntu0.7) ...
Selecting previously unselected package libffi6:amd64.
Preparing to unpack .../libffi6_3.2.1-4_amd64.deb ...
Unpacking libffi6:amd64 (3.2.1-4) ...
Selecting previously unselected package libgmp10:amd64.
Preparing to unpack .../libgmp10_2%3a6.1.0+dfsg-2_amd64.deb ...
Unpacking libgmp10:amd64 (2:6.1.0+dfsg-2) ...
Selecting previously unselected package libnettle6:amd64.
Preparing to unpack .../libnettle6_3.2-1ubuntu0.16.04.1_amd64.deb ...
Unpacking libnettle6:amd64 (3.2-1ubuntu0.16.04.1) ...
Selecting previously unselected package libhogweed4:amd64.
Preparing to unpack .../libhogweed4_3.2-1ubuntu0.16.04.1_amd64.deb ...
Unpacking libhogweed4:amd64 (3.2-1ubuntu0.16.04.1) ...
Selecting previously unselected package libidn11:amd64.
Preparing to unpack .../libidn11_1.32-3ubuntu1.2_amd64.deb ...
Unpacking libidn11:amd64 (1.32-3ubuntu1.2) ...
Selecting previously unselected package libp11-kit0:amd64.
Preparing to unpack .../libp11-kit0_0.23.2-5~ubuntu16.04.1_amd64.deb ...
Unpacking libp11-kit0:amd64 (0.23.2-5~ubuntu16.04.1) ...
Selecting previously unselected package libtasn1-6:amd64.
Preparing to unpack .../libtasn1-6_4.7-3ubuntu0.16.04.2_amd64.deb ...
Unpacking libtasn1-6:amd64 (4.7-3ubuntu0.16.04.2) ...
Selecting previously unselected package libgnutls30:amd64.
Preparing to unpack .../libgnutls30_3.4.10-4ubuntu1.4_amd64.deb ...
Unpacking libgnutls30:amd64 (3.4.10-4ubuntu1.4) ...
Selecting previously unselected package lsb-release.
Preparing to unpack .../lsb-release_9.20160110ubuntu0.2_all.deb ...
Unpacking lsb-release (9.20160110ubuntu0.2) ...
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Unpacking unzip (6.0-20ubuntu1) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Setting up mime-support (3.59ubuntu1) ...
Setting up libmpdec2:amd64 (2.4.2-1) ...
Setting up libsqlite3-0:amd64 (3.11.0-1ubuntu1) ...
Setting up libpython3.5-stdlib:amd64 (3.5.2-2ubuntu0~16.04.4) ...
Setting up python3.5 (3.5.2-2ubuntu0~16.04.4) ...
Setting up libpython3-stdlib:amd64 (3.5.1-3) ...
Setting up libgdbm3:amd64 (1.8.3-13.1) ...
Setting up perl-modules-5.22 (5.22.1-9ubuntu0.2) ...
Setting up libperl5.22:amd64 (5.22.1-9ubuntu0.2) ...
Setting up perl (5.22.1-9ubuntu0.2) ...
update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode
Setting up libapt-inst2.0:amd64 (1.2.24) ...
Setting up apt-utils (1.2.24) ...
Setting up bzip2 (1.0.6-8) ...
Setting up distro-info-data (0.28ubuntu0.7) ...
Setting up libffi6:amd64 (3.2.1-4) ...
Setting up libgmp10:amd64 (2:6.1.0+dfsg-2) ...
Setting up libnettle6:amd64 (3.2-1ubuntu0.16.04.1) ...
Setting up libhogweed4:amd64 (3.2-1ubuntu0.16.04.1) ...
Setting up libidn11:amd64 (1.32-3ubuntu1.2) ...
Setting up libp11-kit0:amd64 (0.23.2-5~ubuntu16.04.1) ...
Setting up libtasn1-6:amd64 (4.7-3ubuntu0.16.04.2) ...
Setting up libgnutls30:amd64 (3.4.10-4ubuntu1.4) ...
Setting up sudo (1.8.16-0ubuntu1.5) ...
Setting up libkrb5support0:amd64 (1.13.2+dfsg-5ubuntu2) ...
Setting up libk5crypto3:amd64 (1.13.2+dfsg-5ubuntu2) ...
Setting up libkeyutils1:amd64 (1.5.9-8ubuntu1) ...
Setting up libkrb5-3:amd64 (1.13.2+dfsg-5ubuntu2) ...
Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-5ubuntu2) ...
Setting up libroken18-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libasn1-8-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libhcrypto4-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libheimbase1-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libwind0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libhx509-5-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libkrb5-26-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libheimntlm0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libgssapi3-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-14build1) ...
Setting up libsasl2-2:amd64 (2.1.26.dfsg1-14build1) ...
Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2ubuntu3.2) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d-1ubuntu0.1) ...
Setting up libcurl3-gnutls:amd64 (7.47.0-1ubuntu2.5) ...
Setting up apt-transport-https (1.2.24) ...
Setting up openssl (1.0.2g-1ubuntu4.10) ...
Setting up ca-certificates (20170717~16.04.1) ...
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76.)
debconf: falling back to frontend: Readline
Setting up libglib2.0-0:amd64 (2.48.2-0ubuntu1) ...
No schema files found: doing nothing.
Setting up libgirepository-1.0-1:amd64 (1.46.0-3ubuntu1) ...
Setting up gir1.2-glib-2.0:amd64 (1.46.0-3ubuntu1) ...
Setting up iso-codes (3.65-1) ...
Setting up libdbus-1-3:amd64 (1.10.6-1ubuntu3.3) ...
Setting up libdbus-glib-1-2:amd64 (0.106-1) ...
Setting up wget (1.17.1-1ubuntu1.3) ...
Setting up curl (7.47.0-1ubuntu2.5) ...
Setting up liberror-perl (0.17-1.2) ...
Setting up git-man (1:2.7.4-0ubuntu1.3) ...
Setting up git (1:2.7.4-0ubuntu1.3) ...
Setting up unzip (6.0-20ubuntu1) ...
Setting up python3 (3.5.1-3) ...
running python rtupdate hooks for python3.5...
running python post-rtupdate hooks for python3.5...
Setting up lsb-release (9.20160110ubuntu0.2) ...
Setting up python-apt-common (1.1.0~beta1build1) ...
Setting up python3-apt (1.1.0~beta1build1) ...
Setting up python3-dbus (1.2.0-3) ...
Setting up python3-gi (3.20.0-0ubuntu1) ...
Setting up python3-pycurl (7.43.0-1ubuntu1) ...
Setting up python3-software-properties (0.96.20.7) ...
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Setting up dh-python (2.20151103ubuntu1.1) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Processing triggers for ca-certificates (20170717~16.04.1) ...
Updating certificates in /etc/ssl/certs...
148 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+ apt-get dist-upgrade -y
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
dpkg libc-bin libc6 libdb5.3 libseccomp2 multiarch-support
6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 6020 kB of archives.
After this operation, 30.7 kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 dpkg amd64 1.18.4ubuntu1.3 [2084 kB]
Get:2 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libc6 amd64 2.23-0ubuntu10 [2580 kB]
Get:3 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libc-bin amd64 2.23-0ubuntu10 [641 kB]
Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdb5.3 amd64 5.3.28-11ubuntu0.1 [670 kB]
Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libseccomp2 amd64 2.3.1-2.1ubuntu2~16.04.1 [38.7 kB]
Get:6 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 multiarch-support amd64 2.23-0ubuntu10 [6826 B]
Fetched 6020 kB in 3s (1962 kB/s)
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76, <> line 6.)
debconf: falling back to frontend: Readline
Preconfiguring packages ...
(Reading database ... 9784 files and directories currently installed.)
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Unpacking dpkg (1.18.4ubuntu1.3) over (1.18.4ubuntu1.2) ...
Setting up dpkg (1.18.4ubuntu1.3) ...
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debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76.)
debconf: falling back to frontend: Readline
Unpacking libc6:amd64 (2.23-0ubuntu10) over (2.23-0ubuntu9) ...
Setting up libc6:amd64 (2.23-0ubuntu10) ...
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76.)
debconf: falling back to frontend: Readline
Processing triggers for libc-bin (2.23-0ubuntu9) ...
(Reading database ... 9784 files and directories currently installed.)
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Unpacking libc-bin (2.23-0ubuntu10) over (2.23-0ubuntu9) ...
Setting up libc-bin (2.23-0ubuntu10) ...
(Reading database ... 9784 files and directories currently installed.)
Preparing to unpack .../libdb5.3_5.3.28-11ubuntu0.1_amd64.deb ...
Unpacking libdb5.3:amd64 (5.3.28-11ubuntu0.1) over (5.3.28-11) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Setting up libdb5.3:amd64 (5.3.28-11ubuntu0.1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
(Reading database ... 9784 files and directories currently installed.)
Preparing to unpack .../libseccomp2_2.3.1-2.1ubuntu2~16.04.1_amd64.deb ...
Unpacking libseccomp2:amd64 (2.3.1-2.1ubuntu2~16.04.1) over (2.2.3-3ubuntu3) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Setting up libseccomp2:amd64 (2.3.1-2.1ubuntu2~16.04.1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
(Reading database ... 9784 files and directories currently installed.)
Preparing to unpack .../multiarch-support_2.23-0ubuntu10_amd64.deb ...
Unpacking multiarch-support (2.23-0ubuntu10) over (2.23-0ubuntu9) ...
Setting up multiarch-support (2.23-0ubuntu10) ...
+ echo 'export PATH=/opt/conda/bin:$PATH'
+ wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /root/miniconda.sh
+ /bin/bash /root/miniconda.sh -b -p /opt/conda
PREFIX=/opt/conda
installing: python-3.6.3-h6c0c0dc_5 ...
Python 3.6.3 :: Anaconda, Inc.
installing: ca-certificates-2017.08.26-h1d4fec5_0 ...
installing: conda-env-2.6.0-h36134e3_1 ...
installing: libgcc-ng-7.2.0-h7cc24e2_2 ...
installing: libstdcxx-ng-7.2.0-h7a57d05_2 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.0-h9df7e31_2 ...
installing: openssl-1.0.2n-hb7f436b_0 ...
installing: tk-8.6.7-hc745277_3 ...
installing: xz-5.2.3-h55aa19d_2 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-ha838bed_2 ...
installing: libedit-3.1-heed3624_0 ...
installing: readline-7.0-ha6073c6_4 ...
installing: sqlite-3.20.1-hb898158_2 ...
installing: asn1crypto-0.23.0-py36h4639342_0 ...
installing: certifi-2017.11.5-py36hf29ccca_0 ...
installing: chardet-3.0.4-py36h0f667ec_1 ...
installing: idna-2.6-py36h82fb2a8_1 ...
installing: pycosat-0.6.3-py36h0a5515d_0 ...
installing: pycparser-2.18-py36hf9f622e_1 ...
installing: pysocks-1.6.7-py36hd97a5b1_1 ...
installing: ruamel_yaml-0.11.14-py36ha2fb22d_2 ...
installing: six-1.11.0-py36h372c433_1 ...
installing: cffi-1.11.2-py36h2825082_0 ...
installing: setuptools-36.5.0-py36he42e2e1_0 ...
installing: cryptography-2.1.4-py36hd09be54_0 ...
installing: wheel-0.30.0-py36hfd4bba0_1 ...
installing: pip-9.0.1-py36h6c6f9ce_4 ...
installing: pyopenssl-17.5.0-py36h20ba746_0 ...
installing: urllib3-1.22-py36hbe7ace6_0 ...
installing: requests-2.18.4-py36he2e5f8d_1 ...
installing: conda-4.3.31-py36_0 ...
installation finished.
+ export PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ conda create -y -n beakerx 'python>=3' nodejs pandas openjdk maven
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /opt/conda/envs/beakerx:
The following NEW packages will be INSTALLED:
ca-certificates: 2017.08.26-h1d4fec5_0
certifi: 2017.11.5-py36hf29ccca_0
intel-openmp: 2018.0.0-hc7b2577_8
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc: 7.2.0-h69d50b8_2
libgcc-ng: 7.2.0-h7cc24e2_2
libgfortran-ng: 7.2.0-h9f7466a_2
libstdcxx-ng: 7.2.0-h7a57d05_2
maven: 3.5.0-0
mkl: 2018.0.1-h19d6760_4
ncurses: 6.0-h9df7e31_2
nodejs: 6.11.2-h3db8ef7_0
numpy: 1.14.0-py36h3dfced4_0
openjdk: 8.0.152-h46b5887_1
openssl: 1.0.2n-hb7f436b_0
pandas: 0.22.0-py36hf484d3e_0
pip: 9.0.1-py36h6c6f9ce_4
python: 3.6.4-hc3d631a_1
python-dateutil: 2.6.1-py36h88d3b88_1
pytz: 2017.3-py36h63b9c63_0
readline: 7.0-ha6073c6_4
setuptools: 38.4.0-py36_0
six: 1.11.0-py36h372c433_1
sqlite: 3.21.0-h1bed415_0
tk: 8.6.7-hc745277_3
wheel: 0.30.0-py36hfd4bba0_1
xz: 5.2.3-h55aa19d_2
zlib: 1.2.11-ha838bed_2
intel-openmp-2 100% |###########################################################################| Time: 0:00:00 1.17 MB/s
libgfortran-ng 100% |###########################################################################| Time: 0:00:00 1.71 MB/s
openjdk-8.0.15 100% |###########################################################################| Time: 0:01:12 1.87 MB/s
libgcc-7.2.0-h 100% |###########################################################################| Time: 0:00:00 1.98 MB/s
maven-3.5.0-0. 100% |###########################################################################| Time: 0:00:04 1.74 MB/s
mkl-2018.0.1-h 100% |###########################################################################| Time: 0:02:06 1.53 MB/s
nodejs-6.11.2- 100% |###########################################################################| Time: 0:00:06 1.75 MB/s
sqlite-3.21.0- 100% |###########################################################################| Time: 0:00:00 1.87 MB/s
python-3.6.4-h 100% |###########################################################################| Time: 0:00:14 2.15 MB/s
numpy-1.14.0-p 100% |###########################################################################| Time: 0:00:01 2.55 MB/s
pytz-2017.3-py 100% |###########################################################################| Time: 0:00:00 3.35 MB/s
python-dateuti 100% |###########################################################################| Time: 0:00:00 3.67 MB/s
setuptools-38. 100% |###########################################################################| Time: 0:00:00 2.84 MB/s
pandas-0.22.0- 100% |###########################################################################| Time: 0:00:03 2.95 MB/s
#
# To activate this environment, use:
# > source activate beakerx
#
# To deactivate an active environment, use:
# > source deactivate
#
+ conda install -y -n beakerx -c conda-forge ipywidgets pyzmq pytest beakerx
Fetching package metadata .............
Solving package specifications: .
Package plan for installation in environment /opt/conda/envs/beakerx:
The following NEW packages will be INSTALLED:
attrs: 17.4.0-py_0 conda-forge
beakerx: 0.11.1-py36_1 conda-forge
bleach: 2.0.0-py36_0 conda-forge
dbus: 1.10.22-0 conda-forge
decorator: 4.1.2-py36_0 conda-forge
entrypoints: 0.2.3-py36_1 conda-forge
expat: 2.2.5-0 conda-forge
fontconfig: 2.12.1-4 conda-forge
freetype: 2.7-1 conda-forge
gettext: 0.19.7-1 conda-forge
glib: 2.55.0-0 conda-forge
gmp: 6.1.2-0 conda-forge
gst-plugins-base: 1.8.0-0 conda-forge
gstreamer: 1.8.0-1 conda-forge
html5lib: 1.0.1-py_0 conda-forge
icu: 58.2-0 conda-forge
ipykernel: 4.7.0-py36_0 conda-forge
ipython: 6.2.1-py36_1 conda-forge
ipython_genutils: 0.2.0-py36_0 conda-forge
ipywidgets: 7.1.1-py36_0 conda-forge
jedi: 0.10.2-py36_0 conda-forge
jinja2: 2.10-py36_0 conda-forge
jpeg: 9b-2 conda-forge
jsonschema: 2.6.0-py36_0 conda-forge
jupyter: 1.0.0-py36_0 conda-forge
jupyter_client: 5.2.1-py36_0 conda-forge
jupyter_console: 5.2.0-py36_0 conda-forge
jupyter_core: 4.4.0-py_0 conda-forge
libiconv: 1.15-0 conda-forge
libpng: 1.6.34-0 conda-forge
libsodium: 1.0.15-1 conda-forge
libxcb: 1.12-1 conda-forge
libxml2: 2.9.7-0 conda-forge
markupsafe: 1.0-py36_0 conda-forge
mistune: 0.8.3-py_0 conda-forge
nbconvert: 5.3.1-py_1 conda-forge
nbformat: 4.4.0-py36_0 conda-forge
notebook: 5.3.1-py36_1 conda-forge
pandoc: 2.1.1-0 conda-forge
pandocfilters: 1.4.1-py36_0 conda-forge
pcre: 8.39-0 conda-forge
pexpect: 4.3.1-py36_0 conda-forge
pickleshare: 0.7.4-py36_0 conda-forge
pluggy: 0.6.0-py_0 conda-forge
prompt_toolkit: 1.0.15-py36_0 conda-forge
ptyprocess: 0.5.2-py36_0 conda-forge
py: 1.5.2-py_0 conda-forge
pygments: 2.2.0-py36_0 conda-forge
pyqt: 5.6.0-py36_4 conda-forge
pytest: 3.3.2-py36_0 conda-forge
pyzmq: 16.0.2-py36_3 conda-forge
qt: 5.6.2-3 conda-forge
qtconsole: 4.3.1-py36_0 conda-forge
send2trash: 1.4.2-py_0 conda-forge
simplegeneric: 0.8.1-py36_0 conda-forge
sip: 4.18-py36_1 conda-forge
terminado: 0.8.1-py36_0 conda-forge
testpath: 0.3.1-py36_0 conda-forge
tornado: 4.5.3-py36_0 conda-forge
traitlets: 4.3.2-py36_0 conda-forge
wcwidth: 0.1.7-py36_0 conda-forge
webencodings: 0.5-py36_0 conda-forge
widgetsnbextension: 3.1.3-py36_0 conda-forge
xorg-libxau: 1.0.8-3 conda-forge
xorg-libxdmcp: 1.1.2-3 conda-forge
zeromq: 4.2.1-1 conda-forge
The following packages will be DOWNGRADED:
openjdk: 8.0.152-h46b5887_1 --> 8.0.121-1
expat-2.2.5-0. 100% |###########################################################################| Time: 0:00:00 685.17 kB/s
gettext-0.19.7 100% |###########################################################################| Time: 0:00:04 1.43 MB/s
gmp-6.1.2-0.ta 100% |###########################################################################| Time: 0:00:00 1.28 MB/s
icu-58.2-0.tar 100% |###########################################################################| Time: 0:00:16 1.44 MB/s
jpeg-9b-2.tar. 100% |###########################################################################| Time: 0:00:00 1.55 MB/s
libiconv-1.15- 100% |###########################################################################| Time: 0:00:01 1.31 MB/s
libsodium-1.0. 100% |###########################################################################| Time: 0:00:01 1.12 MB/s
openjdk-8.0.12 100% |###########################################################################| Time: 0:00:28 2.40 MB/s
pcre-8.39-0.ta 100% |###########################################################################| Time: 0:00:01 723.34 kB/s
xorg-libxau-1. 100% |###########################################################################| Time: 0:00:00 573.57 kB/s
xorg-libxdmcp- 100% |###########################################################################| Time: 0:00:00 505.58 kB/s
dbus-1.10.22-0 100% |###########################################################################| Time: 0:00:01 1.08 MB/s
libxcb-1.12-1. 100% |###########################################################################| Time: 0:00:00 806.12 kB/s
zeromq-4.2.1-1 100% |###########################################################################| Time: 0:00:00 1.39 MB/s
glib-2.55.0-0. 100% |###########################################################################| Time: 0:00:06 1.37 MB/s
libpng-1.6.34- 100% |###########################################################################| Time: 0:00:00 811.73 kB/s
libxml2-2.9.7- 100% |###########################################################################| Time: 0:00:03 1.36 MB/s
pandoc-2.1.1-0 100% |###########################################################################| Time: 0:00:19 1.10 MB/s
freetype-2.7-1 100% |###########################################################################| Time: 0:00:02 1.18 MB/s
gstreamer-1.8. 100% |###########################################################################| Time: 0:00:02 1.28 MB/s
fontconfig-2.1 100% |###########################################################################| Time: 0:00:00 1.11 MB/s
gst-plugins-ba 100% |###########################################################################| Time: 0:00:03 1.27 MB/s
attrs-17.4.0-p 100% |###########################################################################| Time: 0:00:00 992.72 kB/s
decorator-4.1. 100% |###########################################################################| Time: 0:00:00 572.78 kB/s
entrypoints-0. 100% |###########################################################################| Time: 0:00:00 441.60 kB/s
ipython_genuti 100% |###########################################################################| Time: 0:00:00 266.30 kB/s
jedi-0.10.2-py 100% |###########################################################################| Time: 0:00:00 574.74 kB/s
jsonschema-2.6 100% |###########################################################################| Time: 0:00:00 560.60 kB/s
markupsafe-1.0 100% |###########################################################################| Time: 0:00:00 287.65 kB/s
mistune-0.8.3- 100% |###########################################################################| Time: 0:00:00 713.25 kB/s
pandocfilters- 100% |###########################################################################| Time: 0:00:00 438.06 kB/s
pickleshare-0. 100% |###########################################################################| Time: 0:00:00 488.50 kB/s
pluggy-0.6.0-p 100% |###########################################################################| Time: 0:00:00 218.37 kB/s
ptyprocess-0.5 100% |###########################################################################| Time: 0:00:00 194.17 kB/s
py-1.5.2-py_0. 100% |###########################################################################| Time: 0:00:00 297.42 kB/s
pyzmq-16.0.2-p 100% |###########################################################################| Time: 0:00:00 1.03 MB/s
qt-5.6.2-3.tar 100% |###########################################################################| Time: 0:00:34 1.36 MB/s
send2trash-1.4 100% |###########################################################################| Time: 0:00:00 499.29 kB/s
simplegeneric- 100% |###########################################################################| Time: 0:00:00 381.54 kB/s
sip-4.18-py36_ 100% |###########################################################################| Time: 0:00:00 560.62 kB/s
testpath-0.3.1 100% |###########################################################################| Time: 0:00:00 546.72 kB/s
tornado-4.5.3- 100% |###########################################################################| Time: 0:00:00 825.94 kB/s
wcwidth-0.1.7- 100% |###########################################################################| Time: 0:00:00 834.26 kB/s
webencodings-0 100% |###########################################################################| Time: 0:00:00 747.65 kB/s
html5lib-1.0.1 100% |###########################################################################| Time: 0:00:00 404.68 kB/s
pexpect-4.3.1- 100% |###########################################################################| Time: 0:00:00 579.44 kB/s
pyqt-5.6.0-py3 100% |###########################################################################| Time: 0:00:04 1.30 MB/s
terminado-0.8. 100% |###########################################################################| Time: 0:00:00 1.14 MB/s
traitlets-4.3. 100% |###########################################################################| Time: 0:00:00 763.08 kB/s
bleach-2.0.0-p 100% |###########################################################################| Time: 0:00:00 727.57 kB/s
jinja2-2.10-py 100% |###########################################################################| Time: 0:00:00 480.78 kB/s
jupyter_core-4 100% |###########################################################################| Time: 0:00:00 384.31 kB/s
pygments-2.2.0 100% |###########################################################################| Time: 0:00:01 1.04 MB/s
pytest-3.3.2-p 100% |###########################################################################| Time: 0:00:00 1.27 MB/s
jupyter_client 100% |###########################################################################| Time: 0:00:00 568.76 kB/s
nbformat-4.4.0 100% |###########################################################################| Time: 0:00:00 652.29 kB/s
prompt_toolkit 100% |###########################################################################| Time: 0:00:00 599.63 kB/s
ipython-6.2.1- 100% |###########################################################################| Time: 0:00:01 1.01 MB/s
nbconvert-5.3. 100% |###########################################################################| Time: 0:00:00 793.05 kB/s
ipykernel-4.7. 100% |###########################################################################| Time: 0:00:00 588.88 kB/s
jupyter_consol 100% |###########################################################################| Time: 0:00:00 757.04 kB/s
notebook-5.3.1 100% |###########################################################################| Time: 0:00:05 1.30 MB/s
qtconsole-4.3. 100% |###########################################################################| Time: 0:00:00 596.06 kB/s
widgetsnbexten 100% |###########################################################################| Time: 0:00:01 1.16 MB/s
ipywidgets-7.1 100% |###########################################################################| Time: 0:00:00 1.29 MB/s
jupyter-1.0.0- 100% |###########################################################################| Time: 0:00:00 156.08 kB/s
beakerx-0.11.1 100% |###########################################################################| Time: 0:01:19 1.33 MB/s
+ /opt/conda/envs/beakerx/bin/beakerx-install
Installing /opt/conda/envs/beakerx/lib/python3.6/site-packages/beakerx/static -> beakerx
Symlinking: /opt/conda/envs/beakerx/share/jupyter/nbextensions/beakerx -> /opt/conda/envs/beakerx/lib/python3.6/site-packages/beakerx/static
- Validating: OK
Installing /opt/conda/envs/beakerx/lib/python3.6/site-packages/beakerx/static -> beakerx
- Validating: OK
To initialize this nbextension in the browser every time the notebook (or other app) loads:
jupyter nbextension enable beakerx --py --sys-prefix
Enabling tree extension beakerx/tree...
- Validating: OK
Enabling notebook extension beakerx/extension...
- Validating: OK
Enabling: beakerx
- Writing config: /opt/conda/envs/beakerx/etc/jupyter
- Validating...
beakerx OK
[InstallKernelSpec] Installed kernelspec scala in /opt/conda/envs/beakerx/share/jupyter/kernels/scala
[InstallKernelSpec] Installed kernelspec java in /opt/conda/envs/beakerx/share/jupyter/kernels/java
[InstallKernelSpec] Installed kernelspec clojure in /opt/conda/envs/beakerx/share/jupyter/kernels/clojure
[InstallKernelSpec] Installed kernelspec groovy in /opt/conda/envs/beakerx/share/jupyter/kernels/groovy
[InstallKernelSpec] Installed kernelspec sql in /opt/conda/envs/beakerx/share/jupyter/kernels/sql
[InstallKernelSpec] Installed kernelspec kotlin in /opt/conda/envs/beakerx/share/jupyter/kernels/kotlin
(beakerx) ~/src/beakerx(master)$ cat install_test
#!/bin/bash
set -ex
apt-get update
apt-get install -y --no-install-recommends apt-utils sudo curl unzip software-properties-common apt-transport-https git bzip2 wget
apt-get dist-upgrade -y
echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
/bin/bash ~/miniconda.sh -b -p /opt/conda
export PATH=/opt/conda/bin:$PATH
conda create -y -n beakerx 'python>=3' nodejs pandas openjdk maven
conda install -y -n beakerx -c conda-forge ipywidgets pyzmq pytest beakerx
@jmsdnns
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jmsdnns commented Jan 24, 2018

Not entirely relevant to twosigma/beakerx#6715, but I noticed this log still lists jedi 0.10.2, so I went to check on the status of jedi in conda-forge and it seems they got halfway to releasing a new version and then didn't complete it.

I asked them to finish doing that: conda-forge/jedi-feedstock#6

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