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April 1, 2019 12:09
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test_marker_overlap heisenbug log output
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| travis_fold:start:worker_info | |
| [0K[33;1mWorker information[0m | |
| hostname: 4c70b58b-1d92-4cdb-8dc0-547cc4c52f41@1.production-1-worker-org-gce-xd4f | |
| version: v6.2.0 https://github.com/travis-ci/worker/tree/5e5476e01646095f48eec13196fdb3faf8f5cbf7 | |
| instance: travis-job-1c73a386-5e3e-4462-9423-877511d99d2d travis-ci-garnet-trusty-1512502259-986baf0 (via amqp) | |
| startup: 6.583484338s | |
| travis_fold:end:worker_info | |
| [0Ktravis_fold:start:system_info | |
| [0K[33;1mBuild system information[0m | |
| Build language: python | |
| Build group: stable | |
| Build dist: trusty | |
| Build id: 514097605 | |
| Job id: 514097606 | |
| Runtime kernel version: 4.4.0-101-generic | |
| travis-build version: d6b12fc73 | |
| [34m[1mBuild image provisioning date and time[0m | |
| Tue Dec 5 19:58:13 UTC 2017 | |
| [34m[1mOperating System Details[0m | |
| Distributor ID: Ubuntu | |
| Description: Ubuntu 14.04.5 LTS | |
| Release: 14.04 | |
| Codename: trusty | |
| [34m[1mCookbooks Version[0m | |
| 7c2c6a6 https://github.com/travis-ci/travis-cookbooks/tree/7c2c6a6 | |
| [34m[1mgit version[0m | |
| git version 2.15.1 | |
| [34m[1mbash version[0m | |
| GNU bash, version 4.3.11(1)-release (x86_64-pc-linux-gnu) | |
| [34m[1mgcc version[0m | |
| gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4 | |
| Copyright (C) 2013 Free Software Foundation, Inc. | |
| This is free software; see the source for copying conditions. There is NO | |
| warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | |
| [34m[1mdocker version[0m | |
| Client: | |
| Version: 17.09.0-ce | |
| API version: 1.32 | |
| Go version: go1.8.3 | |
| Git commit: afdb6d4 | |
| Built: Tue Sep 26 22:42:38 2017 | |
| OS/Arch: linux/amd64 | |
| Server: | |
| Version: 17.09.0-ce | |
| API version: 1.32 (minimum version 1.12) | |
| Go version: go1.8.3 | |
| Git commit: afdb6d4 | |
| Built: Tue Sep 26 22:41:20 2017 | |
| OS/Arch: linux/amd64 | |
| Experimental: false | |
| [34m[1mclang version[0m | |
| clang version 5.0.0 (tags/RELEASE_500/final) | |
| Target: x86_64-unknown-linux-gnu | |
| Thread model: posix | |
| InstalledDir: /usr/local/clang-5.0.0/bin | |
| [34m[1mjq version[0m | |
| jq-1.5 | |
| [34m[1mbats version[0m | |
| Bats 0.4.0 | |
| [34m[1mshellcheck version[0m | |
| 0.4.6 | |
| [34m[1mshfmt version[0m | |
| v2.0.0 | |
| [34m[1mccache version[0m | |
| ccache version 3.1.9 | |
| Copyright (C) 2002-2007 Andrew Tridgell | |
| Copyright (C) 2009-2011 Joel Rosdahl | |
| This program is free software; you can redistribute it and/or modify it under | |
| the terms of the GNU General Public License as published by the Free Software | |
| Foundation; either version 3 of the License, or (at your option) any later | |
| version. | |
| [34m[1mcmake version[0m | |
| cmake version 3.9.2 | |
| CMake suite maintained and supported by Kitware (kitware.com/cmake). | |
| [34m[1mheroku version[0m | |
| heroku-cli/6.14.39-addc925 (linux-x64) node-v9.2.0 | |
| [34m[1mimagemagick version[0m | |
| Version: ImageMagick 6.7.7-10 2017-07-31 Q16 http://www.imagemagick.org | |
| [34m[1mmd5deep version[0m | |
| 4.2 | |
| [34m[1mmercurial version[0m | |
| Mercurial Distributed SCM (version 4.2.2) | |
| (see https://mercurial-scm.org for more information) | |
| Copyright (C) 2005-2017 Matt Mackall and others | |
| This is free software; see the source for copying conditions. There is NO | |
| warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | |
| [34m[1mmysql version[0m | |
| mysql Ver 14.14 Distrib 5.6.33, for debian-linux-gnu (x86_64) using EditLine wrapper | |
| [34m[1mopenssl version[0m | |
| OpenSSL 1.0.1f 6 Jan 2014 | |
| [34m[1mpacker version[0m | |
| Packer v1.0.2 | |
| Your version of Packer is out of date! The latest version | |
| is 1.1.2. You can update by downloading from www.packer.io | |
| [34m[1mpostgresql client version[0m | |
| psql (PostgreSQL) 9.6.6 | |
| [34m[1mragel version[0m | |
| Ragel State Machine Compiler version 6.8 Feb 2013 | |
| Copyright (c) 2001-2009 by Adrian Thurston | |
| [34m[1msubversion version[0m | |
| svn, version 1.8.8 (r1568071) | |
| compiled Aug 10 2017, 17:20:39 on x86_64-pc-linux-gnu | |
| Copyright (C) 2013 The Apache Software Foundation. | |
| This software consists of contributions made by many people; | |
| see the NOTICE file for more information. | |
| Subversion is open source software, see http://subversion.apache.org/ | |
| The following repository access (RA) modules are available: | |
| * ra_svn : Module for accessing a repository using the svn network protocol. | |
| - with Cyrus SASL authentication | |
| - handles 'svn' scheme | |
| * ra_local : Module for accessing a repository on local disk. | |
| - handles 'file' scheme | |
| * ra_serf : Module for accessing a repository via WebDAV protocol using serf. | |
| - using serf 1.3.3 | |
| - handles 'http' scheme | |
| - handles 'https' scheme | |
| [34m[1msudo version[0m | |
| Sudo version 1.8.9p5 | |
| Configure options: --prefix=/usr -v --with-all-insults --with-pam --with-fqdn --with-logging=syslog --with-logfac=authpriv --with-env-editor --with-editor=/usr/bin/editor --with-timeout=15 --with-password-timeout=0 --with-passprompt=[sudo] password for %p: --without-lecture --with-tty-tickets --disable-root-mailer --enable-admin-flag --with-sendmail=/usr/sbin/sendmail --with-timedir=/var/lib/sudo --mandir=/usr/share/man --libexecdir=/usr/lib/sudo --with-sssd --with-sssd-lib=/usr/lib/x86_64-linux-gnu --with-selinux | |
| Sudoers policy plugin version 1.8.9p5 | |
| Sudoers file grammar version 43 | |
| Sudoers path: /etc/sudoers | |
| Authentication methods: 'pam' | |
| Syslog facility if syslog is being used for logging: authpriv | |
| Syslog priority to use when user authenticates successfully: notice | |
| Syslog priority to use when user authenticates unsuccessfully: alert | |
| Send mail if the user is not in sudoers | |
| Use a separate timestamp for each user/tty combo | |
| Lecture user the first time they run sudo | |
| Root may run sudo | |
| Allow some information gathering to give useful error messages | |
| Require fully-qualified hostnames in the sudoers file | |
| Visudo will honor the EDITOR environment variable | |
| Set the LOGNAME and USER environment variables | |
| Length at which to wrap log file lines (0 for no wrap): 80 | |
| Authentication timestamp timeout: 15.0 minutes | |
| Password prompt timeout: 0.0 minutes | |
| Number of tries to enter a password: 3 | |
| Umask to use or 0777 to use user's: 022 | |
| Path to mail program: /usr/sbin/sendmail | |
| Flags for mail program: -t | |
| Address to send mail to: root | |
| Subject line for mail messages: *** SECURITY information for %h *** | |
| Incorrect password message: Sorry, try again. | |
| Path to authentication timestamp dir: /var/lib/sudo | |
| Default password prompt: [sudo] password for %p: | |
| Default user to run commands as: root | |
| Value to override user's $PATH with: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin | |
| Path to the editor for use by visudo: /usr/bin/editor | |
| When to require a password for 'list' pseudocommand: any | |
| When to require a password for 'verify' pseudocommand: all | |
| File descriptors >= 3 will be closed before executing a command | |
| Environment variables to check for sanity: | |
| TZ | |
| TERM | |
| LINGUAS | |
| LC_* | |
| LANGUAGE | |
| LANG | |
| COLORTERM | |
| Environment variables to remove: | |
| RUBYOPT | |
| RUBYLIB | |
| PYTHONUSERBASE | |
| PYTHONINSPECT | |
| PYTHONPATH | |
| PYTHONHOME | |
| TMPPREFIX | |
| ZDOTDIR | |
| READNULLCMD | |
| NULLCMD | |
| FPATH | |
| PERL5DB | |
| PERL5OPT | |
| PERL5LIB | |
| PERLLIB | |
| PERLIO_DEBUG | |
| JAVA_TOOL_OPTIONS | |
| SHELLOPTS | |
| GLOBIGNORE | |
| PS4 | |
| BASH_ENV | |
| ENV | |
| TERMCAP | |
| TERMPATH | |
| TERMINFO_DIRS | |
| TERMINFO | |
| _RLD* | |
| LD_* | |
| PATH_LOCALE | |
| NLSPATH | |
| HOSTALIASES | |
| RES_OPTIONS | |
| LOCALDOMAIN | |
| CDPATH | |
| IFS | |
| Environment variables to preserve: | |
| JAVA_HOME | |
| TRAVIS | |
| CI | |
| DEBIAN_FRONTEND | |
| XAUTHORIZATION | |
| XAUTHORITY | |
| PS2 | |
| PS1 | |
| PATH | |
| LS_COLORS | |
| KRB5CCNAME | |
| HOSTNAME | |
| HOME | |
| DISPLAY | |
| COLORS | |
| Locale to use while parsing sudoers: C | |
| Directory in which to store input/output logs: /var/log/sudo-io | |
| File in which to store the input/output log: %{seq} | |
| Add an entry to the utmp/utmpx file when allocating a pty | |
| PAM service name to use | |
| PAM service name to use for login shells | |
| Create a new PAM session for the command to run in | |
| Maximum I/O log sequence number: 0 | |
| Local IP address and netmask pairs: | |
| 10.240.0.28/255.255.255.255 | |
| 172.17.0.1/255.255.0.0 | |
| Sudoers I/O plugin version 1.8.9p5 | |
| [34m[1mgzip version[0m | |
| gzip 1.6 | |
| Copyright (C) 2007, 2010, 2011 Free Software Foundation, Inc. | |
| Copyright (C) 1993 Jean-loup Gailly. | |
| This is free software. You may redistribute copies of it under the terms of | |
| the GNU General Public License <http://www.gnu.org/licenses/gpl.html>. | |
| There is NO WARRANTY, to the extent permitted by law. | |
| Written by Jean-loup Gailly. | |
| [34m[1mzip version[0m | |
| Copyright (c) 1990-2008 Info-ZIP - Type 'zip "-L"' for software license. | |
| This is Zip 3.0 (July 5th 2008), by Info-ZIP. | |
| Currently maintained by E. Gordon. Please send bug reports to | |
| the authors using the web page at www.info-zip.org; see README for details. | |
| Latest sources and executables are at ftp://ftp.info-zip.org/pub/infozip, | |
| as of above date; see http://www.info-zip.org/ for other sites. | |
| Compiled with gcc 4.8.2 for Unix (Linux ELF) on Oct 21 2013. | |
| Zip special compilation options: | |
| USE_EF_UT_TIME (store Universal Time) | |
| BZIP2_SUPPORT (bzip2 library version 1.0.6, 6-Sept-2010) | |
| bzip2 code and library copyright (c) Julian R Seward | |
| (See the bzip2 license for terms of use) | |
| SYMLINK_SUPPORT (symbolic links supported) | |
| LARGE_FILE_SUPPORT (can read and write large files on file system) | |
| ZIP64_SUPPORT (use Zip64 to store large files in archives) | |
| UNICODE_SUPPORT (store and read UTF-8 Unicode paths) | |
| STORE_UNIX_UIDs_GIDs (store UID/GID sizes/values using new extra field) | |
| UIDGID_NOT_16BIT (old Unix 16-bit UID/GID extra field not used) | |
| [encryption, version 2.91 of 05 Jan 2007] (modified for Zip 3) | |
| Encryption notice: | |
| The encryption code of this program is not copyrighted and is | |
| put in the public domain. It was originally written in Europe | |
| and, to the best of our knowledge, can be freely distributed | |
| in both source and object forms from any country, including | |
| the USA under License Exception TSU of the U.S. Export | |
| Administration Regulations (section 740.13(e)) of 6 June 2002. | |
| Zip environment options: | |
| ZIP: [none] | |
| ZIPOPT: [none] | |
| [34m[1mvim version[0m | |
| VIM - Vi IMproved 7.4 (2013 Aug 10, compiled Nov 24 2016 16:43:18) | |
| Included patches: 1-52 | |
| Extra patches: 8.0.0056 | |
| Modified by [email protected] | |
| Compiled by buildd@ | |
| Huge version without GUI. Features included (+) or not (-): | |
| +acl +farsi +mouse_netterm +syntax | |
| +arabic +file_in_path +mouse_sgr +tag_binary | |
| +autocmd +find_in_path -mouse_sysmouse +tag_old_static | |
| -balloon_eval +float +mouse_urxvt -tag_any_white | |
| -browse +folding +mouse_xterm -tcl | |
| ++builtin_terms -footer +multi_byte +terminfo | |
| +byte_offset +fork() +multi_lang +termresponse | |
| +cindent +gettext -mzscheme +textobjects | |
| -clientserver -hangul_input +netbeans_intg +title | |
| -clipboard +iconv +path_extra -toolbar | |
| +cmdline_compl +insert_expand -perl +user_commands | |
| +cmdline_hist +jumplist +persistent_undo +vertsplit | |
| +cmdline_info +keymap +postscript +virtualedit | |
| +comments +langmap +printer +visual | |
| +conceal +libcall +profile +visualextra | |
| +cryptv +linebreak +python +viminfo | |
| +cscope +lispindent -python3 +vreplace | |
| +cursorbind +listcmds +quickfix +wildignore | |
| +cursorshape +localmap +reltime +wildmenu | |
| +dialog_con -lua +rightleft +windows | |
| +diff +menu -ruby +writebackup | |
| +digraphs +mksession +scrollbind -X11 | |
| -dnd +modify_fname +signs -xfontset | |
| -ebcdic +mouse +smartindent -xim | |
| +emacs_tags -mouseshape -sniff -xsmp | |
| +eval +mouse_dec +startuptime -xterm_clipboard | |
| +ex_extra +mouse_gpm +statusline -xterm_save | |
| +extra_search -mouse_jsbterm -sun_workshop -xpm | |
| system vimrc file: "$VIM/vimrc" | |
| user vimrc file: "$HOME/.vimrc" | |
| 2nd user vimrc file: "~/.vim/vimrc" | |
| user exrc file: "$HOME/.exrc" | |
| fall-back for $VIM: "/usr/share/vim" | |
| Compilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 | |
| Linking: gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--as-needed -o vim -lm -ltinfo -lnsl -lselinux -lacl -lattr -lgpm -ldl -L/usr/lib/python2.7/config-x86_64-linux-gnu -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions | |
| [34m[1miptables version[0m | |
| iptables v1.4.21 | |
| [34m[1mcurl version[0m | |
| curl 7.35.0 (x86_64-pc-linux-gnu) libcurl/7.35.0 OpenSSL/1.0.1f zlib/1.2.8 libidn/1.28 librtmp/2.3 | |
| [34m[1mwget version[0m | |
| GNU Wget 1.15 built on linux-gnu. | |
| [34m[1mrsync version[0m | |
| rsync version 3.1.0 protocol version 31 | |
| [34m[1mgimme version[0m | |
| v1.2.0 | |
| [34m[1mnvm version[0m | |
| 0.33.6 | |
| [34m[1mperlbrew version[0m | |
| /home/travis/perl5/perlbrew/bin/perlbrew - App::perlbrew/0.80 | |
| [34m[1mphpenv version[0m | |
| rbenv 1.1.1-25-g6aa70b6 | |
| [34m[1mrvm version[0m | |
| rvm 1.29.3 (latest) by Michal Papis, Piotr Kuczynski, Wayne E. Seguin [https://rvm.io] | |
| [34m[1mdefault ruby version[0m | |
| ruby 2.4.1p111 (2017-03-22 revision 58053) [x86_64-linux] | |
| [34m[1mCouchDB version[0m | |
| couchdb 1.6.1 | |
| [34m[1mElasticSearch version[0m | |
| 5.5.0 | |
| [34m[1mInstalled Firefox version[0m | |
| firefox 56.0.2 | |
| [34m[1mMongoDB version[0m | |
| MongoDB 3.4.10 | |
| [34m[1mPhantomJS version[0m | |
| 2.1.1 | |
| [34m[1mPre-installed PostgreSQL versions[0m | |
| 9.2.24 | |
| 9.3.20 | |
| 9.4.15 | |
| 9.5.10 | |
| 9.6.6 | |
| [34m[1mRabbitMQ Version[0m | |
| 3.6.14 | |
| [34m[1mRedis version[0m | |
| redis-server 4.0.6 | |
| [34m[1mriak version[0m | |
| 2.2.3 | |
| [34m[1mPre-installed Go versions[0m | |
| 1.7.4 | |
| [34m[1mant version[0m | |
| Apache Ant(TM) version 1.9.3 compiled on April 8 2014 | |
| [34m[1mmvn version[0m | |
| Apache Maven 3.5.2 (138edd61fd100ec658bfa2d307c43b76940a5d7d; 2017-10-18T07:58:13Z) | |
| Maven home: /usr/local/maven-3.5.2 | |
| Java version: 1.8.0_151, vendor: Oracle Corporation | |
| Java home: /usr/lib/jvm/java-8-oracle/jre | |
| Default locale: en_US, platform encoding: UTF-8 | |
| OS name: "linux", version: "4.4.0-98-generic", arch: "amd64", family: "unix" | |
| [34m[1mgradle version[0m | |
| ------------------------------------------------------------ | |
| Gradle 4.0.1 | |
| ------------------------------------------------------------ | |
| Build time: 2017-07-07 14:02:41 UTC | |
| Revision: 38e5dc0f772daecca1d2681885d3d85414eb6826 | |
| Groovy: 2.4.11 | |
| Ant: Apache Ant(TM) version 1.9.6 compiled on June 29 2015 | |
| JVM: 1.8.0_151 (Oracle Corporation 25.151-b12) | |
| OS: Linux 4.4.0-98-generic amd64 | |
| [34m[1mlein version[0m | |
| Leiningen 2.8.1 on Java 1.8.0_151 Java HotSpot(TM) 64-Bit Server VM | |
| [34m[1mPre-installed Node.js versions[0m | |
| v4.8.6 | |
| v6.12.0 | |
| v6.12.1 | |
| v8.9 | |
| v8.9.1 | |
| [34m[1mphpenv versions[0m | |
| system | |
| 5.6 | |
| * 5.6.32 (set by /home/travis/.phpenv/version) | |
| 7.0 | |
| 7.0.25 | |
| 7.1 | |
| 7.1.11 | |
| hhvm | |
| hhvm-stable | |
| [34m[1mcomposer --version[0m | |
| Composer version 1.5.2 2017-09-11 16:59:25 | |
| [34m[1mPre-installed Ruby versions[0m | |
| ruby-2.2.7 | |
| ruby-2.3.4 | |
| ruby-2.4.1 | |
| travis_fold:end:system_info | |
| [0K | |
| [33;1m3.5 is not installed; attempting download[0m | |
| [33;1mDownloading archive: https://storage.googleapis.com/travis-ci-language-archives/python/binaries/ubuntu/14.04/x86_64/python-3.5.tar.bz2[0m | |
| travis_time:start:014c5b30 | |
| [0K$ curl -sSf -o python-3.5.tar.bz2 ${archive_url} | |
| travis_time:end:014c5b30:start=1554118495084123470,finish=1554118495710128731,duration=626005261 | |
| [0Ktravis_time:start:1e8a1ac4 | |
| [0K$ sudo tar xjf python-3.5.tar.bz2 --directory / | |
| travis_time:end:1e8a1ac4:start=1554118495714061616,finish=1554118507701942360,duration=11987880744 | |
| [0K | |
| travis_fold:start:git.checkout | |
| [0Ktravis_time:start:257460d8 | |
| [0K$ git clone --depth=50 https://github.com/theislab/scanpy.git theislab/scanpy | |
| Cloning into 'theislab/scanpy'... | |
| remote: Enumerating objects: 1657, done.[K | |
| remote: Counting objects: 0% (1/1657) [K | |
| remote: Counting objects: 1% (17/1657) [K | |
| remote: Counting objects: 2% (34/1657) [K | |
| remote: Counting objects: 3% (50/1657) [K | |
| remote: Counting objects: 4% (67/1657) [K | |
| remote: Counting objects: 5% (83/1657) [K | |
| remote: Counting objects: 6% (100/1657) [K | |
| remote: Counting objects: 7% (116/1657) [K | |
| remote: Counting objects: 8% (133/1657) [K | |
| remote: Counting objects: 9% (150/1657) [K | |
| remote: Counting objects: 10% (166/1657) [K | |
| remote: Counting objects: 11% (183/1657) [K | |
| remote: Counting objects: 12% (199/1657) [K | |
| remote: Counting objects: 13% (216/1657) [K | |
| remote: Counting objects: 14% (232/1657) [K | |
| remote: Counting objects: 15% (249/1657) [K | |
| remote: Counting objects: 16% (266/1657) [K | |
| remote: Counting objects: 17% (282/1657) [K | |
| remote: Counting objects: 18% (299/1657) [K | |
| remote: Counting objects: 19% (315/1657) [K | |
| remote: Counting objects: 20% (332/1657) [K | |
| remote: Counting objects: 21% (348/1657) [K | |
| remote: Counting objects: 22% (365/1657) [K | |
| remote: Counting objects: 23% (382/1657) [K | |
| remote: Counting objects: 24% (398/1657) [K | |
| remote: Counting objects: 25% (415/1657) [K | |
| remote: Counting objects: 26% (431/1657) [K | |
| remote: Counting objects: 27% (448/1657) [K | |
| remote: Counting objects: 28% (464/1657) [K | |
| remote: Counting objects: 29% (481/1657) [K | |
| remote: Counting objects: 30% (498/1657) [K | |
| remote: Counting objects: 31% (514/1657) [K | |
| remote: Counting objects: 32% (531/1657) [K | |
| remote: Counting objects: 33% (547/1657) [K | |
| remote: Counting objects: 34% (564/1657) [K | |
| remote: Counting objects: 35% (580/1657) [K | |
| remote: Counting objects: 36% (597/1657) [K | |
| remote: Counting objects: 37% (614/1657) [K | |
| remote: Counting objects: 38% (630/1657) [K | |
| remote: Counting objects: 39% (647/1657) [K | |
| remote: Counting objects: 40% (663/1657) [K | |
| remote: Counting objects: 41% (680/1657) [K | |
| remote: Counting objects: 42% (696/1657) [K | |
| remote: Counting objects: 43% (713/1657) [K | |
| remote: Counting objects: 44% (730/1657) [K | |
| remote: Counting objects: 45% (746/1657) [K | |
| remote: Counting objects: 46% (763/1657) [K | |
| remote: Counting objects: 47% (779/1657) [K | |
| remote: Counting objects: 48% (796/1657) [K | |
| remote: Counting objects: 49% (812/1657) [K | |
| remote: Counting objects: 50% (829/1657) [K | |
| remote: Counting objects: 51% (846/1657) [K | |
| remote: Counting objects: 52% (862/1657) [K | |
| remote: Counting objects: 53% (879/1657) [K | |
| remote: Counting objects: 54% (895/1657) [K | |
| remote: Counting objects: 55% (912/1657) [K | |
| remote: Counting objects: 56% (928/1657) [K | |
| remote: Counting objects: 57% (945/1657) [K | |
| remote: Counting objects: 58% (962/1657) [K | |
| remote: Counting objects: 59% (978/1657) [K | |
| remote: Counting objects: 60% (995/1657) [K | |
| remote: Counting objects: 61% (1011/1657) [K | |
| remote: Counting objects: 62% (1028/1657) [K | |
| remote: Counting objects: 63% (1044/1657) [K | |
| remote: Counting objects: 64% (1061/1657) [K | |
| remote: Counting objects: 65% (1078/1657) [K | |
| remote: Counting objects: 66% (1094/1657) [K | |
| remote: Counting objects: 67% (1111/1657) [K | |
| remote: Counting objects: 68% (1127/1657) [K | |
| remote: Counting objects: 69% (1144/1657) [K | |
| remote: Counting objects: 70% (1160/1657) [K | |
| remote: Counting objects: 71% (1177/1657) [K | |
| remote: Counting objects: 72% (1194/1657) [K | |
| remote: Counting objects: 73% (1210/1657) [K | |
| remote: Counting objects: 74% (1227/1657) [K | |
| remote: Counting objects: 75% (1243/1657) [K | |
| remote: Counting objects: 76% (1260/1657) [K | |
| remote: Counting objects: 77% (1276/1657) [K | |
| remote: Counting objects: 78% (1293/1657) [K | |
| remote: Counting objects: 79% (1310/1657) [K | |
| remote: Counting objects: 80% (1326/1657) [K | |
| remote: Counting objects: 81% (1343/1657) [K | |
| remote: Counting objects: 82% (1359/1657) [K | |
| remote: Counting objects: 83% (1376/1657) [K | |
| remote: Counting objects: 84% (1392/1657) [K | |
| remote: Counting objects: 85% (1409/1657) [K | |
| remote: Counting objects: 86% (1426/1657) [K | |
| remote: Counting objects: 87% (1442/1657) [K | |
| remote: Counting objects: 88% (1459/1657) [K | |
| remote: Counting objects: 89% (1475/1657) [K | |
| remote: Counting objects: 90% (1492/1657) [K | |
| remote: Counting objects: 91% (1508/1657) [K | |
| remote: Counting objects: 92% (1525/1657) [K | |
| remote: Counting objects: 93% (1542/1657) [K | |
| remote: Counting objects: 94% (1558/1657) [K | |
| remote: Counting objects: 95% (1575/1657) [K | |
| remote: Counting objects: 96% (1591/1657) [K | |
| remote: Counting objects: 97% (1608/1657) [K | |
| remote: Counting objects: 98% (1624/1657) [K | |
| remote: Counting objects: 99% (1641/1657) [K | |
| remote: Counting objects: 100% (1657/1657) [K | |
| remote: Counting objects: 100% (1657/1657), done.[K | |
| remote: Compressing objects: 0% (1/679) [K | |
| remote: Compressing objects: 1% (7/679) [K | |
| remote: Compressing objects: 2% (14/679) [K | |
| remote: Compressing objects: 3% (21/679) [K | |
| remote: Compressing objects: 4% (28/679) [K | |
| remote: Compressing objects: 5% (34/679) [K | |
| remote: Compressing objects: 6% (41/679) [K | |
| remote: Compressing objects: 7% (48/679) [K | |
| remote: Compressing objects: 8% (55/679) [K | |
| remote: Compressing objects: 9% (62/679) [K | |
| remote: Compressing objects: 10% (68/679) [K | |
| remote: Compressing objects: 11% (75/679) [K | |
| remote: Compressing objects: 12% (82/679) [K | |
| remote: Compressing objects: 13% (89/679) [K | |
| remote: Compressing objects: 14% (96/679) [K | |
| remote: Compressing objects: 15% (102/679) [K | |
| remote: Compressing objects: 16% (109/679) [K | |
| remote: Compressing objects: 17% (116/679) [K | |
| remote: Compressing objects: 18% (123/679) [K | |
| remote: Compressing objects: 19% (130/679) [K | |
| remote: Compressing objects: 20% (136/679) [K | |
| remote: Compressing objects: 21% (143/679) [K | |
| remote: Compressing objects: 22% (150/679) [K | |
| remote: Compressing objects: 23% (157/679) [K | |
| remote: Compressing objects: 24% (163/679) [K | |
| remote: Compressing objects: 25% (170/679) [K | |
| remote: Compressing objects: 26% (177/679) [K | |
| remote: Compressing objects: 27% (184/679) [K | |
| remote: Compressing objects: 28% (191/679) [K | |
| remote: Compressing objects: 29% (197/679) [K | |
| remote: Compressing objects: 30% (204/679) [K | |
| remote: Compressing objects: 31% (211/679) [K | |
| remote: Compressing objects: 32% (218/679) [K | |
| remote: Compressing objects: 33% (225/679) [K | |
| remote: Compressing objects: 34% (231/679) [K | |
| remote: Compressing objects: 35% (238/679) [K | |
| remote: Compressing objects: 36% (245/679) [K | |
| remote: Compressing objects: 37% (252/679) [K | |
| remote: Compressing objects: 38% (259/679) [K | |
| remote: Compressing objects: 39% (265/679) [K | |
| remote: Compressing objects: 40% (272/679) [K | |
| remote: Compressing objects: 41% (279/679) [K | |
| remote: Compressing objects: 42% (286/679) [K | |
| remote: Compressing objects: 43% (292/679) [K | |
| remote: Compressing objects: 44% (299/679) [K | |
| remote: Compressing objects: 45% (306/679) [K | |
| remote: Compressing objects: 46% (313/679) [K | |
| remote: Compressing objects: 47% (320/679) [K | |
| remote: Compressing objects: 48% (326/679) [K | |
| remote: Compressing objects: 49% (333/679) [K | |
| remote: Compressing objects: 50% (340/679) [K | |
| remote: Compressing objects: 51% (347/679) [K | |
| remote: Compressing objects: 52% (354/679) [K | |
| remote: Compressing objects: 53% (360/679) [K | |
| remote: Compressing objects: 54% (367/679) [K | |
| remote: Compressing objects: 55% (374/679) [K | |
| remote: Compressing objects: 56% (381/679) [K | |
| remote: Compressing objects: 57% (388/679) [K | |
| remote: Compressing objects: 58% (394/679) [K | |
| remote: Compressing objects: 59% (401/679) [K | |
| remote: Compressing objects: 60% (408/679) [K | |
| remote: Compressing objects: 61% (415/679) [K | |
| remote: Compressing objects: 62% (421/679) [K | |
| remote: Compressing objects: 63% (428/679) [K | |
| remote: Compressing objects: 64% (435/679) [K | |
| remote: Compressing objects: 65% (442/679) [K | |
| remote: Compressing objects: 66% (449/679) [K | |
| remote: Compressing objects: 67% (455/679) [K | |
| remote: Compressing objects: 68% (462/679) [K | |
| remote: Compressing objects: 69% (469/679) [K | |
| remote: Compressing objects: 70% (476/679) [K | |
| remote: Compressing objects: 71% (483/679) [K | |
| remote: Compressing objects: 72% (489/679) [K | |
| remote: Compressing objects: 73% (496/679) [K | |
| remote: Compressing objects: 74% (503/679) [K | |
| remote: Compressing objects: 75% (510/679) [K | |
| remote: Compressing objects: 76% (517/679) [K | |
| remote: Compressing objects: 77% (523/679) [K | |
| remote: Compressing objects: 78% (530/679) [K | |
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| remote: Compressing objects: 80% (544/679) [K | |
| remote: Compressing objects: 81% (550/679) [K | |
| remote: Compressing objects: 82% (557/679) [K | |
| remote: Compressing objects: 83% (564/679) [K | |
| remote: Compressing objects: 84% (571/679) [K | |
| remote: Compressing objects: 85% (578/679) [K | |
| remote: Compressing objects: 86% (584/679) [K | |
| remote: Compressing objects: 87% (591/679) [K | |
| remote: Compressing objects: 88% (598/679) [K | |
| remote: Compressing objects: 89% (605/679) [K | |
| remote: Compressing objects: 90% (612/679) [K | |
| remote: Compressing objects: 91% (618/679) [K | |
| remote: Compressing objects: 92% (625/679) [K | |
| remote: Compressing objects: 93% (632/679) [K | |
| remote: Compressing objects: 94% (639/679) [K | |
| remote: Compressing objects: 95% (646/679) [K | |
| remote: Compressing objects: 96% (652/679) [K | |
| remote: Compressing objects: 97% (659/679) [K | |
| remote: Compressing objects: 98% (666/679) [K | |
| remote: Compressing objects: 99% (673/679) [K | |
| remote: Compressing objects: 100% (679/679) [K | |
| remote: Compressing objects: 100% (679/679), done.[K | |
| Receiving objects: 0% (1/1657) | |
| Receiving objects: 1% (17/1657) | |
| Receiving objects: 2% (34/1657) | |
| Receiving objects: 3% (50/1657) | |
| Receiving objects: 4% (67/1657) | |
| Receiving objects: 5% (83/1657) | |
| Receiving objects: 6% (100/1657) | |
| Receiving objects: 7% (116/1657) | |
| Receiving objects: 8% (133/1657) | |
| Receiving objects: 9% (150/1657) | |
| Receiving objects: 10% (166/1657) | |
| Receiving objects: 11% (183/1657) | |
| Receiving objects: 12% (199/1657) | |
| Receiving objects: 13% (216/1657) | |
| Receiving objects: 14% (232/1657) | |
| Receiving objects: 15% (249/1657) | |
| Receiving objects: 16% (266/1657) | |
| Receiving objects: 17% (282/1657) | |
| Receiving objects: 18% (299/1657) | |
| Receiving objects: 19% (315/1657) | |
| Receiving objects: 20% (332/1657) | |
| Receiving objects: 21% (348/1657) | |
| Receiving objects: 22% (365/1657) | |
| Receiving objects: 23% (382/1657) | |
| Receiving objects: 24% (398/1657) | |
| Receiving objects: 25% (415/1657) | |
| Receiving objects: 26% (431/1657) | |
| Receiving objects: 27% (448/1657) | |
| Receiving objects: 28% (464/1657) | |
| Receiving objects: 29% (481/1657) | |
| Receiving objects: 30% (498/1657) | |
| Receiving objects: 31% (514/1657) | |
| Receiving objects: 32% (531/1657) | |
| Receiving objects: 33% (547/1657) | |
| Receiving objects: 34% (564/1657) | |
| Receiving objects: 35% (580/1657) | |
| Receiving objects: 36% (597/1657) | |
| Receiving objects: 37% (614/1657) | |
| Receiving objects: 38% (630/1657) | |
| Receiving objects: 39% (647/1657) | |
| Receiving objects: 40% (663/1657) | |
| Receiving objects: 41% (680/1657) | |
| Receiving objects: 42% (696/1657) | |
| Receiving objects: 43% (713/1657) | |
| Receiving objects: 44% (730/1657) | |
| Receiving objects: 45% (746/1657) | |
| Receiving objects: 46% (763/1657) | |
| Receiving objects: 47% (779/1657) | |
| Receiving objects: 48% (796/1657) | |
| Receiving objects: 49% (812/1657) | |
| Receiving objects: 50% (829/1657) | |
| Receiving objects: 51% (846/1657) | |
| Receiving objects: 52% (862/1657) | |
| Receiving objects: 53% (879/1657) | |
| Receiving objects: 54% (895/1657) | |
| Receiving objects: 55% (912/1657) | |
| Receiving objects: 56% (928/1657) | |
| Receiving objects: 57% (945/1657) | |
| Receiving objects: 58% (962/1657) | |
| Receiving objects: 59% (978/1657) | |
| Receiving objects: 60% (995/1657) | |
| Receiving objects: 61% (1011/1657) | |
| Receiving objects: 62% (1028/1657) | |
| Receiving objects: 63% (1044/1657) | |
| Receiving objects: 64% (1061/1657) | |
| Receiving objects: 65% (1078/1657) | |
| Receiving objects: 66% (1094/1657) | |
| Receiving objects: 67% (1111/1657) | |
| Receiving objects: 68% (1127/1657) | |
| Receiving objects: 69% (1144/1657) | |
| Receiving objects: 70% (1160/1657) | |
| Receiving objects: 71% (1177/1657) | |
| Receiving objects: 72% (1194/1657) | |
| Receiving objects: 73% (1210/1657) | |
| Receiving objects: 74% (1227/1657) | |
| Receiving objects: 75% (1243/1657) | |
| Receiving objects: 76% (1260/1657) | |
| Receiving objects: 77% (1276/1657) | |
| Receiving objects: 78% (1293/1657) | |
| Receiving objects: 79% (1310/1657) | |
| Receiving objects: 80% (1326/1657) | |
| Receiving objects: 81% (1343/1657) | |
| Receiving objects: 82% (1359/1657) | |
| Receiving objects: 83% (1376/1657) | |
| Receiving objects: 84% (1392/1657) | |
| Receiving objects: 85% (1409/1657) | |
| Receiving objects: 86% (1426/1657) | |
| Receiving objects: 87% (1442/1657) | |
| Receiving objects: 88% (1459/1657) | |
| Receiving objects: 89% (1475/1657) | |
| Receiving objects: 90% (1492/1657) | |
| Receiving objects: 91% (1508/1657) | |
| Receiving objects: 92% (1525/1657) | |
| Receiving objects: 93% (1542/1657) | |
| Receiving objects: 94% (1558/1657) | |
| Receiving objects: 95% (1575/1657) | |
| remote: Total 1657 (delta 1058), reused 1448 (delta 950), pack-reused 0[K | |
| Receiving objects: 96% (1591/1657) | |
| Receiving objects: 97% (1608/1657) | |
| Receiving objects: 98% (1624/1657) | |
| Receiving objects: 99% (1641/1657) | |
| Receiving objects: 100% (1657/1657) | |
| Receiving objects: 100% (1657/1657), 7.26 MiB | 24.61 MiB/s, done. | |
| Resolving deltas: 0% (0/1058) | |
| Resolving deltas: 6% (69/1058) | |
| Resolving deltas: 14% (152/1058) | |
| Resolving deltas: 16% (179/1058) | |
| Resolving deltas: 20% (217/1058) | |
| Resolving deltas: 22% (240/1058) | |
| Resolving deltas: 23% (245/1058) | |
| Resolving deltas: 32% (343/1058) | |
| Resolving deltas: 33% (351/1058) | |
| Resolving deltas: 34% (367/1058) | |
| Resolving deltas: 35% (377/1058) | |
| Resolving deltas: 36% (388/1058) | |
| Resolving deltas: 38% (412/1058) | |
| Resolving deltas: 39% (414/1058) | |
| Resolving deltas: 40% (430/1058) | |
| Resolving deltas: 56% (596/1058) | |
| Resolving deltas: 63% (668/1058) | |
| Resolving deltas: 66% (702/1058) | |
| Resolving deltas: 67% (711/1058) | |
| Resolving deltas: 70% (746/1058) | |
| Resolving deltas: 71% (754/1058) | |
| Resolving deltas: 72% (764/1058) | |
| Resolving deltas: 73% (775/1058) | |
| Resolving deltas: 74% (784/1058) | |
| Resolving deltas: 76% (812/1058) | |
| Resolving deltas: 77% (820/1058) | |
| Resolving deltas: 78% (831/1058) | |
| Resolving deltas: 80% (852/1058) | |
| Resolving deltas: 81% (858/1058) | |
| Resolving deltas: 82% (869/1058) | |
| Resolving deltas: 83% (885/1058) | |
| Resolving deltas: 84% (889/1058) | |
| Resolving deltas: 85% (902/1058) | |
| Resolving deltas: 87% (922/1058) | |
| Resolving deltas: 88% (939/1058) | |
| Resolving deltas: 89% (942/1058) | |
| Resolving deltas: 90% (953/1058) | |
| Resolving deltas: 91% (966/1058) | |
| Resolving deltas: 92% (974/1058) | |
| Resolving deltas: 93% (984/1058) | |
| Resolving deltas: 94% (995/1058) | |
| Resolving deltas: 95% (1011/1058) | |
| Resolving deltas: 96% (1018/1058) | |
| Resolving deltas: 97% (1027/1058) | |
| Resolving deltas: 98% (1039/1058) | |
| Resolving deltas: 99% (1051/1058) | |
| Resolving deltas: 100% (1058/1058) | |
| Resolving deltas: 100% (1058/1058), done. | |
| travis_time:end:257460d8:start=1554118507724877522,finish=1554118509282134528,duration=1557257006 | |
| [0K$ cd theislab/scanpy | |
| travis_time:start:245cdb5c | |
| [0K$ git fetch origin +refs/pull/579/merge: | |
| remote: Enumerating objects: 17, done.[K | |
| remote: Counting objects: 5% (1/17) [K | |
| remote: Counting objects: 11% (2/17) [K | |
| remote: Counting objects: 17% (3/17) [K | |
| remote: Counting objects: 23% (4/17) [K | |
| remote: Counting objects: 29% (5/17) [K | |
| remote: Counting objects: 35% (6/17) [K | |
| remote: Counting objects: 41% (7/17) [K | |
| remote: Counting objects: 47% (8/17) [K | |
| remote: Counting objects: 52% (9/17) [K | |
| remote: Counting objects: 58% (10/17) [K | |
| remote: Counting objects: 64% (11/17) [K | |
| remote: Counting objects: 70% (12/17) [K | |
| remote: Counting objects: 76% (13/17) [K | |
| remote: Counting objects: 82% (14/17) [K | |
| remote: Counting objects: 88% (15/17) [K | |
| remote: Counting objects: 94% (16/17) [K | |
| remote: Counting objects: 100% (17/17) [K | |
| remote: Counting objects: 100% (17/17), done.[K | |
| remote: Compressing objects: 14% (1/7) [K | |
| remote: Compressing objects: 28% (2/7) [K | |
| remote: Compressing objects: 42% (3/7) [K | |
| remote: Compressing objects: 57% (4/7) [K | |
| remote: Compressing objects: 71% (5/7) [K | |
| remote: Compressing objects: 85% (6/7) [K | |
| remote: Compressing objects: 100% (7/7) [K | |
| remote: Compressing objects: 100% (7/7), done.[K | |
| remote: Total 7 (delta 5), reused 0 (delta 0), pack-reused 0[K | |
| Unpacking objects: 14% (1/7) | |
| Unpacking objects: 28% (2/7) | |
| Unpacking objects: 42% (3/7) | |
| Unpacking objects: 57% (4/7) | |
| Unpacking objects: 71% (5/7) | |
| Unpacking objects: 85% (6/7) | |
| Unpacking objects: 100% (7/7) | |
| Unpacking objects: 100% (7/7), done. | |
| From https://github.com/theislab/scanpy | |
| * branch refs/pull/579/merge -> FETCH_HEAD | |
| travis_time:end:245cdb5c:start=1554118509286708571,finish=1554118509744376836,duration=457668265 | |
| [0K$ git checkout -qf FETCH_HEAD | |
| travis_fold:end:git.checkout | |
| [0K | |
| [33;1mSetting environment variables from .travis.yml[0m | |
| $ export MPLBACKEND=Agg | |
| travis_time:start:04d32b30 | |
| [0K$ source ~/virtualenv/python3.5/bin/activate | |
| travis_time:end:04d32b30:start=1554118509811774442,finish=1554118509817004820,duration=5230378 | |
| [0Ktravis_fold:start:cache.1 | |
| [0KSetting up build cache | |
| $ export CASHER_DIR=${TRAVIS_HOME}/.casher | |
| travis_time:start:0742f8de | |
| [0K$ Installing caching utilities | |
| travis_time:end:0742f8de:start=1554118514397731409,finish=1554118514544546104,duration=146814695 | |
| [0Ktravis_time:start:160fe894 | |
| [0Ktravis_time:end:160fe894:start=1554118514550354826,finish=1554118514553643868,duration=3289042 | |
| [0Ktravis_time:start:0443e6c0 | |
| [0K[32;1mattempting to download cache archive[0m | |
| [32;1mfetching PR.579/cache-linux-trusty-af97160760c6a1f71d47d7257ec5900e97fcc7d2b78b0e11646772eb55c1deb7--python-3.5.tgz[0m | |
| [32;1mfetching PR.579/cache--python-3.5.tgz[0m | |
| [32;1mfetching master/cache-linux-trusty-af97160760c6a1f71d47d7257ec5900e97fcc7d2b78b0e11646772eb55c1deb7--python-3.5.tgz[0m | |
| [32;1mfound cache[0m | |
| travis_time:end:0443e6c0:start=1554118514557912555,finish=1554118517206213951,duration=2648301396 | |
| [0Ktravis_fold:end:cache.1 | |
| [0K | |
| travis_fold:start:cache.pip | |
| [0K | |
| travis_time:start:0ddbfab8 | |
| [0Ktravis_time:end:0ddbfab8:start=1554118517213105520,finish=1554118517216541470,duration=3435950 | |
| [0Ktravis_time:start:09743268 | |
| [0K[32;1madding /home/travis/.cache/pip to cache[0m | |
| travis_time:end:09743268:start=1554118517220751660,finish=1554118523072487770,duration=5851736110 | |
| [0Ktravis_fold:end:cache.pip | |
| [0K$ python --version | |
| Python 3.5.6 | |
| $ pip --version | |
| pip 18.0 from /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pip (python 3.5) | |
| travis_fold:start:install.1 | |
| [0Ktravis_time:start:28e34df8 | |
| [0K$ pip install docutils | |
| Collecting docutils | |
| Using cached https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl | |
| Installing collected packages: docutils | |
| Successfully installed docutils-0.14 | |
| travis_time:end:28e34df8:start=1554118523495316679,finish=1554118524905506329,duration=1410189650 | |
| [0Ktravis_fold:end:install.1 | |
| [0Ktravis_fold:start:install.2 | |
| [0Ktravis_time:start:0c22d928 | |
| [0K$ pip install -e .[test,louvain,leiden] | |
| Obtaining file:///home/travis/build/theislab/scanpy | |
| Collecting anndata>=0.6.15 (from scanpy==1.4+219.g339d4df) | |
| Collecting matplotlib>=3.0.0 (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/89/61/465fb3bfba684b0f53b5c4829c3c89e86e6fe9fdcdfda93e38f1788090f0/matplotlib-3.0.3-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting pandas>=0.21 (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/74/24/0cdbf8907e1e3bc5a8da03345c23cbed7044330bb8f73bb12e711a640a00/pandas-0.24.2-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting scipy (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/f0/30/526bee2ce18c066f9ff13ba89603f6c2b96c9fd406b57a21a7ba14bf5679/scipy-1.2.1-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting seaborn (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/a8/76/220ba4420459d9c4c9c9587c6ce607bf56c25b3d3d2de62056efe482dadc/seaborn-0.9.0-py3-none-any.whl | |
| Collecting h5py (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/4c/77/c4933e12dca0f61bcdafc207c7532e1250b8d12719459fd85132f3daa9fd/h5py-2.9.0-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting tables (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/ab/b8/2848cd92d50d07bbc1cae4cd3ea33281332b3a701a3776648ead94c6c833/tables-3.5.1-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting scikit-learn>=0.19.1 (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/38/7f/7d21bd89a97603a14d3770ca912d4402c394a8e50642f9b8b5cc6867a61a/scikit_learn-0.20.3-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting statsmodels (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/a5/75/758f980df4d971b909d2bc516d22494a2e871fe1f3968ff9798b52d20fb9/statsmodels-0.9.0-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting patsy (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl | |
| Collecting networkx (from scanpy==1.4+219.g339d4df) | |
| Collecting natsort (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/e7/13/a66bfa0ebf00e17778ca0319d081be686a33384d1f612fc8e0fc542ac5d8/natsort-6.0.0-py2.py3-none-any.whl | |
| Collecting joblib (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/cd/c1/50a758e8247561e58cb87305b1e90b171b8c767b15b12a1734001f41d356/joblib-0.13.2-py2.py3-none-any.whl | |
| Collecting numba>=0.41.0 (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/6d/4d/b54079bc0abb347a24e0080745da04efb2df3350544b91cffac2fe1c2651/numba-0.43.1-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting python-igraph (from scanpy==1.4+219.g339d4df) | |
| Collecting leidenalg (from scanpy==1.4+219.g339d4df) | |
| Collecting louvain>=0.6 (from scanpy==1.4+219.g339d4df) | |
| Collecting pytest>=3.9 (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/7e/16/83b2a35c427b838df9836c9e7e4ae6dfbcbdea643db44652f693b1c57d70/pytest-4.4.0-py2.py3-none-any.whl | |
| Collecting dask[array] (from scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/0e/c3/dc200eac6927d99b2ba7746ac173b238d56fef7c89d811b5e842560def90/dask-1.1.5-py2.py3-none-any.whl | |
| Collecting zappy (from scanpy==1.4+219.g339d4df) | |
| Collecting zarr (from scanpy==1.4+219.g339d4df) | |
| Requirement already satisfied: numpy~=1.14 in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from anndata>=0.6.15->scanpy==1.4+219.g339d4df) (1.15.0) | |
| Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=3.0.0->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl | |
| Collecting python-dateutil>=2.1 (from matplotlib>=3.0.0->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl | |
| Collecting cycler>=0.10 (from matplotlib>=3.0.0->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl | |
| Collecting kiwisolver>=1.0.1 (from matplotlib>=3.0.0->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/7e/31/d6fedd4fb2c94755cd101191e581af30e1650ccce7a35bddb7930fed6574/kiwisolver-1.0.1-cp35-cp35m-manylinux1_x86_64.whl | |
| Collecting pytz>=2011k (from pandas>=0.21->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl | |
| Requirement already satisfied: six in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from h5py->scanpy==1.4+219.g339d4df) (1.11.0) | |
| Collecting numexpr>=2.6.2 (from tables->scanpy==1.4+219.g339d4df) | |
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| Requirement already satisfied: mock>=2.0 in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from tables->scanpy==1.4+219.g339d4df) (2.0.0) | |
| Collecting decorator>=4.3.0 (from networkx->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl | |
| Collecting llvmlite>=0.28.0dev0 (from numba>=0.41.0->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/d1/0e/d0ed03146d441ce92c62367c29c0e77c8b1e78f9a17c77d9015b959cff02/llvmlite-0.28.0-1-cp35-cp35m-manylinux1_x86_64.whl | |
| Requirement already satisfied: attrs>=17.4.0 in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from pytest>=3.9->scanpy==1.4+219.g339d4df) (18.1.0) | |
| Requirement already satisfied: setuptools in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from pytest>=3.9->scanpy==1.4+219.g339d4df) (40.0.0) | |
| Collecting pluggy>=0.9 (from pytest>=3.9->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/84/e8/4ddac125b5a0e84ea6ffc93cfccf1e7ee1924e88f53c64e98227f0af2a5f/pluggy-0.9.0-py2.py3-none-any.whl | |
| Requirement already satisfied: py>=1.5.0 in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from pytest>=3.9->scanpy==1.4+219.g339d4df) (1.5.4) | |
| Requirement already satisfied: more-itertools>=4.0.0; python_version > "2.7" in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from pytest>=3.9->scanpy==1.4+219.g339d4df) (4.3.0) | |
| Requirement already satisfied: pathlib2>=2.2.0; python_version < "3.6" in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from pytest>=3.9->scanpy==1.4+219.g339d4df) (2.3.2) | |
| Requirement already satisfied: atomicwrites>=1.0 in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from pytest>=3.9->scanpy==1.4+219.g339d4df) (1.1.5) | |
| Collecting toolz>=0.7.3; extra == "array" (from dask[array]->scanpy==1.4+219.g339d4df) | |
| Collecting numcodecs>=0.6.2 (from zarr->scanpy==1.4+219.g339d4df) | |
| Collecting asciitree (from zarr->scanpy==1.4+219.g339d4df) | |
| Collecting fasteners (from zarr->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/14/3a/096c7ad18e102d4f219f5dd15951f9728ca5092a3385d2e8f79a7c1e1017/fasteners-0.14.1-py2.py3-none-any.whl | |
| Requirement already satisfied: pbr>=0.11 in /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages (from mock>=2.0->tables->scanpy==1.4+219.g339d4df) (4.2.0) | |
| Collecting monotonic>=0.1 (from fasteners->zarr->scanpy==1.4+219.g339d4df) | |
| Using cached https://files.pythonhosted.org/packages/ac/aa/063eca6a416f397bd99552c534c6d11d57f58f2e94c14780f3bbf818c4cf/monotonic-1.5-py2.py3-none-any.whl | |
| Installing collected packages: python-dateutil, pytz, pandas, natsort, h5py, scipy, anndata, pyparsing, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, scikit-learn, patsy, statsmodels, decorator, networkx, joblib, llvmlite, numba, python-igraph, leidenalg, louvain, pluggy, pytest, toolz, dask, zappy, numcodecs, asciitree, monotonic, fasteners, zarr, scanpy | |
| Found existing installation: pluggy 0.7.1 | |
| Uninstalling pluggy-0.7.1: | |
| Successfully uninstalled pluggy-0.7.1 | |
| Found existing installation: pytest 3.7.1 | |
| Uninstalling pytest-3.7.1: | |
| Successfully uninstalled pytest-3.7.1 | |
| Running setup.py develop for scanpy | |
| Successfully installed anndata-0.6.19 asciitree-0.3.3 cycler-0.10.0 dask-1.1.5 decorator-4.4.0 fasteners-0.14.1 h5py-2.9.0 joblib-0.13.2 kiwisolver-1.0.1 leidenalg-0.7.0 llvmlite-0.28.0 louvain-0.6.1 matplotlib-3.0.3 monotonic-1.5 natsort-6.0.0 networkx-2.2 numba-0.43.1 numcodecs-0.6.3 numexpr-2.6.9 pandas-0.24.2 patsy-0.5.1 pluggy-0.9.0 pyparsing-2.3.1 pytest-4.4.0 python-dateutil-2.8.0 python-igraph-0.7.1.post6 pytz-2018.9 scanpy scikit-learn-0.20.3 scipy-1.2.1 seaborn-0.9.0 statsmodels-0.9.0 tables-3.5.1 toolz-0.9.0 zappy-0.2.0 zarr-2.3.1 | |
| travis_time:end:0c22d928:start=1554118524910673378,finish=1554118553405607979,duration=28494934601 | |
| [0Ktravis_fold:end:install.2 | |
| [0Ktravis_time:start:11083c02 | |
| [0K$ pytest --ignore=scanpy/tests/_images | |
| [1m============================= test session starts ==============================[0m | |
| platform linux -- Python 3.5.6, pytest-4.4.0, py-1.5.4, pluggy-0.9.0 | |
| rootdir: /home/travis/build/theislab/scanpy, inifile: pytest.ini, testpaths: scanpy | |
| [1mcollecting ... [0m[1m | |
| collecting 0 items [0m[1m | |
| collected 72 items [0m | |
| scanpy/tests/test_clustering.py [32m.[0m[32m.[0m[32m.[0m[36m [ 4%][0m | |
| scanpy/tests/test_combat.py [32m.[0m[32m.[0m[36m [ 6%][0m | |
| scanpy/tests/test_embedding_density.py [32m.[0m[32m.[0m[36m [ 9%][0m | |
| scanpy/tests/test_highly_variable_genes.py [32m.[0m[32m.[0m[32m.[0m[36m [ 13%][0m | |
| scanpy/tests/test_marker_gene_overlap.py [31mF[0m[36m [ 15%][0m | |
| scanpy/tests/test_neighbors.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 20%][0m | |
| scanpy/tests/test_pca.py [32m.[0m[32m.[0m[36m [ 23%][0m | |
| scanpy/tests/test_plotting.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 38%][0m | |
| scanpy/tests/test_preprocessing.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 50%][0m | |
| scanpy/tests/test_preprocessing_distributed.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 63%][0m | |
| scanpy/tests/test_qc_metrics.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 73%][0m | |
| scanpy/tests/test_rank_genes_groups.py [32m.[0m[32m.[0m[36m [ 76%][0m | |
| scanpy/tests/test_rank_genes_groups_logreg.py [32m.[0m[36m [ 77%][0m | |
| scanpy/tests/test_read_10x.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 84%][0m | |
| scanpy/tests/test_readwrite.py [32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[36m [ 93%][0m | |
| scanpy/tests/test_score_genes.py [32m.[0m[36m [ 94%][0m | |
| scanpy/tests/test_sim.py [32m.[0m[36m [ 95%][0m | |
| scanpy/tests/test_utils.py [32m.[0m[36m [ 97%][0m | |
| scanpy/tests/notebooks/test_paga_paul15_subsampled.py [32m.[0m[36m [ 98%][0m | |
| scanpy/tests/notebooks/test_pbmc3k.py [32m.[0m[36m [100%][0m | |
| =================================== FAILURES =================================== | |
| [31m[1m_____________________________ test_marker_overlap ______________________________[0m | |
| [1m def test_marker_overlap():[0m | |
| [1m # Test all overlap calculations on artificial data[0m | |
| [1m test_data = sc.AnnData(X = np.ones((9,10)))[0m | |
| [1m test_data.uns['rank_genes_groups'] = dict()[0m | |
| [1m test_data.uns['rank_genes_groups']['names'] = np.rec.fromarrays([0m | |
| [1m [['a', 'b','c','d','e'], ['a','f','g','h','i']])[0m | |
| [1m test_data.uns['rank_genes_groups']['pvals_adj'] = np.rec.fromarrays([0m | |
| [1m [[0.001, 0.01, 0.02, 0.05, 0.6], [0.001, 0.01, 0.02, 0.05, 0.6]])[0m | |
| [1m [0m | |
| [1m marker_genes = {'type 1':{'a','b','c'}, 'type 2':{'a','f','g'}}[0m | |
| [1m [0m | |
| [1m t1 = sc.tl.marker_gene_overlap(test_data, marker_genes)[0m | |
| [1m t2 = sc.tl.marker_gene_overlap(test_data, marker_genes, normalize='reference')[0m | |
| [1m t3 = sc.tl.marker_gene_overlap(test_data, marker_genes, method='overlap_coef')[0m | |
| [1m t4 = sc.tl.marker_gene_overlap(test_data, marker_genes, method='jaccard')[0m | |
| [1m t5 = sc.tl.marker_gene_overlap(test_data, marker_genes, top_n_markers=2)[0m | |
| [1m t6 = sc.tl.marker_gene_overlap(test_data, marker_genes, adj_pval_threshold=0.01)[0m | |
| [1m [0m | |
| [1m> assert t1.iloc[1,1] == 3.0[0m | |
| [31m[1mE assert 1.0 == 3.0[0m | |
| [31m[1mscanpy/tests/test_marker_gene_overlap.py[0m:22: AssertionError | |
| [33m=============================== warnings summary ===============================[0m | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222 | |
| scanpy/tests/test_clustering.py::test_leiden_basic | |
| scanpy/tests/test_combat.py::test_norm | |
| scanpy/tests/test_preprocessing.py::test_regress_out_ordinal | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/igraph/configuration.py:288 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/igraph/configuration.py:288 | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/igraph/configuration.py:288: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. | |
| self._config = SafeConfigParser() | |
| scanpy/tests/test_clustering.py::test_leiden_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_partition_type | |
| scanpy/tests/test_highly_variable_genes.py::test_higly_variable_genes_compare_to_seurat | |
| scanpy/tests/test_highly_variable_genes.py::test_filter_genes_dispersion_compare_to_seurat | |
| scanpy/tests/test_plotting.py::test_dotplot | |
| scanpy/tests/test_plotting.py::test_violin | |
| scanpy/tests/test_plotting.py::test_dendrogram | |
| scanpy/tests/test_plotting.py::test_correlation | |
| scanpy/tests/test_plotting.py::test_rank_genes_groups | |
| scanpy/tests/test_plotting.py::test_scatterplots | |
| scanpy/tests/notebooks/test_pbmc3k.py::test_pbmc3k | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/anndata/readwrite/read.py:439: DeprecationWarning: In a future version, read_h5ad will no longer explicitly support boolean arguments. Specify the read mode, or leave `backed=None`. | |
| DeprecationWarning, | |
| scanpy/tests/test_clustering.py::test_leiden_basic | |
| scanpy/tests/test_clustering.py::test_leiden_basic | |
| scanpy/tests/test_clustering.py::test_leiden_basic | |
| scanpy/tests/test_clustering.py::test_leiden_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_louvain_basic | |
| scanpy/tests/test_clustering.py::test_partition_type | |
| scanpy/tests/test_clustering.py::test_partition_type | |
| scanpy/tests/test_clustering.py::test_partition_type | |
| scanpy/tests/test_clustering.py::test_partition_type | |
| scanpy/tests/test_clustering.py::test_partition_type | |
| scanpy/tests/test_embedding_density.py::test_embedding_density_plot | |
| scanpy/tests/test_embedding_density.py::test_embedding_density_plot | |
| scanpy/tests/test_highly_variable_genes.py::test_higly_variable_genes_compare_to_seurat | |
| scanpy/tests/test_highly_variable_genes.py::test_higly_variable_genes_compare_to_seurat | |
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| scanpy/tests/test_highly_variable_genes.py::test_filter_genes_dispersion_compare_to_seurat | |
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| scanpy/tests/test_rank_genes_groups_logreg.py::test_rank_genes_groups_with_renamed_categories | |
| scanpy/tests/test_read_10x.py::test_read_10x_h5_v1 | |
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| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/matrixlib/defmatrix.py:68: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| return matrix(data, dtype=dtype, copy=False) | |
| scanpy/tests/test_combat.py::test_shilhouette | |
| scanpy/tests/test_combat.py::test_shilhouette | |
| /home/travis/build/theislab/scanpy/scanpy/preprocessing/_combat.py:232: NumbaWarning: Function "_it_sol" failed type inference: Cannot unify array(float64, 2d, C) and array(float64, 1d, C) for 'sum2', defined at /home/travis/build/theislab/scanpy/scanpy/preprocessing/_combat.py (274) | |
| File "scanpy/preprocessing/_combat.py", line 274: | |
| def _it_sol(s_data, g_hat, d_hat, g_bar, t2, a, b, conv=0.0001): | |
| <source elided> | |
| g_new = (t2*n*g_hat + d_old*g_bar) / (t2*n + d_old) | |
| sum2 = s_data - g_new.reshape((g_new.shape[0], 1)) @ np.ones((1, s_data.shape[1])) | |
| ^ | |
| [1] During: typing of assignment at /home/travis/build/theislab/scanpy/scanpy/preprocessing/_combat.py (276) | |
| File "scanpy/preprocessing/_combat.py", line 276: | |
| def _it_sol(s_data, g_hat, d_hat, g_bar, t2, a, b, conv=0.0001): | |
| <source elided> | |
| sum2 = sum2 ** 2 | |
| sum2 = sum2.sum(axis=1) | |
| ^ | |
| @numba.jit | |
| scanpy/tests/test_combat.py::test_shilhouette | |
| /home/travis/build/theislab/scanpy/scanpy/preprocessing/_combat.py:232: NumbaWarning: Function "_it_sol" failed type inference: cannot determine Numba type of <class 'numba.dispatcher.LiftedLoop'> | |
| File "scanpy/preprocessing/_combat.py", line 268: | |
| def _it_sol(s_data, g_hat, d_hat, g_bar, t2, a, b, conv=0.0001): | |
| <source elided> | |
| change = 1 | |
| count = 0 | |
| ^ | |
| @numba.jit | |
| scanpy/tests/test_combat.py::test_shilhouette | |
| /home/travis/build/theislab/scanpy/scanpy/preprocessing/_combat.py:232: NumbaWarning: Function "_it_sol" was compiled in object mode without forceobj=True, but has lifted loops. | |
| @numba.jit | |
| scanpy/tests/test_combat.py::test_shilhouette | |
| /home/travis/build/theislab/scanpy/scanpy/preprocessing/_combat.py:232: NumbaWarning: Function "_it_sol" was compiled in object mode without forceobj=True. | |
| @numba.jit | |
| scanpy/tests/test_plotting.py::test_heatmap | |
| scanpy/tests/test_plotting.py::test_heatmap | |
| scanpy/tests/test_plotting.py::test_heatmap | |
| scanpy/tests/test_plotting.py::test_heatmap | |
| scanpy/tests/test_plotting.py::test_rank_genes_groups | |
| scanpy/tests/test_plotting.py::test_rank_genes_symbols | |
| /home/travis/build/theislab/scanpy/scanpy/plotting/_anndata.py:2660: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| groupby_ax.imshow(np.matrix([label2code[lab] for lab in obs_tidy.index]).T, aspect='auto', cmap=groupby_cmap, norm=norm) | |
| scanpy/tests/test_plotting.py::test_heatmap | |
| scanpy/tests/test_plotting.py::test_tracksplot | |
| scanpy/tests/test_plotting.py::test_rank_genes_groups | |
| scanpy/tests/test_plotting.py::test_rank_genes_groups | |
| scanpy/tests/test_plotting.py::test_rank_genes_symbols | |
| /home/travis/build/theislab/scanpy/scanpy/plotting/_anndata.py:2678: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| groupby_ax.imshow(np.matrix([label2code[lab] for lab in obs_tidy.index]), aspect='auto', cmap=groupby_cmap, norm=norm) | |
| scanpy/tests/test_plotting.py::test_rank_genes_groups | |
| /home/travis/build/theislab/scanpy/scanpy/plotting/_anndata.py:1308: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| gene_groups_ax.imshow(np.matrix(arr).T, aspect='auto', cmap=groupby_cmap, norm=norm) | |
| scanpy/tests/test_plotting.py::test_rank_genes_groups | |
| /home/travis/build/theislab/scanpy/scanpy/plotting/_anndata.py:1984: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| gene_groups_ax.imshow(np.matrix(arr).T, aspect='auto', cmap=groupby_cmap, norm=norm) | |
| scanpy/tests/test_preprocessing_distributed.py::TestPreprocessingDistributed::test_write_zarr[direct] | |
| scanpy/tests/test_preprocessing_distributed.py::TestPreprocessingDistributed::test_write_zarr[dask] | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/zarr/storage.py:388: UserWarning: an object_codec is only needed for object arrays | |
| warnings.warn('an object_codec is only needed for object arrays') | |
| scanpy/tests/test_preprocessing_distributed.py::TestPreprocessingDistributed::test_write_zarr[dask] | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/anndata/readwrite/write.py:190: UserWarning: Could not save field with key = "X" to hdf5 file: int() argument must be a string, a bytes-like object or a number, not 'tuple' | |
| 'to hdf5 file: {}'.format(key, e)) | |
| scanpy/tests/test_rank_genes_groups_logreg.py::test_rank_genes_groups_with_renamed_categories | |
| scanpy/tests/test_rank_genes_groups_logreg.py::test_rank_genes_groups_with_renamed_categories | |
| scanpy/tests/notebooks/test_pbmc3k.py::test_pbmc3k | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/sklearn/linear_model/logistic.py:433: FutureWarning: Default solver will be changed to 'lbfgs' in 0.22. Specify a solver to silence this warning. | |
| FutureWarning) | |
| scanpy/tests/test_rank_genes_groups_logreg.py::test_rank_genes_groups_with_renamed_categories | |
| scanpy/tests/test_rank_genes_groups_logreg.py::test_rank_genes_groups_with_renamed_categories | |
| scanpy/tests/notebooks/test_pbmc3k.py::test_pbmc3k | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/sklearn/linear_model/logistic.py:460: FutureWarning: Default multi_class will be changed to 'auto' in 0.22. Specify the multi_class option to silence this warning. | |
| "this warning.", FutureWarning) | |
| scanpy/tests/test_rank_genes_groups_logreg.py::test_rank_genes_groups_with_renamed_categories | |
| /home/travis/build/theislab/scanpy/scanpy/tools/_rank_genes_groups.py:224: RuntimeWarning: invalid value encountered in log2 | |
| rankings_gene_logfoldchanges.append(np.log2(foldchanges[global_indices])) | |
| -- Docs: https://docs.pytest.org/en/latest/warnings.html | |
| [31m[1m============= 1 failed, 71 passed, 322 warnings in 130.43 seconds ==============[0m | |
| travis_time:end:11083c02:start=1554118553410299154,finish=1554118685125052387,duration=131714753233 | |
| [0K[31;1mThe command "pytest --ignore=scanpy/tests/_images" exited with 1.[0m | |
| travis_time:start:068fe1d8 | |
| [0K$ python setup.py check --restructuredtext --strict | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 | |
| return f(*args, **kwds) | |
| /home/travis/virtualenv/python3.5.6/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 | |
| return f(*args, **kwds) | |
| running check | |
| travis_time:end:068fe1d8:start=1554118685131202438,finish=1554118687596419592,duration=2465217154 | |
| [0K[32;1mThe command "python setup.py check --restructuredtext --strict" exited with 0.[0m | |
| travis_time:start:0cadbf78 | |
| [0K$ rst2html.py --halt=2 README.rst >/dev/null | |
| travis_time:end:0cadbf78:start=1554118687602455281,finish=1554118687784410946,duration=181955665 | |
| [0K[32;1mThe command "rst2html.py --halt=2 README.rst >/dev/null" exited with 0.[0m | |
| travis_fold:start:cache.2 | |
| [0Kstore build cache | |
| travis_time:start:047f717b | |
| [0Ktravis_time:end:047f717b:start=1554118687789257672,finish=1554118687792346157,duration=3088485 | |
| [0Ktravis_time:start:1777578c | |
| [0K[32;1mchange detected (content changed, file is created, or file is deleted): | |
| /home/travis/.cache/pip/http/0/c/2/1/8/0c218d526767991766d9b365a4f3e4449ce3579fd8b0f96a707d5a52 | |
| /home/travis/.cache/pip/http/0/f/b/9/e/0fb9e3091de4f40ea9031e23c8e25fea79ee5e5b34dcff8f41dc7eae | |
| /home/travis/.cache/pip/http/2/f/f/d/d/2ffdd395dcb3a7e8edba3e0e56d3b4fe4ab9cf77874b9a82f9ab3534 | |
| /home/travis/.cache/pip/http/3/3/3/a/6/333a6a167445d3fe4d9ec04168abfd5cb0692c8d023f686d619d63eb | |
| /home/travis/.cache/pip/http/3/3/9/7/4/33974f84394d9a943f68359da08431dab4af9f86c33962982ea21b5f | |
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| /home/travis/.cache/pip/http/3/c/d/e/8/3cde89ac405bfd9ac5cb6923d04b85ae2c188e1365361fc60623c282 | |
| /home/travis/.cache/pip/http/4/6/7/8/2/46782699abbec5872b7532f8fdb60b49d903fe55317d456987dab6fe | |
| /home/travis/.cache/pip/http/4/6/d/d/6/46dd6c7d38d9678c38989b4cd14dca9da87ef21be758c0f56968decd | |
| /home/travis/.cache/pip/http/4/e/2/9/8/4e | |
| [0m | |
| [32;1m... | |
| [0m | |
| [32;1mchanges detected, packing new archive[0m | |
| . | |
| . | |
| [32;1muploading PR.579/cache-linux-trusty-af97160760c6a1f71d47d7257ec5900e97fcc7d2b78b0e11646772eb55c1deb7--python-3.5.tgz[0m | |
| [32;1mcache uploaded[0m | |
| travis_time:end:1777578c:start=1554118687796595195,finish=1554118707088128961,duration=19291533766 | |
| [0Ktravis_fold:end:cache.2 | |
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| Done. Your build exited with 1. |
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