https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18341877 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-026 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 5 Jan 10:43:38 ntpdate[1940]: adjust time server 10.211.37.1 offset -0.021017 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18341877 --image-type chroot /home/buildd/filecache-default/e96c25c651525abc9f0cabeb95ea71010abf4ecb Creating target for build PACKAGEBUILD-18341877 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18341877 Starting target for build PACKAGEBUILD-18341877 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18341877 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18341877 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18341877 Updating target for build PACKAGEBUILD-18341877 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 Packages [966 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted amd64 Packages [18.4 kB] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [5768 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe amd64 Packages [8671 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse amd64 Packages [152 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [110 kB] Fetched 15.9 MB in 3s (4963 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 94 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 70.2 MB of archives. After this operation, 51.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main amd64 libc6-dev amd64 2.30-0ubuntu3 [2549 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 libc-dev-bin amd64 2.30-0ubuntu3 [71.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 linux-libc-dev amd64 5.3.0-24.26 [1096 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 libisl22 amd64 0.22-2 [592 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 libcc1-0 amd64 9.2.1-21ubuntu1 [49.0 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-x86-64-linux-gnu amd64 2.33.1-6ubuntu3 [1639 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libbinutils amd64 2.33.1-6ubuntu3 [474 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-common amd64 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 binutils amd64 2.33.1-6ubuntu3 [3400 B] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9-base amd64 9.2.1-21ubuntu1 [19.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc1 amd64 1:9.2.1-21ubuntu1 [40.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 libgomp1 amd64 9.2.1-21ubuntu1 [89.3 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 libitm1 amd64 9.2.1-21ubuntu1 [28.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 libatomic1 amd64 9.2.1-21ubuntu1 [9236 B] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 libasan5 amd64 9.2.1-21ubuntu1 [395 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 liblsan0 amd64 9.2.1-21ubuntu1 [139 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 libtsan0 amd64 9.2.1-21ubuntu1 [301 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 libubsan1 amd64 9.2.1-21ubuntu1 [130 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main amd64 libquadmath0 amd64 9.2.1-21ubuntu1 [146 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 g++-9 amd64 9.2.1-21ubuntu1 [11.0 MB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++-9-dev amd64 9.2.1-21ubuntu1 [1709 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc-9-dev amd64 9.2.1-21ubuntu1 [2362 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9 amd64 9.2.1-21ubuntu1 [10.4 MB] Get:24 http://ftpmaster.internal/ubuntu focal/main amd64 cpp-9 amd64 9.2.1-21ubuntu1 [9729 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++6 amd64 9.2.1-21ubuntu1 [512 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libc6 amd64 2.30-0ubuntu3 [2725 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 base-files amd64 11ubuntu2 [60.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 debianutils amd64 4.9.1 [85.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 bash amd64 5.0-5ubuntu1 [639 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 bsdutils amd64 1:2.34-0.1ubuntu4 [63.8 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 gzip amd64 1.10-0ubuntu4 [95.3 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 hostname amd64 3.23 [11.4 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-bin amd64 6.1+20191019-1ubuntu1 [172 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libperl5.30 amd64 5.30.0-9 [3950 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 perl amd64 5.30.0-9 [224 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 perl-base amd64 5.30.0-9 [1511 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 bzip2 amd64 1.0.8-2 [34.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-1.0 amd64 1.0.8-2 [32.3 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 libblkid1 amd64 2.34-0.1ubuntu4 [137 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 libuuid1 amd64 2.34-0.1ubuntu4 [20.5 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libfdisk1 amd64 2.34-0.1ubuntu4 [175 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-8-0 amd64 10.34-7 [197 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libselinux1 amd64 3.0-1 [68.7 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libmount1 amd64 2.34-0.1ubuntu4 [149 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses6 amd64 6.1+20191019-1ubuntu1 [101 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libtinfo6 amd64 6.1+20191019-1ubuntu1 [85.9 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libncursesw6 amd64 6.1+20191019-1ubuntu1 [132 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libsmartcols1 amd64 2.34-0.1ubuntu4 [101 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 fdisk amd64 2.34-0.1ubuntu4 [120 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 util-linux amd64 2.34-0.1ubuntu4 [1022 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libdebconfclient0 amd64 0.250ubuntu2 [6336 B] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 base-passwd amd64 3.5.47 [47.7 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libc-bin amd64 2.30-0ubuntu3 [625 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 sysvinit-utils amd64 2.96-1ubuntu1 [20.8 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 liblz4-1 amd64 1.9.2-2 [55.9 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 systemd-sysv amd64 244-3ubuntu1 [9368 B] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libacl1 amd64 2.2.53-5ubuntu1 [18.7 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libapparmor1 amd64 2.13.3-7ubuntu1 [34.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libcap-ng0 amd64 0.7.9-2.1 [11.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit1 amd64 1:2.8.5-2ubuntu5 [39.1 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libcap2 amd64 1:2.27-1 [14.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 libudev1 amd64 244-3ubuntu1 [76.3 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-2ubuntu7 [127 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 libjson-c4 amd64 0.13.1+dfsg-6 [29.2 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libcryptsetup12 amd64 2:2.2.2-1ubuntu1 [182 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 libnettle7 amd64 3.5.1+really3.5.1-2 [114 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libhogweed5 amd64 3.5.1+really3.5.1-2 [138 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libp11-kit0 amd64 0.23.18.1-2 [189 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libtasn1-6 amd64 4.15.0-2 [37.7 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 libgnutls30 amd64 3.6.11.1-2 [793 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libkmod2 amd64 26-3ubuntu1 [42.9 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libpam0g amd64 1.3.1-5ubuntu4 [55.4 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 libseccomp2 amd64 2.4.2-2ubuntu1 [39.4 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 mount amd64 2.34-0.1ubuntu4 [115 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 systemd amd64 244-3ubuntu1 [3677 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 libsystemd0 amd64 244-3ubuntu1 [260 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 libzstd1 amd64 1.4.4+dfsg-1 [237 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 libapt-pkg5.90 amd64 1.9.5 [851 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 libgcrypt20 amd64 1.8.5-3ubuntu1 [419 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 gpgv amd64 2.2.17-3ubuntu1 [200 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 apt amd64 1.9.5 [1281 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules-bin amd64 1.3.1-5ubuntu4 [37.7 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules amd64 1.3.1-5ubuntu4 [250 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libattr1 amd64 1:2.4.48-5 [12.7 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 libsepol1 amd64 3.0-1 [252 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage-common all 3.0-1 [9880 B] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage1 amd64 3.0-1 [85.3 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libsqlite3-0 amd64 3.30.1-1ubuntu1 [540 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 gpg amd64 2.2.17-3ubuntu1 [479 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 gpgconf amd64 2.2.17-3ubuntu1 [124 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 gpg-agent amd64 2.2.17-3ubuntu1 [232 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile-bin amd64 1.16-1.1 [11.7 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile1 amd64 1.16-1.1 [6680 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.2 MB in 2s (30.3 MB/s) (Reading database ... 12741 files and directories currently installed.) 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Setting up libstdc++-9-dev:amd64 (9.2.1-21ubuntu1) ... Setting up systemd (244-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-21ubuntu1) ... Setting up systemd-sysv (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18341877 amd64 focal -c chroot:build-PACKAGEBUILD-18341877 --arch=amd64 --dist=focal --nolog -A pybel_0.12.1-1.dsc Initiating build PACKAGEBUILD-18341877 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-026.buildd +==============================================================================+ | pybel 0.12.1-1 (amd64) 05 Jan 2020 10:44 | +==============================================================================+ Package: pybel Version: 0.12.1-1 Source Version: 0.12.1-1 Distribution: focal Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/pybel-bHT1bp/pybel-0.12.1' with '<>' I: NOTICE: Log filtering will replace 'build/pybel-bHT1bp' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18341877/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pybel_0.12.1-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-C_dpHj/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-C_dpHj/apt_archive ./ InRelease Get:2 copy:/<>/resolver-C_dpHj/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-C_dpHj/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-C_dpHj/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-C_dpHj/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-C_dpHj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14652 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11), dh-python, python3-all, python3-setuptools, python3-click-plugins, python3-networkx, python3-pyparsing, python3-requests-file, python3-six, python3-sqlalchemy, python3-tqdm Filtered Build-Depends: debhelper (>= 11), dh-python, python3-all, python3-setuptools, python3-click-plugins, python3-networkx, python3-pyparsing, python3-requests-file, python3-six, python3-sqlalchemy, python3-tqdm dpkg-deb: building package 'sbuild-build-depends-pybel-dummy' in '/<>/resolver-RhhvJu/apt_archive/sbuild-build-depends-pybel-dummy.deb'. Ign:1 copy:/<>/resolver-RhhvJu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-RhhvJu/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-RhhvJu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-RhhvJu/apt_archive ./ Sources [280 B] Get:5 copy:/<>/resolver-RhhvJu/apt_archive ./ Packages [606 B] Fetched 3005 B in 0s (285 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install pybel build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support po-debconf python3 python3-all python3-certifi python3-chardet python3-click python3-click-plugins python3-colorama python3-decorator python3-distutils python3-idna python3-lib2to3 python3-minimal python3-networkx python3-pkg-resources python3-pyparsing python3-requests python3-requests-file python3-setuptools python3-six python3-sqlalchemy python3-tqdm python3-urllib3 python3.7 python3.7-minimal python3.8 python3.8-minimal Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3-gdal python3-scipy python-networkx-doc python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-setuptools-doc python-sqlalchemy-doc python3-psycopg2 python3-mysqldb python3-fdb python3.7-venv python3.7-doc binfmt-support python3.8-venv python3.8-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl python3-numpy python3-yaml python3-sqlalchemy-ext The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support po-debconf python3 python3-all python3-certifi python3-chardet python3-click python3-click-plugins python3-colorama python3-decorator python3-distutils python3-idna python3-lib2to3 python3-minimal python3-networkx python3-pkg-resources python3-pyparsing python3-requests python3-requests-file python3-setuptools python3-six python3-sqlalchemy python3-tqdm python3-urllib3 python3.7 python3.7-minimal python3.8 python3.8-minimal sbuild-build-depends-pybel-dummy 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 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Setting up libpipeline1:amd64 (1.5.1-3) ... Setting up libpython3.8-minimal:amd64 (3.8.0-5) ... Setting up mime-support (3.64ubuntu1) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.63.3-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.7.1ubuntu1) ... Setting up libmagic1:amd64 (1:5.37-6) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.37-6) ... Setting up libicu63:amd64 (63.2-2) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-10) ... Setting up python3.8-minimal (3.8.0-5) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libpython3.8-stdlib:amd64 (3.8.0-5) ... Setting up python3.8 (3.8.0-5) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-8ubuntu1) ... Setting up libfile-stripnondeterminism-perl (1.6.3-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.5-2) ... Setting up libtool (2.4.6-11) ... Setting up m4 (1.4.18-4) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libpython3-stdlib:amd64 (3.7.5-1ubuntu1) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.5-2) ... Setting up gettext (0.19.8.1-10) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-sqlalchemy (1.2.18+ds1-2ubuntu3) ... /usr/lib/python3/dist-packages/sqlalchemy/orm/query.py:195: SyntaxWarning: "is not" with a literal. Did you mean "!="? if entities is not (): Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-2build1) ... Setting up python3-decorator (4.3.0-1.1build1) ... Setting up python3-pyparsing (2.4.2-1) ... Setting up python3-certifi (2019.11.28-1) ... Setting up python3-idna (2.6-2build1) ... Setting up python3-urllib3 (1.24.1-1ubuntu2) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu1) ... Setting up python3-setuptools (41.4.0-1) ... Setting up python3-colorama (0.3.7-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-tqdm (4.30.0-1) ... Setting up python3-all (3.7.5-1ubuntu1) ... Setting up python3-click (7.0-2) ... Setting up python3-networkx (2.2-1ubuntu4) ... /usr/lib/python3/dist-packages/networkx/convert_matrix.py:567: SyntaxWarning: "is" with a literal. Did you mean "=="? if python_type is 'void': /usr/lib/python3/dist-packages/networkx/drawing/nx_pydot.py:210: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is '': Setting up python3-chardet (3.0.4-4) ... Setting up python3-requests (2.21.0-1) ... Setting up python3-click-plugins (1.1.1-2) ... Setting up python3-requests-file (1.4.3-2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up sbuild-build-depends-pybel-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic amd64 (x86_64) Toolchain package versions: binutils_2.33.1-6ubuntu3 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-21ubuntu1 gcc-9_9.2.1-21ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 linux-libc-dev_5.3.0-24.26 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 binutils-x86-64-linux-gnu_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-21ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017ubuntu1 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu2 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu4 file_1:5.37-6 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-21ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-21ubuntu1 gcc-9-base_9.2.1-21ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.3-1build1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.5 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-21ubuntu1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-21ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.33.1-6ubuntu3 libblkid1_2.34-0.1ubuntu4 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcc1-0_9.2.1-21ubuntu1 libcom-err2_1.45.3-4ubuntu2 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu2 libdebhelper-perl_12.7.1ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu2 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu4 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-21ubuntu1 libgcc1_1:9.2.1-21ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.63.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-21ubuntu1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_9.2.1-21ubuntu1 libjson-c4_0.13.1+dfsg-6 libkmod2_26-3ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_9.2.1-21ubuntu1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1ubuntu4 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libpython3.8-minimal_3.8.0-5 libpython3.8-stdlib_3.8.0-5 libquadmath0_9.2.1-21ubuntu1 libreadline8_8.0-3 libseccomp2_2.4.2-2ubuntu1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu4 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu2 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244-3ubuntu1 libtasn1-6_4.15.0-2 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-11 libtsan0_9.2.1-21ubuntu1 libubsan1_9.2.1-21ubuntu1 libuchardet0_0.0.6-3 libudev1_244-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu4 libxml2_2.9.4+dfsg1-8ubuntu1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.0-24.26 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python3_3.7.5-1ubuntu1 python3-all_3.7.5-1ubuntu1 python3-certifi_2019.11.28-1 python3-chardet_3.0.4-4 python3-click_7.0-2 python3-click-plugins_1.1.1-2 python3-colorama_0.3.7-1 python3-decorator_4.3.0-1.1build1 python3-distutils_3.8.0-1 python3-idna_2.6-2build1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-1ubuntu1 python3-networkx_2.2-1ubuntu4 python3-pkg-resources_41.4.0-1 python3-pyparsing_2.4.2-1 python3-requests_2.21.0-1 python3-requests-file_1.4.3-2 python3-setuptools_41.4.0-1 python3-six_1.12.0-2build1 python3-sqlalchemy_1.2.18+ds1-2ubuntu3 python3-tqdm_4.30.0-1 python3-urllib3_1.24.1-1ubuntu2 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 python3.8_3.8.0-5 python3.8-minimal_3.8.0-5 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pybel-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu4 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Oct 23 12:16:04 2018 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pybel_0.12.1-1.dsc dpkg-source: info: extracting pybel in pybel-0.12.1 dpkg-source: info: unpacking pybel_0.12.1.orig.tar.gz dpkg-source: info: unpacking pybel_0.12.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying not_testing_what_fails.patch dpkg-source: info: applying python3_compat.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18341877 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18341877 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18341877 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pybel dpkg-buildpackage: info: source version 0.12.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from pybel-0.12.1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base:217: python3.8 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.8_pybel/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.7_pybel/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -rf src/PyBEL.egg-info/ make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3.8 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/canonicalize.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/tokens.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/cli.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/__main__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/language.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/constants.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel copying src/pybel/exceptions.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/mocks.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/mock_manager.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/generate.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/cases.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing copying src/pybel/testing/constants.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/nodes.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/edges.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/node_classes.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/namespaces.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl copying src/pybel/dsl/constants.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/dsl creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources copying src/pybel/resources/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources copying src/pybel/resources/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources copying src/pybel/resources/document.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources copying src/pybel/resources/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources copying src/pybel/resources/constants.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/parse_metadata.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/parse_bel.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/parse_identifier.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/parse_control.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser copying src/pybel/parser/baseparser.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/gpickle.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/extras.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/web.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/neo4j.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/line_utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/indra.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/nodelink.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/lines.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io copying src/pybel/io/jgif.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/io creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/cache_manager.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/database_io.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/base_manager.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/models.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/query_manager.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/defaults.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/lookup_manager.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/citation_utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager copying src/pybel/manager/make_json_serializable.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/manager creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/homology_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/egf_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/sialic_acid_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/various_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/braf_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/tloc_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples copying src/pybel/examples/statin_example.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/examples creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct copying src/pybel/struct/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct copying src/pybel/struct/operations.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct copying src/pybel/struct/graph.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct copying src/pybel/struct/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/annotation.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/definitions.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/namespace.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/write_utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/resources/definitions creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/variant.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_modification.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/location.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/fusion.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_modification.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_substitution.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/truncation.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_substitution.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/fragment.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/constants.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/modifiers creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/transfer.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/metadata.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/induction_expansion.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query copying src/pybel/struct/query/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query copying src/pybel/struct/query/query.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query copying src/pybel/struct/query/selection.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query copying src/pybel/struct/query/seeding.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query copying src/pybel/struct/query/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query copying src/pybel/struct/query/constants.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/query creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/edge_summary.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/provenance.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/errors.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/node_summary.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/graph_summary.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/summary creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/annotations.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/provenance.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/grouping creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/exc.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/pipeline.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/decorators.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/pipeline creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_predicates.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_predicate_builders.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_filters.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_selection.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/edge_predicate_builders.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/edge_predicates.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/edge_filters.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/filters creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/collapse.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/protein_rna_origins.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/collapse creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/upstream.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/neighborhood.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/expansion creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/deletion.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/protein_rna_origins.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/deletion creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/protein_rna_origins.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/inference creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/utils.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/annotations.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/upstream.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/__init__.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/neighborhood.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/paths.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/random_subgraph.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/citation.py -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/struct/mutation/induction running egg_info creating src/PyBEL.egg-info writing src/PyBEL.egg-info/PKG-INFO writing dependency_links to src/PyBEL.egg-info/dependency_links.txt writing entry points to src/PyBEL.egg-info/entry_points.txt writing requirements to src/PyBEL.egg-info/requires.txt writing top-level names to src/PyBEL.egg-info/top_level.txt writing manifest file 'src/PyBEL.egg-info/SOURCES.txt' reading manifest file 'src/PyBEL.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'scripts' warning: no files found matching '*.bel' under directory 'src/pybel/testing/bel' warning: no files found matching '*.belanno' under directory 'src/pybel/testing/belanno' warning: no files found matching '*.belns' under directory 'src/pybel/testing/belns' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.dylib' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no previously-included files matching '*.gpickle' found anywhere in distribution warning: no previously-included files found matching '.bumpversion.cfg' writing manifest file 'src/PyBEL.egg-info/SOURCES.txt' creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/isolated.bel -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/misordered.bel -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/slushy.bel -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/test_bel.bel -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/thorough.bel -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/bel creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/cell-line.belanno -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/confidence-1.0.0.belanno -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/mesh-diseases.belanno -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/species-taxonomy-id.belanno -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/test_an_1.belanno -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno creating /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/chebi.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/disease-ontology.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/go-biological-process.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/go-cellular-component.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/hgnc-human-genes.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/mesh-diseases.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_nocache.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1_updated.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_2.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_empty.belns -> /<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/canonicalize.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/tokens.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/cli.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/__main__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/language.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/constants.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel copying src/pybel/exceptions.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/mocks.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/mock_manager.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/generate.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/cases.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing copying src/pybel/testing/constants.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/nodes.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/edges.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/node_classes.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/namespaces.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl copying src/pybel/dsl/constants.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/dsl creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources copying src/pybel/resources/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources copying src/pybel/resources/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources copying src/pybel/resources/document.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources copying src/pybel/resources/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources copying src/pybel/resources/constants.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/parse_metadata.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/parse_bel.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/parse_identifier.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/parse_control.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser copying src/pybel/parser/baseparser.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/gpickle.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/extras.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/web.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/neo4j.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/line_utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/indra.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/nodelink.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/lines.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io copying src/pybel/io/jgif.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/io creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/cache_manager.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/database_io.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/base_manager.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/models.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/query_manager.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/defaults.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/lookup_manager.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/citation_utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager copying src/pybel/manager/make_json_serializable.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/manager creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/homology_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/egf_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/sialic_acid_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/various_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/braf_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/tloc_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples copying src/pybel/examples/statin_example.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/examples creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct copying src/pybel/struct/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct copying src/pybel/struct/operations.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct copying src/pybel/struct/graph.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct copying src/pybel/struct/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/annotation.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/definitions.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/namespace.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources/definitions copying src/pybel/resources/definitions/write_utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/resources/definitions creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/variant.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_modification.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/location.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/fusion.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_modification.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_substitution.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/truncation.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_substitution.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/fragment.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers copying src/pybel/parser/modifiers/constants.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/parser/modifiers creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/transfer.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/metadata.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation copying src/pybel/struct/mutation/induction_expansion.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query copying src/pybel/struct/query/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query copying src/pybel/struct/query/query.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query copying src/pybel/struct/query/selection.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query copying src/pybel/struct/query/seeding.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query copying src/pybel/struct/query/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query copying src/pybel/struct/query/constants.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/query creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/edge_summary.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/provenance.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/errors.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/node_summary.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary copying src/pybel/struct/summary/graph_summary.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/summary creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/annotations.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/provenance.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/grouping copying src/pybel/struct/grouping/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/grouping creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/exc.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/pipeline.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/pipeline copying src/pybel/struct/pipeline/decorators.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/pipeline creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_predicates.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_predicate_builders.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_filters.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/node_selection.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/edge_predicate_builders.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/edge_predicates.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters copying src/pybel/struct/filters/edge_filters.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/filters creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/collapse.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/protein_rna_origins.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/collapse creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/upstream.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/neighborhood.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/expansion creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/deletion.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/protein_rna_origins.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/deletion creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/protein_rna_origins.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/inference creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/utils.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/annotations.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/upstream.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/__init__.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/neighborhood.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/paths.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/random_subgraph.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/citation.py -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/struct/mutation/induction running egg_info writing src/PyBEL.egg-info/PKG-INFO writing dependency_links to src/PyBEL.egg-info/dependency_links.txt writing entry points to src/PyBEL.egg-info/entry_points.txt writing requirements to src/PyBEL.egg-info/requires.txt writing top-level names to src/PyBEL.egg-info/top_level.txt reading manifest file 'src/PyBEL.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'scripts' warning: no files found matching '*.bel' under directory 'src/pybel/testing/bel' warning: no files found matching '*.belanno' under directory 'src/pybel/testing/belanno' warning: no files found matching '*.belns' under directory 'src/pybel/testing/belns' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.dylib' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no previously-included files matching '*.gpickle' found anywhere in distribution warning: no previously-included files found matching '.bumpversion.cfg' writing manifest file 'src/PyBEL.egg-info/SOURCES.txt' creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/isolated.bel -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/misordered.bel -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/slushy.bel -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/test_bel.bel -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/thorough.bel -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/bel creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/cell-line.belanno -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/confidence-1.0.0.belanno -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/mesh-diseases.belanno -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/species-taxonomy-id.belanno -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/test_an_1.belanno -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belanno creating /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/chebi.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/disease-ontology.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/go-biological-process.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/go-cellular-component.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/hgnc-human-genes.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/mesh-diseases.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_nocache.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1_updated.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_2.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_empty.belns -> /<>/.pybuild/cpython3_3.7_pybel/build/pybel/testing/resources/belns dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /<>/.pybuild/cpython3_3.8_pybel/build; python3.8 -m unittest discover -v test_abundance (tests.test_canonicalization.TestCanonicalize) Test canonicalization of abundances. ... ok test_bioprocess (tests.test_canonicalization.TestCanonicalize) ... ok test_canonicalize_fusion_range_dsl (tests.test_canonicalization.TestCanonicalize) Test canonicalization of enumerated fusion ranges. ... ok test_canonicalize_variant_dsl (tests.test_canonicalization.TestCanonicalize) Use the __str__ functions in the DSL to create BEL instead of external pybel.canonicalize. ... ok test_complex_abundance (tests.test_canonicalization.TestCanonicalize) ... ok test_composite_abundance (tests.test_canonicalization.TestCanonicalize) ... ok test_gene_fusion_specified (tests.test_canonicalization.TestCanonicalize) ... ok test_gene_reference (tests.test_canonicalization.TestCanonicalize) ... ok test_mirna_reference (tests.test_canonicalization.TestCanonicalize) ... ok test_named_complex_abundance (tests.test_canonicalization.TestCanonicalize) ... ok test_pathology (tests.test_canonicalization.TestCanonicalize) ... ok test_postpend_location_failure (tests.test_canonicalization.TestCanonicalize) ... ok test_protein_fragment (tests.test_canonicalization.TestCanonicalize) ... ok test_protein_pmod (tests.test_canonicalization.TestCanonicalize) ... ok test_protein_reference (tests.test_canonicalization.TestCanonicalize) ... ok test_reaction (tests.test_canonicalization.TestCanonicalize) ... ok test_rna_fusion_specified (tests.test_canonicalization.TestCanonicalize) ... ok test_rna_fusion_unspecified (tests.test_canonicalization.TestCanonicalize) ... ok test_canonicalize_edge_info (tests.test_canonicalization.TestCanonicalizeEdge) ... ok test_failure (tests.test_canonicalization.TestCanonicalizeEdge) ... ok test_subject_degradation_location (tests.test_canonicalization.TestCanonicalizeEdge) ... ok test_translocation (tests.test_canonicalization.TestCanonicalizeEdge) ... ok test_multiple_annotations (tests.test_canonicalization.TestSerializeBEL) ... ok test_simple (tests.test_canonicalization.TestSerializeBEL) Tests a scenario with a qualified edge, but no annotaitons ... ok test_single_annotation (tests.test_canonicalization.TestSerializeBEL) Tests a scenario with a qualified edge, but no annotaitons ... ok test_get_parent (tests.test_dsl.TestCentralDogma) Test the get_parent function in :class:`CentralDogmaAbundance`s. ... ok test_with_variants (tests.test_dsl.TestCentralDogma) Test the `with_variant` function in :class:`CentralDogmaAbundance`s. ... ok test_with_variants_list (tests.test_dsl.TestCentralDogma) Test the `with_variant` function in :class:`CentralDogmaAbundance`s. ... ok test_abundance_as_bel (tests.test_dsl.TestDSL) Test converting an abundance to BEL with a name that does not need quotation. ... ok test_abundance_as_bel_quoted (tests.test_dsl.TestDSL) Test converting an abundance to BEL with a name that needs quotation. ... ok test_add_identified_node (tests.test_dsl.TestDSL) Test what happens when a node with only an identifier is added to a graph. ... ok test_add_named_node (tests.test_dsl.TestDSL) Test adding a named node to a BEL graph. ... ok test_add_robust_node (tests.test_dsl.TestDSL) Test adding a node with both a name and identifier. ... ok test_as_tuple (tests.test_dsl.TestDSL) ... ok test_complex_with_name (tests.test_dsl.TestDSL) Test what happens with a named complex. ... ok test_gene_fusion (tests.test_dsl.TestDSL) Test serialization of a gene fusion to BEL with a explicit fusion ranges. ... ok test_gene_fusion_missing_explicit (tests.test_dsl.TestDSL) Test serialization of a gene fusion to BEL with an explicit missing fusion ranges. ... ok test_gene_fusion_missing_implicit (tests.test_dsl.TestDSL) Test serialization of a gene fusion to BEL with a implicit missing fusion ranges. ... ok test_missing_information (tests.test_dsl.TestDSL) Test that entity and abundance functions raise on missing name/identifier. ... ok test_str_has_both (tests.test_dsl.TestDSL) ... ok test_str_has_identifier (tests.test_dsl.TestDSL) ... ok test_example_bytes (tests.test_io.test_import.TestExampleInterchange) Test the round-trip through bytes. ... ok test_example_pickle (tests.test_io.test_import.TestExampleInterchange) Test the round-trip through a pickle. ... ok test_thorough_json (tests.test_io.test_import.TestExampleInterchange) Test the round-trip through node-link JSON. ... ok test_thorough_json_file (tests.test_io.test_import.TestExampleInterchange) Test the round-trip through a node-link JSON file. ... ok test_thorough_jsons (tests.test_io.test_import.TestExampleInterchange) Test the round-trip through a node-link JSON string. ... ok test_annotations (tests.test_io.test_import.TestFull) ... ok test_annotations_with_list (tests.test_io.test_import.TestFull) ... ok test_annotations_with_multilist (tests.test_io.test_import.TestFull) ... ok test_missing_citation (tests.test_io.test_import.TestFull) ... ok test_regex_match (tests.test_io.test_import.TestFull) ... ok test_regex_mismatch (tests.test_io.test_import.TestFull) ... ok test_semantic_failure (tests.test_io.test_import.TestFull) ... ok Line 0000039 - General Failure: a(CHEBI:"oxygen atom") -> geneAbundance(HGNC:AKT1,gmod(M)) Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/io/line_utils.py", line 204, in parse_statements bel_parser.parseString(line, line_number=line_number) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/baseparser.py", line 50, in parseString return self.language.parseString(line) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1929, in parseString loc, tokens = self._parse(instring, 0) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4222, in parseImpl ret = e._parse(instring, loc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1702, in _parseNoCache tokens = fn(instring, tokensStart, retTokens) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1308, in wrapper ret = func(*args[limit[0]:]) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 837, in _handle_relation_harness self._handle_relation(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 790, in _handle_relation object_node_dsl = self.ensure_node(tokens[OBJECT]) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 886, in ensure_node node_dsl = parse_result_to_dsl(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 35, in parse_result_to_dsl return _variant_po_to_dict(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 123, in _variant_po_to_dict variants=[ File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 124, in _variant_to_dsl_helper(variant_tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 143, in _variant_to_dsl_helper name=tokens[IDENTIFIER][NAME], File "/usr/lib/python3/dist-packages/pyparsing.py", line 590, in __getitem__ return self.__tokdict[i][-1][0] KeyError: 'name' trunc() is deprecated. Re-encode with reference terminal amino acid in HGVS: p(HGNC:AKT1, trunc(40)) -> p(HGNC:CHCHD4, fusion(HGNC:AIFM1)) trunc() is deprecated. Re-encode with reference terminal amino acid in HGVS: p(HGNC:AKT1, trunc(40)) -> p(HGNC:CHCHD4, fusion(HGNC:AIFM1)) trunc() is deprecated. Re-encode with reference terminal amino acid in HGVS: p(HGNC:AKT1, trunc(40)) -> p(HGNC:CHCHD4, fusion(HGNC:AIFM1)) trunc() is deprecated. Re-encode with reference terminal amino acid in HGVS: p(HGNC:AKT1, trunc(40)) -> p(HGNC:CHCHD4, fusion(HGNC:AIFM1)) Line 0000003 - VersionFormatWarning: Version string "0.0" neither is a date like YYYYMMDD nor adheres to semantic versioning. See http://semver.org/ Missing required document metadata: ContactInfo Line 0000026 - MissingAnnotationKeyWarning: "STATEMENT_GROUP" is not set, so it can't be unset Line 0000029 - MissingAnnotationKeyWarning: "Citation" is not set, so it can't be unset Line 0000034 - CitationTooShortException: [pos:4] Citation is missing required fields: SET Citation = {"PubMed"} Line 0000037 - InvalidCitationType: [pos:4] "Pubmed" is not a valid citation type Line 0000040 - InvalidPubMedIdentifierWarning: [pos:4] "Fake Reference" is not a valid PubMed identifier Line 0000043 - MissingCitationException: Missing citation; can't add: p(HGNC:AKT1) -- p(HGNC:AKT2) Line 0000048 - MissingAnnotationKeyWarning: "Evidence" is not set, so it can't be unset Line 0000051 - MissingAnnotationKeyWarning: "PowerLevel" is not set, so it can't be unset Line 0000054 - MissingSupportWarning: Missing evidence; can't add: p(HGNC:AKT1) -- p(HGNC:AKT2) Line 0000059 - NakedNameWarning: [pos:18] "response to oxidative stress" should be qualified with a valid namespace Line 0000062 - UndefinedNamespaceWarning: "UNDEFINED" is not a defined namespace Line 0000065 - MissingNamespaceNameWarning: "maybe response to oxidative stress" is not in the GO namespace Line 0000068 - UndefinedAnnotationWarning: "UNDEFINED_ANNOTATION" is not defined Line 0000071 - MissingAnnotationKeyWarning: "TextLocation" is not set, so it can't be unset Line 0000074 - IllegalAnnotationValueWarning: "Nope" is not defined in the TextLocation annotation Line 0000077 - MissingAnnotationRegexWarning: "Nine Thousand" doesn't match the regex for PowerLevel annotation Line 0000080 - MissingNamespaceRegexWarning: "rs123123-A" doesn't match the regex for dbSNP namespace Line 0000083 - MalformedTranslocationWarning: [pos:4] Unqualified translocation: tloc(p(HGNC:AKT1)) -- p(HGNC:AKT2) [['Protein', 'HGNC', 'AKT1']] Line 0000086 - PlaceholderAminoAcidWarning: [pos:23] Placeholder amino acid found: X Line 0000089 - NestedRelationWarning: Nesting is not supported. Split this statement: p(HGNC:AKT1) -> (p(HGNC:AKT2) -> biologicalProcess(GO:"response to oxidative stress")) Line 0000092 - InvalidFunctionSemantic: BiologicalProcess HGNC:AKT1 should be encoded as one of: RNA, miRNA, Gene, Protein Line 0000098 - General Parser Failure: p(HGNC:TP53,sub(Q,R,248)) directlyDecreases transcriptionalActivity(proteinAbundance(HGNC:TP53)) test_isolated_compile (tests.test_io.test_import.TestInterchange) ... ok test_isolated_upgrade (tests.test_io.test_import.TestInterchange) ... ok test_misordered_compile (tests.test_io.test_import.TestInterchange) Test that non-citation clearing mode works. ... ok test_simple_compile (tests.test_io.test_import.TestInterchange) ... ok test_slushy (tests.test_io.test_import.TestInterchange) ... ok test_slushy_bytes (tests.test_io.test_import.TestInterchange) ... ok test_slushy_graphml (tests.test_io.test_import.TestInterchange) ... ok test_slushy_json (tests.test_io.test_import.TestInterchange) ... ok test_slushy_syntax_errors (tests.test_io.test_import.TestInterchange) ... ok test_thorough_bytes (tests.test_io.test_import.TestInterchange) ... FAIL test_thorough_csv (tests.test_io.test_import.TestInterchange) ... ok test_thorough_graphml (tests.test_io.test_import.TestInterchange) ... ok test_thorough_gsea (tests.test_io.test_import.TestInterchange) ... ok test_thorough_json (tests.test_io.test_import.TestInterchange) ... FAIL test_thorough_json_file (tests.test_io.test_import.TestInterchange) ... FAIL test_thorough_jsons (tests.test_io.test_import.TestInterchange) ... FAIL test_thorough_path (tests.test_io.test_import.TestInterchange) ... FAIL test_thorough_pickle (tests.test_io.test_import.TestInterchange) ... FAIL test_thorough_sif (tests.test_io.test_import.TestInterchange) ... ok test_thorough_upgrade (tests.test_io.test_import.TestInterchange) ... FAIL test_import_warning (tests.test_io.test_import.TestRandom) Tests an error is thrown when the version is set wrong ... ok test_jgif_interchange (tests.test_io.test_jgif.TestJgif) Tests data from CBN ... ok test_sanitize_1 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY Mon DD. ... ok test_sanitize_2 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY Mon. ... ok test_sanitize_3 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY. ... ok test_sanitize_4 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY Mon-Mon. ... ok test_sanitize_5 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY Season. ... ok test_sanitize_6 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY Mon DD-DD. ... ok test_sanitize_7 (tests.test_manager.test_citation_utils.TestSanitizeDate) Test YYYY Mon DD-Mon DD. ... ok test_sanitize_nope (tests.test_manager.test_citation_utils.TestSanitizeDate) Test failure. ... ok test_fail_connection_none (tests.test_manager.test_connection.TestInstantiation) Test that a None causes a huge error. ... ok test_instantiate_init (tests.test_manager.test_connection.TestInstantiation) Test what happens when no connection is specified for the normal constructor. ... ok test_instantiate_manager_connection_fail_too_many_keyword (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_engine_fail_too_many_keywords (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_engine_missing (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_fail_positional (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_keyword (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_positional (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_positional_with_keyword (tests.test_manager.test_connection.TestInstantiation) ... ok test_instantiate_manager_session_missing (tests.test_manager.test_connection.TestInstantiation) ... ok test_get_annotation_entries_no_data (tests.test_manager.test_manager_definitions.TestDefinitionManagers) Test that if there's no ANNOTATIONS entry in the data, it just returns none. ... ok test_insert_annotation (tests.test_manager.test_manager_definitions.TestDefinitionManagers) ... ok test_insert_namespace_nocache (tests.test_manager.test_manager_definitions.TestDefinitionManagers) Test that this namespace isn't cached ... /usr/lib/python3/dist-packages/sqlalchemy/sql/elements.py:1870: ResourceWarning: unclosed file <_io.FileIO name='/<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns/test_nocache.belns' mode='rb' closefd=True> return list(itertools.chain(*[c._from_objects for c in self.clauses])) ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_insert_namespace_persistent (tests.test_manager.test_manager_definitions.TestDefinitionManagers) ... ok test_drop_all_networks (tests.test_manager.test_manager_drop.TestCascades) When all networks are dropped, make sure all the edges and network_edge mappings are gone too ... ok test_drop_edge (tests.test_manager.test_manager_drop.TestCascades) When an edge gets dropped, make sure the network doesn't have as many edges, but nodes get to stay ... ok test_drop_modification (tests.test_manager.test_manager_drop.TestCascades) Don't let this happen ... ok test_drop_namespace (tests.test_manager.test_manager_drop.TestCascades) ... ok test_drop_network_1 (tests.test_manager.test_manager_drop.TestCascades) When a network gets dropped, drop all of the edges if they don't appear in other networks ... ok test_drop_network_2 (tests.test_manager.test_manager_drop.TestCascades) When a network gets dropped, drop all of the edges if they don't appear in other networks ... ok test_drop_node (tests.test_manager.test_manager_drop.TestCascades) Makes sure that when a node gets dropped, its in-edges AND out-edges also do ... ok test_drop_property (tests.test_manager.test_manager_drop.TestCascades) Don't let this happen ... ok test_get_orphan_edges (tests.test_manager.test_manager_drop.TestCascades) ... ok test_simple (tests.test_manager.test_manager_drop.TestReconstituteNodeTuples) This test checks that the network can be added and dropped ... ok test_complex (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_composite (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_dimer_complex (tests.test_manager.test_manager_graph.TestAddNodeFromData) Tests what happens if a BEL statement complex(p(X), p(X)) is added ... ok test_fusion (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_multiple_variants (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_nested_complex (tests.test_manager.test_manager_graph.TestAddNodeFromData) Checks what happens if a theoretical BEL statement `complex(p(X), complex(p(Y), p(Z)))` is added ... ok test_reaction (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_simple (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_single_variant (tests.test_manager.test_manager_graph.TestAddNodeFromData) ... ok test_authors (tests.test_manager.test_manager_graph.TestEdgeStore) ... ok test_citations (tests.test_manager.test_manager_graph.TestEdgeStore) ... ok test_edges (tests.test_manager.test_manager_graph.TestEdgeStore) ... ok test_evidences (tests.test_manager.test_manager_graph.TestEdgeStore) ... ok test_nodes (tests.test_manager.test_manager_graph.TestEdgeStore) ... ok test_reconstitute (tests.test_manager.test_manager_graph.TestEdgeStore) ... ok test_get_or_create_author (tests.test_manager.test_manager_graph.TestEnsure) This tests getting or creating author with unicode characters ... ok test_get_or_create_citation (tests.test_manager.test_manager_graph.TestEnsure) ... ok test_get_or_create_citation_full (tests.test_manager.test_manager_graph.TestEnsure) ... ok test_get_or_create_evidence (tests.test_manager.test_manager_graph.TestEnsure) ... ok test_direct_has_namespace (tests.test_manager.test_manager_graph.TestEquivalentNodes) ... ok test_indirect_has_namespace (tests.test_manager.test_manager_graph.TestEquivalentNodes) ... ok test_triangle_has_namespace (tests.test_manager.test_manager_graph.TestEquivalentNodes) ... ok test_get_graph_missing (tests.test_manager.test_manager_graph.TestNetworkCache) ... ok test_get_network_missing (tests.test_manager.test_manager_graph.TestNetworkCache) ... ok test_reload (tests.test_manager.test_manager_graph.TestNetworkCache) Tests that a graph with the same name and version can't be added twice ... ok test_upload_with_tloc (tests.test_manager.test_manager_graph.TestNetworkCache) Test that the RAS translocation example graph can be uploaded. ... ok test_no_activity (tests.test_manager.test_manager_graph.TestNoAddNode) Test that when an uncached custom namespace is used in the activity on an edge, the edge doesn't get ... uncached namespace e04f5634-7301-4 in fusion() ok test_no_gene_modification (tests.test_manager.test_manager_graph.TestNoAddNode) Test that a gene node whose gmod variant is in the uncached namespaces set can't be added. ... uncached namespace c0a26e8a-299c-4 in fusion() could not create g(HGNC:YFG, gmod(e227f6aa-df41-4:dummy)) because had an uncachable modification can not add node g(HGNC:YFG, gmod(e227f6aa-df41-4:dummy)) ok test_no_location (tests.test_manager.test_manager_graph.TestNoAddNode) Test that when using a custom namespace in the location the edge doesn't get stored. ... uncached namespace efbc4fa5-cad9-4 in loc() on line None ok test_no_node_fusion_3p (tests.test_manager.test_manager_graph.TestNoAddNode) Test that a fusion node whose 3P partner's namespace is in the uncached namespaces set can't be added. ... uncached namespace 36fe5303-00e5-4 in fusion() could not create p(fus(HGNC:YFG, "?", 45299d82-146f-4:AKT1, "?")) because had an uncachable modification can not add node p(fus(HGNC:YFG, "?", 45299d82-146f-4:AKT1, "?")) ok test_no_node_fusion_5p (tests.test_manager.test_manager_graph.TestNoAddNode) Test that a node whose namespace is in the uncached namespaces set can't be added. ... uncached namespace c25da11a-96ff-4 in fusion() could not create p(fus(abcf3eaf-f06b-4:YFG, "?", HGNC:YFG, "?")) because had an uncachable modification can not add node p(fus(abcf3eaf-f06b-4:YFG, "?", HGNC:YFG, "?")) ok test_no_node_name (tests.test_manager.test_manager_graph.TestNoAddNode) Test that a node whose namespace is in the uncached namespaces set can't be added. ... ok test_no_protein_modification (tests.test_manager.test_manager_graph.TestNoAddNode) Test that a protein node whose pmod variant is in the uncached namespaces set can't be added. ... uncached namespace 00e7b938-5bdc-4 in fusion() could not create p(HGNC:YFG, pmod(b47cc6ae-e2df-4:dummy)) because had an uncachable modification can not add node p(HGNC:YFG, pmod(b47cc6ae-e2df-4:dummy)) ok test_no_translocation (tests.test_manager.test_manager_graph.TestNoAddNode) Test that a translocation using custom namespaces doesn't get stored. ... uncached namespace 992cfb99-045d-4 in tloc() on line None ok test_regex_lookup (tests.test_manager.test_manager_graph.TestNoAddNode) Test that regular expression nodes get love too. ... ok test_query_citation_by_reference (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_citation_by_type (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_bel (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_evidence_wildcard (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_mixed (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_mixed_no_result (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_relation_wildcard (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_source_function (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_edge_by_target_function (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_node_bel_1 (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_node_bel_2 (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_node_namespace_wildcard (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_node_type (tests.test_manager.test_manager_graph.TestQuery) ... ok test_query_node_type_missing (tests.test_manager.test_manager_graph.TestQuery) ... ok test_mixed_1 (tests.test_manager.test_manager_graph.TestReconstituteEdges) Test mixed having location and something else. ... ok test_mixed_2 (tests.test_manager.test_manager_graph.TestReconstituteEdges) Tests both subject and object activity with location information as well. ... ok test_object_activity_custom (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_object_activity_default (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_object_degradation (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_subject_activity_custom (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_subject_activity_default (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_subject_degradation (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_subject_location (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_subject_translocation_custom_to_loc (tests.test_manager.test_manager_graph.TestReconstituteEdges) ... ok test_translocation_default (tests.test_manager.test_manager_graph.TestReconstituteEdges) This test checks that a translocation gets in the database properly ... ok test_complex (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_composite (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_fragment_specified (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_fragment_specified_end_only (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_fragment_specified_start_only (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_fragment_unspecified (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_fusion_specified (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_fusion_unspecified (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_gmod_custom (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) Tests a gene modification that uses a non-default namespace ... ok test_gmod_default (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) Tests a gene modification that uses the BEL default namespace ... ok test_hgvs (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_multiple_variants (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_nested_complex (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_pmod_custom_full (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_pmod_custom_simple (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_pmod_custom_with_residue (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_pmod_default_full (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_pmod_default_simple (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_pmod_default_with_residue (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_reaction (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_simple (tests.test_manager.test_manager_graph.TestReconstituteNodeTuples) ... ok test_insert_with_list_annotations (tests.test_manager.test_manager_graph.TestTemporaryInsertNetwork) This test checks that graphs that contain list annotations, which aren't cached, can be loaded properly ... ok test_citation (tests.test_manager.test_manager_model.TestModels) ... ok test_namespace_entry (tests.test_manager.test_manager_model.TestModels) ... ok test_namespace_pattern (tests.test_manager.test_manager_model.TestModels) ... ok test_namespace_url (tests.test_manager.test_manager_model.TestModels) ... ok test_dump (tests.test_manager.test_manager_model.TestNetwork) ... ok test_network (tests.test_manager.test_manager_model.TestNetwork) ... ok test_to_json (tests.test_manager.test_manager_model.TestNetwork) ... ok test_edge_existence (tests.test_manager.test_seeding.TestSeeding) ... ok test_namespace_existence (tests.test_manager.test_seeding.TestSeeding) ... ok test_namespace_existence_b (tests.test_manager.test_seeding.TestSeeding) ... ok test_namespace_existence_c (tests.test_manager.test_seeding.TestSeeding) ... ok test_network_existence (tests.test_manager.test_seeding.TestSeeding) ... ok test_seed_by_induction (tests.test_manager.test_seeding.TestSeeding) Test seeding by inducing over a list of nodes. ... ok test_seed_by_induction_raise (tests.test_manager.test_seeding.TestSeeding) Test that seeding by induction fails when an empty list is given. ... ok test_seed_by_induction_raise_length_one (tests.test_manager.test_seeding.TestSeeding) Test that seeding by induction fails when a list of length one is given. ... ok test_seed_by_neighbors (tests.test_manager.test_seeding.TestSeeding) Test seeding a graph by neighbors of a list of nodes. ... ok test_seed_by_pmid (tests.test_manager.test_seeding.TestSeeding) ... ok test_seed_by_pmid_no_result (tests.test_manager.test_seeding.TestSeeding) ... ok test_sialic_acid_in_node_store (tests.test_manager.test_seeding.TestSeeding) ... ok test_abundance (tests.test_parse.test_parse_bel.TestAbundance) Test short/long abundance name. ... ok test_abundance_with_location (tests.test_parse.test_parse_bel.TestAbundance) Test short/long abundance name and short/long location name. ... ok test_activity_bare (tests.test_parse.test_parse_bel.TestActivity) ... ok test_activity_legacy (tests.test_parse.test_parse_bel.TestActivity) Test BEL 1.0 style molecular activity annotation ... ok test_activity_on_listed_complex (tests.test_parse.test_parse_bel.TestActivity) ... ok test_activity_on_named_complex (tests.test_parse.test_parse_bel.TestActivity) ... ok test_activity_withMolecularActivityCustom (tests.test_parse.test_parse_bel.TestActivity) Tests activity modifier with molecular activity from custom namespaced ... ok test_activity_withMolecularActivityDefault (tests.test_parse.test_parse_bel.TestActivity) Tests activity modifier with molecular activity from default BEL namespace ... ok test_activity_withMolecularActivityDefaultLong (tests.test_parse.test_parse_bel.TestActivity) Tests activity modifier with molecular activity from custom namespaced ... ok test_kinase_activity_on_listed_complex (tests.test_parse.test_parse_bel.TestActivity) ... ok test_kinase_activity_on_named_complex (tests.test_parse.test_parse_bel.TestActivity) ... ok test_231a (tests.test_parse.test_parse_bel.TestBiologicalProcess) ... ok test_complex_list_long (tests.test_parse.test_parse_bel.TestComplex) ... ok test_complex_list_short (tests.test_parse.test_parse_bel.TestComplex) ... ok test_named_complex_singleton (tests.test_parse.test_parse_bel.TestComplex) ... ok test_213a (tests.test_parse.test_parse_bel.TestComposite) Evidence: ``IL-6 and IL-23 synergistically induce Th17 differentiation ... ok test_214a (tests.test_parse.test_parse_bel.TestGene) ... ok test_214b (tests.test_parse.test_parse_bel.TestGene) ... ok test_214c (tests.test_parse.test_parse_bel.TestGene) Test variant ... ok test_214d (tests.test_parse.test_parse_bel.TestGene) Test BEL 1.0 gene substitution ... ok test_gene_fusion_1 (tests.test_parse.test_parse_bel.TestGene) ... ok test_gene_fusion_2 (tests.test_parse.test_parse_bel.TestGene) ... ok test_gene_fusion_3 (tests.test_parse.test_parse_bel.TestGene) ... ok test_gene_fusion_legacy_1 (tests.test_parse.test_parse_bel.TestGene) ... ok test_gene_fusion_legacy_2 (tests.test_parse.test_parse_bel.TestGene) ... ok test_gene_variant_chromosome (tests.test_parse.test_parse_bel.TestGene) 2.2.2 chromosome ... ok test_gene_variant_deletion (tests.test_parse.test_parse_bel.TestGene) 2.2.2 gene-coding DNA reference sequence ... ok test_gene_variant_snp (tests.test_parse.test_parse_bel.TestGene) 2.2.2 SNP ... ok test_gmod (tests.test_parse.test_parse_bel.TestGene) Test Gene Modification ... ERROR test_multiple_variants (tests.test_parse.test_parse_bel.TestGene) Test multiple variants ... ok test_variant_location (tests.test_parse.test_parse_bel.TestGene) Test BEL 1.0 gene substitution with location tag ... ok test_mirna_location (tests.test_parse.test_parse_bel.TestMiRNA) ... ok test_mirna_variant (tests.test_parse.test_parse_bel.TestMiRNA) ... ok test_mirna_variant_location (tests.test_parse.test_parse_bel.TestMiRNA) ... ok test_short (tests.test_parse.test_parse_bel.TestMiRNA) ... ok test_232a (tests.test_parse.test_parse_bel.TestPathology) ... ok test_ensure_no_dup_edges (tests.test_parse.test_parse_bel.TestProtein) Ensure node and edges aren't added twice, even if from different statements and has origin completion ... ok test_multiple_variants (tests.test_parse.test_parse_bel.TestProtein) ... ok test_protein_fragment_descriptor (tests.test_parse.test_parse_bel.TestProtein) 2.2.3 fragment with unknown start/stop and a descriptor ... ok test_protein_fragment_known (tests.test_parse.test_parse_bel.TestProtein) 2.2.3 fragment with known start/stop ... ok test_protein_fragment_unboundTerminal (tests.test_parse.test_parse_bel.TestProtein) 2.2.3 carboxyl-terminal fragment of unknown length ... ok test_protein_fragment_unbounded (tests.test_parse.test_parse_bel.TestProtein) 2.2.3 amino-terminal fragment of unknown length ... ok test_protein_fragment_unknown (tests.test_parse.test_parse_bel.TestProtein) 2.2.3 fragment with unknown start/stop ... ok test_protein_fusion_1 (tests.test_parse.test_parse_bel.TestProtein) ... ok test_protein_fusion_legacy_1 (tests.test_parse.test_parse_bel.TestProtein) ... ok test_protein_fusion_legacy_2 (tests.test_parse.test_parse_bel.TestProtein) ... ok test_protein_pmod_1 (tests.test_parse.test_parse_bel.TestProtein) 2.2.1 Test default BEL namespace and 1-letter amino acid code: ... ok test_protein_pmod_2 (tests.test_parse.test_parse_bel.TestProtein) 2.2.1 Test default BEL namespace and 3-letter amino acid code: ... ok test_protein_pmod_3 (tests.test_parse.test_parse_bel.TestProtein) 2.2.1 Test PSI-MOD namespace and 3-letter amino acid code: ... ok test_protein_pmod_4 (tests.test_parse.test_parse_bel.TestProtein) 2.2.1 Test HRAS palmitoylated at an unspecified residue. Default BEL namespace ... ok test_protein_trunc_1 (tests.test_parse.test_parse_bel.TestProtein) ... trunc() is deprecated. Re-encode with reference terminal amino acid in HGVS: p(HGNC:AKT1, trunc(40)) ok test_protein_trunc_2 (tests.test_parse.test_parse_bel.TestProtein) ... ok test_protein_trunc_3 (tests.test_parse.test_parse_bel.TestProtein) ... ok test_protein_variant_deletion (tests.test_parse.test_parse_bel.TestProtein) 2.2.2 deletion ... ok test_protein_variant_reference (tests.test_parse.test_parse_bel.TestProtein) 2.2.2 Test reference allele ... ok test_protein_variant_substitution (tests.test_parse.test_parse_bel.TestProtein) 2.2.2 Test substitution ... ok test_protein_variant_unspecified (tests.test_parse.test_parse_bel.TestProtein) 2.2.2 Test unspecified variant ... ok test_protein_with_location (tests.test_parse.test_parse_bel.TestProtein) ... ok test_reference (tests.test_parse.test_parse_bel.TestProtein) ... ok test_multiple_variants (tests.test_parse.test_parse_bel.TestRna) Test multiple variants. ... ok test_reference (tests.test_parse.test_parse_bel.TestRna) ... ok test_rna_fusion_known_breakpoints (tests.test_parse.test_parse_bel.TestRna) Test RNA fusions (2.6.1) with known breakpoints (2.6.1). ... ok test_rna_fusion_legacy_1 (tests.test_parse.test_parse_bel.TestRna) ... ok test_rna_fusion_unspecified_breakpoints (tests.test_parse.test_parse_bel.TestRna) Test RNA fusions (2.6.1) with unspecified breakpoints. ... ok test_rna_variant_codingReference (tests.test_parse.test_parse_bel.TestRna) 2.2.2 RNA coding reference sequence ... ok test_lenient_semantic_no_failure (tests.test_parse.test_parse_bel.TestSemantics) ... ok test_clearance (tests.test_parse.test_parse_bel.TestTransformation) Tests that after adding things, the graph and parser can be cleared properly ... ok test_degradation_long (tests.test_parse.test_parse_bel.TestTransformation) Test the long form of degradation works ... ok test_degredation_short (tests.test_parse.test_parse_bel.TestTransformation) Test the short form of degradation works ... ok test_reaction_1 (tests.test_parse.test_parse_bel.TestTransformation) ... ok test_reaction_2 (tests.test_parse.test_parse_bel.TestTransformation) ... ok test_translocation_bare (tests.test_parse.test_parse_bel.TestTransformation) translocation example ... ok test_translocation_secretion (tests.test_parse.test_parse_bel.TestTransformation) cell secretion short form ... ok test_translocation_standard (tests.test_parse.test_parse_bel.TestTransformation) translocation example ... ok test_translocation_surface (tests.test_parse.test_parse_bel.TestTransformation) cell surface expression short form ... ok test_unqualified_translocation_strict (tests.test_parse.test_parse_bel.TestTransformation) Fail on an improperly written single argument translocation ... ok test_unqualified_translocation_relation (tests.test_parse.test_parse_bel.TestTranslocationPermissive) Test translocation in object. ... ok test_unqualified_translocation_single (tests.test_parse.test_parse_bel.TestTranslocationPermissive) translocation example ... ok test_location_undefined_name (tests.test_parse.test_parse_bel_relations.TestCustom) ... ok test_location_undefined_namespace (tests.test_parse.test_parse_bel_relations.TestCustom) ... ok test_tloc_undefined_name (tests.test_parse.test_parse_bel_relations.TestCustom) ... ok test_tloc_undefined_namespace (tests.test_parse.test_parse_bel_relations.TestCustom) ... ok test_cnc_with_subject_variant (tests.test_parse.test_parse_bel_relations.TestRelations) Test a causesNoChange relationship with a variant in the subject. ... ok test_component_list (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_decreases (tests.test_parse.test_parse_bel_relations.TestRelations) Test parsing a decreases relation with a reaction. ... ok test_directlyDecreases (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_directlyDecreases_annotationExpansion (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_directlyIncreases_withTlocObject (tests.test_parse.test_parse_bel_relations.TestRelations) Test translocation in object. See BEL 2.0 specification ... ok test_ensure_no_dup_nodes (tests.test_parse.test_parse_bel_relations.TestRelations) Ensure node isn't added twice, even if from different statements ... ok test_equivalentTo (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_extra_1 (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_has_reaction_component (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_has_variant (tests.test_parse.test_parse_bel_relations.TestRelations) ... ERROR test_increases (tests.test_parse.test_parse_bel_relations.TestRelations) Test composite in subject. See BEL 2.0 specification ... ok test_isA (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_label_1 (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_member_list (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_negativeCorrelation_withObjectVariant (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_nested_failure (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_nested_lenient (tests.test_parse.test_parse_bel_relations.TestRelations) 3.1 \ Test nested statement ... ok test_orthologous (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_partOf (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_positiveCorrelation_withSelfReferential (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_predicate_failure (tests.test_parse.test_parse_bel_relations.TestRelations) Checks that if there's a problem with the relation/object, that an error gets thrown ... ok test_raise_on_relabel (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_rateLimitingStepOf_subjectActivity (tests.test_parse.test_parse_bel_relations.TestRelations) 3.1.5 http://openbel.org/language/web/version_2.0/bel_specification_version_2.0.html#_ratelimitingstepof ... ok test_regulates_with_multiple_nnotations (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_singleton (tests.test_parse.test_parse_bel_relations.TestRelations) Test singleton composite in subject. ... ok test_subProcessOf (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_transcription (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_translation (tests.test_parse.test_parse_bel_relations.TestRelations) ... ok test_descriptor_quoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) fragment with unknown start/stop and a descriptor ... ok test_descriptor_unquoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) fragment with unknown start/stop and a descriptor ... ok test_known_length_quotes (tests.test_parse.test_parse_bel_variants.TestFragmentParser) test known length ... ok test_known_length_unquoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) test known length ... ok test_unknown_length_quoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) amino-terminal fragment of unknown length ... ok test_unknown_length_unquoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) amino-terminal fragment of unknown length ... ok test_unknown_start_stop_quoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) fragment with unknown start/stop ... ok test_unknown_start_stop_unquoted (tests.test_parse.test_parse_bel_variants.TestFragmentParser) fragment with unknown start/stop ... ok test_rna_fusion_known_breakpoints (tests.test_parse.test_parse_bel_variants.TestFusionParser) RNA abundance of fusion with known breakpoints ... ok test_rna_fusion_specified_fuzzy_breakpoints (tests.test_parse.test_parse_bel_variants.TestFusionParser) RNA abundance of fusion with unspecified breakpoints ... ok test_rna_fusion_specified_one_fuzzy_breakpoint (tests.test_parse.test_parse_bel_variants.TestFusionParser) RNA abundance of fusion with unspecified breakpoints ... ok test_rna_fusion_unspecified_breakpoints (tests.test_parse.test_parse_bel_variants.TestFusionParser) RNA abundance of fusion with unspecified breakpoints ... ok test_dsl (tests.test_parse.test_parse_bel_variants.TestGeneModification) ... ok test_gmod_long (tests.test_parse.test_parse_bel_variants.TestGeneModification) ... FAIL test_gmod_short (tests.test_parse.test_parse_bel_variants.TestGeneModification) ... FAIL test_gmod_unabbreviated (tests.test_parse.test_parse_bel_variants.TestGeneModification) ... FAIL test_gsub (tests.test_parse.test_parse_bel_variants.TestGeneSubstitutionParser) ... ok test_chromosome_1 (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_chromosome_2 (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_frameshift (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_protein_del (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_protein_del_quoted (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_protein_mut (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_protein_trunc_legacy (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_protein_trunc_triple (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_rna_del (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_snp (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_unspecified (tests.test_parse.test_parse_bel_variants.TestHGVSParser) ... ok test_a (tests.test_parse.test_parse_bel_variants.TestLocation) ... ok test_bel_name (tests.test_parse.test_parse_bel_variants.TestPmod) ... ok test_full (tests.test_parse.test_parse_bel_variants.TestPmod) ... ok test_full_with_non_standard_namespace (tests.test_parse.test_parse_bel_variants.TestPmod) ... ok test_residue (tests.test_parse.test_parse_bel_variants.TestPmod) ... ok test_psub_1 (tests.test_parse.test_parse_bel_variants.TestProteinSubstitution) ... ok test_psub_2 (tests.test_parse.test_parse_bel_variants.TestProteinSubstitution) ... ok test_trunc_1 (tests.test_parse.test_parse_bel_variants.TestTruncationParser) ... trunc() is deprecated. Re-encode with reference terminal amino acid in HGVS: trunc(40) ok test_citation_invalid_date (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_citation_short (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_citation_too_long (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_citation_too_short (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_citation_with_empty_comment (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_custom_annotation (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_custom_annotation_list (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_double (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_double_with_space (tests.test_parse.test_parse_control.TestParseControl2) Same as test_double, but has a space between the comma and next entry ... ok test_evidence (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_overwrite_evidence (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_reset_citation (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_set_regex (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_set_statement_group (tests.test_parse.test_parse_control.TestParseControl2) Tests a statement group gets set properly ... ok test_unset_custom (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_unset_evidence (tests.test_parse.test_parse_control.TestParseControl2) ... ok test_custom_annotation_list_withInvalid (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) ... ok test_custom_value_failure (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) Tests what happens for a valid annotation key, but an invalid value ... ok test_invalid_citation_type (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) ... ok test_invalid_pmid (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) ... ok test_invalid_pmid_short (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) ... ok test_regex_failure (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) ... ok test_set_missing_statement (tests.test_parse.test_parse_control.TestParseControlSetStatementErrors) ... ok test_unset_invalid_command (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) ... ok test_unset_list_compact (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) Tests unsetting an annotation list, without spaces in it ... ok test_unset_list_spaced (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) Tests unsetting an annotation list, with spaces in it ... ok test_unset_missing_citation (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) ... ok test_unset_missing_command (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) ... ok test_unset_missing_evidence (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) ... ok test_unset_missing_evidence_with_citation (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) Tests that an evidence can't be unset without a citation ... ok test_unset_missing_statement_group (tests.test_parse.test_parse_control.TestParseControlUnsetStatementErrors) ... ok test_111 (tests.test_parse.test_parse_control.TestParseEvidence) ... ok test_131 (tests.test_parse.test_parse_control.TestParseEvidence) ... ok test_132 (tests.test_parse.test_parse_control.TestParseEvidence) ... ok test_133 (tests.test_parse.test_parse_control.TestParseEvidence) ... ok test_141 (tests.test_parse.test_parse_control.TestParseEvidence) ... ok test_142 (tests.test_parse.test_parse_control.TestParseEvidence) ... ok test_parser_double (tests.test_parse.test_parse_control.TestSetCitation) ... ok test_parser_double_spaced (tests.test_parse.test_parse_control.TestSetCitation) ... ok test_parser_triple (tests.test_parse.test_parse_control.TestSetCitation) ... ok test_parser_triple_spaced (tests.test_parse.test_parse_control.TestSetCitation) ... ok test_invalid_1 (tests.test_parse.test_parse_identifier.TestIdentifierParser) ... ok test_invalid_2 (tests.test_parse.test_parse_identifier.TestIdentifierParser) ... ok test_invalid_3 (tests.test_parse.test_parse_identifier.TestIdentifierParser) ... ok test_invalid_4 (tests.test_parse.test_parse_identifier.TestIdentifierParser) ... ok test_valid_1 (tests.test_parse.test_parse_identifier.TestIdentifierParser) ... ok test_valid_2 (tests.test_parse.test_parse_identifier.TestIdentifierParser) ... ok test_not_in_defaultNs (tests.test_parse.test_parse_identifier.TestNamespaceParserDefault) ... ok test_valid_1 (tests.test_parse.test_parse_identifier.TestNamespaceParserDefault) ... ok test_valid_2 (tests.test_parse.test_parse_identifier.TestNamespaceParserDefault) ... ok test_valid_3 (tests.test_parse.test_parse_identifier.TestNamespaceParserDefault) ... ok test_invalid_1 (tests.test_parse.test_parse_identifier.TestNamespaceParserLenient) ... ok test_invalid_2 (tests.test_parse.test_parse_identifier.TestNamespaceParserLenient) ... ok test_not_invalid_3 (tests.test_parse.test_parse_identifier.TestNamespaceParserLenient) ... ok test_not_invalid_4 (tests.test_parse.test_parse_identifier.TestNamespaceParserLenient) ... ok test_valid_1 (tests.test_parse.test_parse_identifier.TestNamespaceParserLenient) ... ok test_valid_2 (tests.test_parse.test_parse_identifier.TestNamespaceParserLenient) ... ok test_annotation_name_persistience_1 (tests.test_parse.test_parse_metadata.TestParseMetadata) Tests that an annotation defined by a URL can't be overwritten by a definition by a list ... ok test_annotation_name_persistience_2 (tests.test_parse.test_parse_metadata.TestParseMetadata) Tests that an annotation defined by a list can't be overwritten by a definition by URL ... ok test_control_compound (tests.test_parse.test_parse_metadata.TestParseMetadata) ... ok test_define_namespace_regex (tests.test_parse.test_parse_metadata.TestParseMetadata) ... ok test_document_metadata_exception (tests.test_parse.test_parse_metadata.TestParseMetadata) ... ok test_namespace_name_persistience (tests.test_parse.test_parse_metadata.TestParseMetadata) Tests that a namespace defined by a URL can't be overwritten by a definition by another URL ... ok test_namespace_nocache (tests.test_parse.test_parse_metadata.TestParseMetadata) Checks namespace is loaded into parser but not cached ... ok test_not_semantic_version (tests.test_parse.test_parse_metadata.TestParseMetadata) ... /usr/lib/python3/dist-packages/pyparsing.py:1549: ResourceWarning: unclosed file <_io.FileIO name='/<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belns/test_nocache.belns' mode='rb' closefd=True> self.parseAction = list(map(_trim_arity, list(fns))) ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_parse_annotation_pattern (tests.test_parse.test_parse_metadata.TestParseMetadata) ... ok test_parse_annotation_url_file (tests.test_parse.test_parse_metadata.TestParseMetadata) Tests parsing an annotation by file URL ... ok test_parse_document (tests.test_parse.test_parse_metadata.TestParseMetadata) ... /usr/lib/python3/dist-packages/sqlalchemy/engine/result.py:1191: ResourceWarning: unclosed file <_io.FileIO name='/<>/.pybuild/cpython3_3.8_pybel/build/pybel/testing/resources/belanno/test_an_1.belanno' mode='rb' closefd=True> return [ ResourceWarning: Enable tracemalloc to get the object allocation traceback Tried to overwrite metadata: Name ok test_parse_namespace_url_file (tests.test_parse.test_parse_metadata.TestParseMetadata) Tests parsing a namespace by file URL ... ok test_squiggly_filepath (tests.test_parse.test_parse_metadata.TestParseMetadata) ... skipped 'Need local files to test local files' test_underscore (tests.test_parse.test_parse_metadata.TestParseMetadata) Tests that an underscore is a valid character in an annotation name ... ok test_parts (tests.test_parse.test_parse_metadata.TestSplitLines) ... ok test_a (tests.test_parse.test_parse_utils.TestSanitize) ... ok test_b (tests.test_parse.test_parse_utils.TestSanitize) ... ok test_c (tests.test_parse.test_parse_utils.TestSanitize) ... ok test_d (tests.test_parse.test_parse_utils.TestSanitize) Test forgotten delimiters ... ok test_e (tests.test_parse.test_parse_utils.TestSanitize) ... ok test_f (tests.test_parse.test_parse_utils.TestSanitize) ... ok test_quote (tests.test_parse.test_parse_utils.TestSanitize) ... ok test_dict_matches_1 (tests.test_parse.test_parse_utils.TestSubdictMatching) ... ok test_dict_matches_2 (tests.test_parse.test_parse_utils.TestSubdictMatching) ... ok test_dict_matches_3 (tests.test_parse.test_parse_utils.TestSubdictMatching) ... ok test_dict_matches_4 (tests.test_parse.test_parse_utils.TestSubdictMatching) ... ok test_dict_matches_5 (tests.test_parse.test_parse_utils.TestSubdictMatching) ... ok test_dict_matches_6 (tests.test_parse.test_parse_utils.TestSubdictMatching) ... ok test_dict_matches_7_exact (tests.test_parse.test_parse_utils.TestSubdictMatching) Test a partial match. ... ok test_dict_matches_7_partial (tests.test_parse.test_parse_utils.TestSubdictMatching) Tests a partial match ... ok test_dict_matches_8_partial (tests.test_parse.test_parse_utils.TestSubdictMatching) Test a partial match. ... ok test_dict_matches_graph (tests.test_parse.test_parse_utils.TestSubdictMatching) Test matching a graph. ... ok test_build_author_inclusion_filter (tests.test_struct.test_filters.test_edge_predicate_builders.TestEdgePredicateBuilders) Test building a predicate for a single author. ... ok test_build_author_set_inclusion_filter (tests.test_struct.test_filters.test_edge_predicate_builders.TestEdgePredicateBuilders) Test building a predicate for multiple authors. ... ok test_build_pmid_inclusion_filter (tests.test_struct.test_filters.test_edge_predicate_builders.TestEdgePredicateBuilders) Test building a predicate for a single PubMed identifier. ... ok test_build_pmid_set_inclusion_filter (tests.test_struct.test_filters.test_edge_predicate_builders.TestEdgePredicateBuilders) Test building a predicate for multiple PubMed identifiers. ... ok test_has_pathology (tests.test_struct.test_filters.test_edge_predicates.TestEdgePredicates) Test for checking edges that have a causal pathology. ... ok test_empty_list_error (tests.test_struct.test_filters.test_node_predicate_builders.TestFunctionInclusionFilterBuilder) Test that a value error is thrown for an empty list. ... ok test_multiple (tests.test_struct.test_filters.test_node_predicate_builders.TestFunctionInclusionFilterBuilder) Test building a node predicate with multiple functions. ... ok test_single (tests.test_struct.test_filters.test_node_predicate_builders.TestFunctionInclusionFilterBuilder) Test building a node predicate with a single function. ... ok test_type_error (tests.test_struct.test_filters.test_node_predicate_builders.TestFunctionInclusionFilterBuilder) Test that a type error is thrown for an invalid argument type. ... ok test_build_node_data_search (tests.test_struct.test_filters.test_node_predicate_builders.TestNodePredicateBuilders) Test build_node_data_search. ... ok test_build_node_key_search (tests.test_struct.test_filters.test_node_predicate_builders.TestNodePredicateBuilders) Test build_node_key_search. ... ok test_data_missing_key_builder (tests.test_struct.test_filters.test_node_predicate_builders.TestNodePredicateBuilders) Test the data_missing_key_builder function. ... ok test_build_is_association (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) Test build_relation_predicate. ... ok test_build_is_increases_or_decreases (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) Test build_relation_predicate with multiple relations. ... ok test_has_activity (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_annotation (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_authors (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_degradation (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_polarity (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_polarity_dict (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_provenance (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_pubmed (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_has_translocation (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_is_association (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_is_causal (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_is_direct_causal (tests.test_struct.test_filters.test_node_predicates.TestEdgePredicate) ... ok test_causal_source (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_fragments (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_g1_variants (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_node_exclusion_data (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_node_exclusion_tuples (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_node_inclusion_data (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_node_inclusion_tuples (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_none (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) Test permissive node predicate with graph and tuple. ... ok test_none_data (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) Test permissive node predicate with a node data dictionary. ... ok test_object_has_secretion (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) p(MGI:Il4) increases sec(p(MGI:Cxcl1)) ... ok test_object_has_translocation (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) p(HGNC: EGF) increases tloc(p(HGNC: VCP), GOCCID: 0005634, GOCCID: 0005737) ... ok test_p1_active (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) cat(p(HGNC:HSD11B1)) increases deg(a(CHEBI:cortisol)) ... ok test_p1_data_variants (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) Test node predicates on BRAF. ... ok test_p1_tuple_variants (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) Test node predicates on the node tuple from BRAF.s ... ok test_p2_data_variants (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_p2_tuple_variants (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_p3 (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) ... ok test_subject_has_secretion (tests.test_struct.test_filters.test_node_predicates.TestNodePredicates) sec(p(MGI:S100b)) increases a(CHEBI:"nitric oxide") ... ok test_a (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_all_filter (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_all_filter_dict (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_all_filter_empty_annotations (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_all_filter_no_annotations (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_all_filter_no_query (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) Test that the all filter returns true when there's no argument ... ok test_any_filter (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_any_filter_empty_annotations (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_any_filter_no_annotations (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_any_filter_no_query (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) Test that the all filter returns true when there's no argument ... ok test_b (tests.test_struct.test_filters.test_struct_filters.TestEdgeFilters) ... ok test_concatenate_multiple_edge_filter (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_concatenate_multiple_node_filters (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_concatenate_single_edge_filter (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_concatenate_single_node_filter (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_keep_edge_permissive (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_keep_edge_unpermissive (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_keep_node_permissive (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_missing_edge_filter (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_missing_node_filter (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_no_edge_filter (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_no_node_filter_argument (tests.test_struct.test_filters.test_struct_filters.TestNodeFilters) ... ok test_get_subgraphs_by_annotation (tests.test_struct.test_grouping.TestAnnotation) ... ok test_get_subgraphs_by_annotation_with_sentinel (tests.test_struct.test_grouping.TestAnnotation) ... ok test_get_subgraphs_by_citation (tests.test_struct.test_grouping.TestProvenance) Test getting sub-graphs by citation. ... ok test_add_graph (tests.test_struct.test_query.test_mocks.TestMockManager) Test adding a graph with insert_graph. ... ok test_make (tests.test_struct.test_query.test_mocks.TestMockManager) Test instantiating the mock query manager. ... ok test_make_with_graph (tests.test_struct.test_query.test_mocks.TestMockManager) Test counting networks in the mock query manager. ... ok test_get_subgraph_by_annotation_value (tests.test_struct.test_query.test_query.QueryTest) ... ok test_pipeline (tests.test_struct.test_query.test_query.QueryTest) ... ok test_pipeline_2 (tests.test_struct.test_query.test_query.QueryTest) ... ok test_query_multiple_networks (tests.test_struct.test_query.test_query.QueryTest) ... ok test_query_multiple_networks_with_api (tests.test_struct.test_query.test_query.QueryTest) ... ok test_seeding_1 (tests.test_struct.test_query.test_query.QueryTest) ... ok test_seeding_with_pipeline (tests.test_struct.test_query.test_query.QueryTest) ... ok test_fail_run_with_no_networks (tests.test_struct.test_query.test_query.QueryTestEgf) ... ok test_no_seeding_no_pipeline (tests.test_struct.test_query.test_query.QueryTestEgf) ... ok test_random_sample (tests.test_struct.test_query.test_query.QueryTestEgf) Test generating multiple random samples and combining them. ... ok test_seed_by_neighbor (tests.test_struct.test_query.test_query.QueryTestEgf) ... ok test_seed_by_neighbors (tests.test_struct.test_query.test_query.QueryTestEgf) ... ok test_network_ids_multiple (tests.test_struct.test_query.test_query.TestQueryConstructor) ... ok test_network_ids_none (tests.test_struct.test_query.test_query.TestQueryConstructor) ... ok test_network_ids_single (tests.test_struct.test_query.test_query.TestQueryConstructor) ... ok test_network_ids_type_error (tests.test_struct.test_query.test_query.TestQueryConstructor) ... ok test_pipeline (tests.test_struct.test_query.test_query.TestQueryConstructor) ... ok test_seeding (tests.test_struct.test_query.test_query.TestQueryConstructor) ... ok test_append_sample (tests.test_struct.test_query.test_query.TestSeedingConstructor) ... ok test_none (tests.test_struct.test_query.test_query.TestSeedingConstructor) Test construction of a seeding container. ... ok test_append_sample (tests.test_struct.test_query.test_seeding.TestSeedingConstructor) ... ok test_no_seeding (tests.test_struct.test_query.test_seeding.TestSeedingConstructor) ... ok test_none (tests.test_struct.test_query.test_seeding.TestSeedingConstructor) ... ok test_random_sample (tests.test_struct.test_query.test_seeding.TestSeedingConstructor) ... ok test_seed_by_neighbor (tests.test_struct.test_query.test_seeding.TestSeedingConstructor) ... ok test_seed_by_neighbors (tests.test_struct.test_query.test_seeding.TestSeedingConstructor) ... ok test_register_deprecated (tests.test_struct.test_query.test_struct_pipeline.TestDeprecation) Test that a deprecation mapping doesn't override a pre-existing mapping. ... ok test_register_deprecation_remapping_error (tests.test_struct.test_query.test_struct_pipeline.TestDeprecation) Test that a deprecation mapping doesn't override a pre-existing mapping. ... ok test_register_missing (tests.test_struct.test_query.test_struct_pipeline.TestDeprecation) Test that a deprecation mapping fails if it's missing a transformation function. ... ok test_append (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) ... ok test_deprecated_central_dogma_is_registered (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) Tests that a deprecated function is properly registered ... ok test_extend (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) ... ok test_pipeline_by_function (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) ... ok test_pipeline_by_string (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) ... ok test_serialize_file (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) ... ok test_serialize_string (tests.test_struct.test_query.test_struct_pipeline.TestPipeline) ... ok test_append_invalid (tests.test_struct.test_query.test_struct_pipeline.TestPipelineFailures) Test when an invalid type is given to a :class:`pybel.struct.Pipeline`. ... ok test_assert_failure (tests.test_struct.test_query.test_struct_pipeline.TestPipelineFailures) ... ok test_assert_success (tests.test_struct.test_query.test_struct_pipeline.TestPipelineFailures) ... ok test_build_meta_failure (tests.test_struct.test_query.test_struct_pipeline.TestPipelineFailures) ... ok test_fail_add (tests.test_struct.test_query.test_struct_pipeline.TestPipelineFailures) ... ok test_get_function_failure (tests.test_struct.test_query.test_struct_pipeline.TestPipelineFailures) ... ok test_add_node_with_variant (tests.test_struct.test_struct_graph.TestGetGraphProperties) Test that the identifier is carried through to the child. ... ok test_get_node_properties (tests.test_struct.test_struct_graph.TestGetGraphProperties) Test looking up node properties. ... ok test_get_qualified_edge (tests.test_struct.test_struct_graph.TestGetGraphProperties) Test adding an edge to a graph. ... ok test_get_unqualified_edge (tests.test_struct.test_struct_graph.TestGetGraphProperties) Test adding an unqualified edge. ... ok test_name (tests.test_struct.test_struct_graph.TestGraphProperties) Test setting of metadata through attributes. ... ok test_str_kwargs (tests.test_struct.test_struct_graph.TestGraphProperties) Test setting of metadata through keyword arguments. ... ok test_add_simple (tests.test_struct.test_struct_graph.TestStruct) Test that a simple node can be added, but not duplicated. ... ok test_citation_type_error (tests.test_struct.test_struct_graph.TestStruct) Test error handling on adding qualified edges. ... ok test_in_place_type_failure (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_initialize (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_intersection_failure (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_intersection_trivial (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_left_node_intersection_join (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_magic (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_node_intersection (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_type_failure (tests.test_struct.test_struct_operations.TestInnerJoin) ... ok test_function (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test full joining two networks using the function. ... ok test_in_place_operator (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test full joining two networks using the BELGraph in-place addition operator. ... ok test_in_place_operator_failure (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test that using the wrong type with the in-place addition operator raises an error. ... ok test_operator (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test full joining two networks using the BELGraph addition operator. ... ok test_operator_failure (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test that using the wrong type with the addition operator raises an error. ... ok test_union (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test that the union of a pair of graphs is the same as the full join. ... ok test_union_failure (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test that the union of no graphs raises a value error. ... ok test_union_trivial (tests.test_struct.test_struct_operations.TestLeftFullJoin) Test that the union of a single graph returns that graph. ... ok test_in_place_type_failure (tests.test_struct.test_struct_operations.TestLeftFullOuterJoin) ... ok test_left_outer_exhaustive_join (tests.test_struct.test_struct_operations.TestLeftFullOuterJoin) ... ok test_left_outer_join (tests.test_struct.test_struct_operations.TestLeftFullOuterJoin) ... ok test_magic (tests.test_struct.test_struct_operations.TestLeftFullOuterJoin) ... ok test_operator (tests.test_struct.test_struct_operations.TestLeftFullOuterJoin) ... ok test_type_failure (tests.test_struct.test_struct_operations.TestLeftFullOuterJoin) ... ok test_count_error_types (tests.test_struct.test_summary.test_errors.TestErrors) Test counting error types. ... ok test_get_naked_names (tests.test_struct.test_summary.test_errors.TestErrors) Retrieve the naked names from a graph. ... ok test_count_citations (tests.test_struct.test_summary.test_provenance.TestProvenance) Test counting citations. ... ok test_1 (tests.test_struct.test_summary.test_struct_summary_edges.TestEdgeSummary) Test iterating over annotation/value pairs. ... ok test_get_annotation_values (tests.test_struct.test_summary.test_struct_summary_edges.TestEdgeSummary) Test getting annotation values. ... ok test_get_unused_annotation_list (tests.test_struct.test_summary.test_struct_summary_edges.TestEdgeSummary) ... ok test_get_unused_annotation_pattern (tests.test_struct.test_summary.test_struct_summary_edges.TestEdgeSummary) ... ok test_get_unused_annotation_url (tests.test_struct.test_summary.test_struct_summary_edges.TestEdgeSummary) ... ok test_count_names_raise (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test that an index error is raised when trying to count a namespace that isn't present. ... ok test_count_pathologies (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test counting pathologies in the graph. ... ok test_count_variants (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test counting the number of variants in a graph. ... ok test_functions_egf (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test counting nodes and grouping by function on the EGF graph. ... ok test_functions_sialic (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test counting nodes and grouping by function on the sialic acid graph. ... ok test_get_names_raise (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test that an index error is raised when trying to get names from a namespace that isn't present. ... ok test_get_top_hubs (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test counting pathologies in the graph. ... ok test_names_fusions (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test that names inside fusions are still found by the iterator. ... ok test_names_sialic (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test getting and counting names by namespace. ... ok test_namespaces_egf (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test getting and counting namespaces' contents on the EGF graph. ... ok test_namespaces_sialic (tests.test_struct.test_summary.test_summary_nodes.TestSummary) Test getting and counting namespaces' contents on the sialic acid graph. ... ok test_collapse_all_variants (tests.test_struct.test_transformations.test_collapse.TestCollapse) Test collapsing all variants to their reference nodes. ... ok test_collapse_by_dict (tests.test_struct.test_transformations.test_collapse.TestCollapse) Test collapsing nodes by a dictionary. ... ok test_collapse_dogma_1 (tests.test_struct.test_transformations.test_collapse.TestCollapse) Test collapsing to genes, only with translations. ... ok test_collapse_dogma_2 (tests.test_struct.test_transformations.test_collapse.TestCollapse) Test collapsing to genes with translations and transcriptions. ... ok test_collapse_dogma_3 (tests.test_struct.test_transformations.test_collapse.TestCollapse) Test collapsing to genes, only with transcriptions. ... ok test_remove_isolated_in_place (tests.test_struct.test_transformations.test_deletions.TestDeletions) Test removing isolated nodes (in-place). ... ok test_remove_isolated_out_of_place (tests.test_struct.test_transformations.test_deletions.TestDeletions) Test removing isolated nodes (out-of-place). ... ok test_remove_pathologies (tests.test_struct.test_transformations.test_deletions.TestDeletions) Test removal of pathologies. ... ok test_infer_on_sialic_acid_example (tests.test_struct.test_transformations.test_deletions.TestProcessing) Test infer_central_dogma on the sialic acid example. ... ok test_no_infer_on_protein_variants (tests.test_struct.test_transformations.test_deletions.TestProcessing) Test that expansion doesn't occur on protein variants. ... ok test_no_infer_on_rna_variants (tests.test_struct.test_transformations.test_deletions.TestProcessing) Test that expansion doesn't occur on RNA variants. ... ok test_no_infer_protein_fusion (tests.test_struct.test_transformations.test_deletions.TestProcessing) Test that no gene is inferred from a RNA fusion node. ... ok test_no_infer_rna_fusion (tests.test_struct.test_transformations.test_deletions.TestProcessing) Test that no RNA nor gene is inferred from a protein fusion node. ... ok test_neighborhood (tests.test_struct.test_transformations.test_expansion.TestExpansion) Test expansion around the neighborhood of a given node. ... ok test_neighborhood_with_predecessors (tests.test_struct.test_transformations.test_expansion.TestExpansion) Test expansion on the predecessors of a given node. ... ok test_neighborhood_with_successors (tests.test_struct.test_transformations.test_expansion.TestExpansion) Test expansion on the successors of a given node. ... ok test_neighborhoods (tests.test_struct.test_transformations.test_expansion.TestExpansion) Test expansion on the neighborhood of given nodes. ... ok test_get_subgraph_by_annotation_value (tests.test_struct.test_transformations.test_induction.TestEdgeInduction) Test getting a subgraph by a single annotation value. ... ok test_get_subgraph_by_annotation_values (tests.test_struct.test_transformations.test_induction.TestEdgeInduction) Test getting a subgraph by multiple annotation value. ... ok test_build_author_inclusion_filter (tests.test_struct.test_transformations.test_induction.TestEdgePredicateBuilders) Test getting a sub-graph by a single author. ... ok test_build_author_set_inclusion_filter (tests.test_struct.test_transformations.test_induction.TestEdgePredicateBuilders) Test getting a sub-graph by a set of authors. ... ok test_build_pmid_inclusion_filter (tests.test_struct.test_transformations.test_induction.TestEdgePredicateBuilders) Test getting a sub-graph by a single PubMed identifier. ... ok test_build_pmid_set_inclusion_filter (tests.test_struct.test_transformations.test_induction.TestEdgePredicateBuilders) Test getting a sub-graph by a set of PubMed identifiers. ... ok test_expand_upstream_causal_subgraph (tests.test_struct.test_transformations.test_induction.TestInduction) Test expanding on the upstream causal subgraph. ... ok test_get_subgraph_by_all_shortest_paths (tests.test_struct.test_transformations.test_induction.TestInduction) Test get_subgraph_by_all_shortest_paths. ... ok test_get_subgraph_by_induction (tests.test_struct.test_transformations.test_induction.TestInduction) Test get_subgraph_by_induction. ... ok test_get_upstream_causal_subgraph (tests.test_struct.test_transformations.test_induction.TestInduction) Test get_upstream_causal_subgraph. ... ok test_add_and_remove_annotation (tests.test_struct.test_transformations.test_metadata.TestMetadata) Test adding and removing annotations. ... ok test_strip_annotations (tests.test_struct.test_transformations.test_metadata.TestMetadata) Test the strip_annotation function. ... ok test_helper_failure (tests.test_struct.test_transformations.test_random.TestRandom) ... infinite loop happening source: None no grow: {1, 2, 3} ok test_random_edges (tests.test_struct.test_transformations.test_random.TestRandom) Test getting a graph by random edges. ... ok test_random_nodes (tests.test_struct.test_transformations.test_random.TestRandom) Test getting random nodes. ... ok test_random_nodes_inverted (tests.test_struct.test_transformations.test_random.TestRandom) Test getting random nodes. ... ok test_random_sample (tests.test_struct.test_transformations.test_random.TestRandom) Test randomly sampling a graph. ... ok test_random_sample_small (tests.test_struct.test_transformations.test_random.TestRandom) Test a graph that is too small to sample. ... ok test_get_random_path (tests.test_struct.test_transformations.test_random.TestRandomPath) Test getting random paths doesn't crash. ... ok test_does_not_redo (tests.test_struct.test_transformations.test_transfer.TestTransfer) Test that :func:`propagate_node_relations` does not add the same edges twice. ... ok test_get_children (tests.test_struct.test_transformations.test_transfer.TestTransfer) Test iterating over the children of a node. ... ok test_infer (tests.test_struct.test_transformations.test_transfer.TestTransfer) Test inferring child relations. ... ok test_bad_aminoAcid (tests.test_utils.TestRandom) ... ok test_get_date (tests.test_utils.TestRandom) ... ok test_nest_failure (tests.test_utils.TestRandom) ... ok test_dev (tests.test_utils.TestTokenizeVersion) Test when there's a dash after. ... ok test_long (tests.test_utils.TestTokenizeVersion) Test when the version pieces have more than 1 digit. ... ok test_simple (tests.test_utils.TestTokenizeVersion) Test the simplest version string case. ... ok test_download_raises_on_empty (tests.test_utils.TestUtils) Test that an error is thrown if an empty resource is downloaded. ... ok test_download_url (tests.test_utils.TestUtils) Test downloading a resource by URL. ... ok test_expand_dict (tests.test_utils.TestUtils) ... ok test_flatten_dict (tests.test_utils.TestUtils) ... ok test_flatten_dict_withLists (tests.test_utils.TestUtils) ... ok ====================================================================== ERROR: test_gmod (tests.test_parse.test_parse_bel.TestGene) Test Gene Modification ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_parse/test_parse_bel.py", line 161, in test_gmod result = self.parser.gene.parseString(statement) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1929, in parseString loc, tokens = self._parse(instring, 0) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1702, in _parseNoCache tokens = fn(instring, tokensStart, retTokens) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1308, in wrapper ret = func(*args[limit[0]:]) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 718, in handle_term self.ensure_node(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 886, in ensure_node node_dsl = parse_result_to_dsl(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 35, in parse_result_to_dsl return _variant_po_to_dict(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 123, in _variant_po_to_dict variants=[ File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 124, in _variant_to_dsl_helper(variant_tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 143, in _variant_to_dsl_helper name=tokens[IDENTIFIER][NAME], File "/usr/lib/python3/dist-packages/pyparsing.py", line 590, in __getitem__ return self.__tokdict[i][-1][0] KeyError: 'name' ====================================================================== ERROR: test_has_variant (tests.test_parse.test_parse_bel_relations.TestRelations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_parse/test_parse_bel_relations.py", line 896, in test_has_variant self.parser.relation.parseString(statement) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1929, in parseString loc, tokens = self._parse(instring, 0) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4222, in parseImpl ret = e._parse(instring, loc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4222, in parseImpl ret = e._parse(instring, loc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4037, in parseImpl loc, exprtokens = e._parse(instring, loc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4430, in parseImpl return self.expr._parse(instring, loc, doActions, callPreParse=False) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4222, in parseImpl ret = e._parse(instring, loc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1669, in _parseNoCache loc, tokens = self.parseImpl(instring, preloc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 4222, in parseImpl ret = e._parse(instring, loc, doActions) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1702, in _parseNoCache tokens = fn(instring, tokensStart, retTokens) File "/usr/lib/python3/dist-packages/pyparsing.py", line 1308, in wrapper ret = func(*args[limit[0]:]) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 718, in handle_term self.ensure_node(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/parser/parse_bel.py", line 886, in ensure_node node_dsl = parse_result_to_dsl(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 35, in parse_result_to_dsl return _variant_po_to_dict(tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 123, in _variant_po_to_dict variants=[ File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 124, in _variant_to_dsl_helper(variant_tokens) File "/<>/.pybuild/cpython3_3.8_pybel/build/pybel/tokens.py", line 143, in _variant_to_dsl_helper name=tokens[IDENTIFIER][NAME], File "/usr/lib/python3/dist-packages/pyparsing.py", line 590, in __getitem__ return self.__tokdict[i][-1][0] KeyError: 'name' ====================================================================== FAIL: test_thorough_bytes (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 111, in test_thorough_bytes self.bel_thorough_reconstituted(graph) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 351, in bel_thorough_reconstituted self.assertEqual(0, len(graph.warnings), AssertionError: 0 != 1 : Document warnings: (39, 'a(CHEBI:"oxygen atom") -> geneAbundance(HGNC:AKT1,gmod(M))', KeyError('name'), {'evidence': 'These are mostly made up', 'citation': {'type': 'PubMed', 'name': 'That one article from last week', 'reference': '123455'}, 'annotations': {'TESTAN1': {'1', '2'}, 'TestRegex': '9000'}}) ====================================================================== FAIL: test_thorough_json (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 123, in test_thorough_json self.bel_thorough_reconstituted(graph) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 369, in bel_thorough_reconstituted self.assertEqual(set(BEL_THOROUGH_NODES), set(graph), msg='Nodes not equal') AssertionError: Items in the first set but not the second: : Nodes not equal ====================================================================== FAIL: test_thorough_json_file (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 135, in test_thorough_json_file self.bel_thorough_reconstituted(graph) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 369, in bel_thorough_reconstituted self.assertEqual(set(BEL_THOROUGH_NODES), set(graph), msg='Nodes not equal') AssertionError: Items in the first set but not the second: : Nodes not equal ====================================================================== FAIL: test_thorough_jsons (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 128, in test_thorough_jsons self.bel_thorough_reconstituted(graph) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 369, in bel_thorough_reconstituted self.assertEqual(set(BEL_THOROUGH_NODES), set(graph), msg='Nodes not equal') AssertionError: Items in the first set but not the second: : Nodes not equal ====================================================================== FAIL: test_thorough_path (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 106, in test_thorough_path self.bel_thorough_reconstituted(self.thorough_graph) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 351, in bel_thorough_reconstituted self.assertEqual(0, len(graph.warnings), AssertionError: 0 != 1 : Document warnings: (39, 'a(CHEBI:"oxygen atom") -> geneAbundance(HGNC:AKT1,gmod(M))', KeyError('name'), {'evidence': 'These are mostly made up', 'citation': {'type': 'PubMed', 'name': 'That one article from last week', 'reference': '123455'}, 'annotations': {'TESTAN1': {'1', '2'}, 'TestRegex': '9000'}}) ====================================================================== FAIL: test_thorough_pickle (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 118, in test_thorough_pickle self.bel_thorough_reconstituted(graph) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 351, in bel_thorough_reconstituted self.assertEqual(0, len(graph.warnings), AssertionError: 0 != 1 : Document warnings: (39, 'a(CHEBI:"oxygen atom") -> geneAbundance(HGNC:AKT1,gmod(M))', KeyError('name'), {'evidence': 'These are mostly made up', 'citation': {'type': 'PubMed', 'name': 'That one article from last week', 'reference': '123455'}, 'annotations': {'TESTAN1': {'1', '2'}, 'TestRegex': '9000'}}) ====================================================================== FAIL: test_thorough_upgrade (tests.test_io.test_import.TestInterchange) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_io/test_import.py", line 176, in test_thorough_upgrade self.bel_thorough_reconstituted(reconstituted, check_citation_name=False) File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/constants.py", line 369, in bel_thorough_reconstituted self.assertEqual(set(BEL_THOROUGH_NODES), set(graph), msg='Nodes not equal') AssertionError: Items in the first set but not the second: : Nodes not equal ====================================================================== FAIL: test_gmod_long (tests.test_parse.test_parse_bel_variants.TestGeneModification) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_parse/test_parse_bel_variants.py", line 229, in test_gmod_long self.assertEqual(self.expected, result.asDict()) AssertionError: {'kind': 'gmod', 'identifier': {'namespace': 'bel', 'name': 'Me'}} != {'kind': 'gmod', 'identifier': [{'namespace': 'bel', 'name': 'Me'}]} ====================================================================== FAIL: test_gmod_short (tests.test_parse.test_parse_bel_variants.TestGeneModification) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_parse/test_parse_bel_variants.py", line 219, in test_gmod_short self.assertEqual(self.expected, result.asDict()) AssertionError: {'kind': 'gmod', 'identifier': {'namespace': 'bel', 'name': 'Me'}} != {'kind': 'gmod', 'identifier': [{'namespace': 'bel', 'name': 'Me'}]} ====================================================================== FAIL: test_gmod_unabbreviated (tests.test_parse.test_parse_bel_variants.TestGeneModification) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.8_pybel/build/tests/test_parse/test_parse_bel_variants.py", line 224, in test_gmod_unabbreviated self.assertEqual(self.expected, result.asDict()) AssertionError: {'kind': 'gmod', 'identifier': {'namespace': 'bel', 'name': 'Me'}} != {'kind': 'gmod', 'identifier': [{'namespace': 'bel', 'name': 'Me'}]} ---------------------------------------------------------------------- Ran 657 tests in 52.336s FAILED (failures=10, errors=2, skipped=1) (, 2) E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /<>/.pybuild/cpython3_3.8_pybel/build; python3.8 -m unittest discover -v dh_auto_test: pybuild --test -i python{version} -p "3.8 3.7" returned exit code 13 make: *** [debian/rules:7: build] Error 255 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200105-1045 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 8260 Build-Time: 56 Distribution: focal Fail-Stage: build Host Architecture: amd64 Install-Time: 21 Job: pybel_0.12.1-1.dsc Machine Architecture: amd64 Package: pybel Package-Time: 79 Source-Version: 0.12.1-1 Space: 8260 Status: attempted Version: 0.12.1-1 -------------------------------------------------------------------------------- Finished at 20200105-1045 Build needed 00:01:19, 8260k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18341877 Scanning for processes to kill in build PACKAGEBUILD-18341877