Wed May 15 14:22:17 UTC 2024 I: starting to build barclay/trixie/amd64 on jenkins on '2024-05-15 14:22' Wed May 15 14:22:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/11929/console.log Wed May 15 14:22:17 UTC 2024 I: Downloading source for trixie/barclay=5.0.0+dfsg-1 --2024-05-15 14:22:17-- http://deb.debian.org/debian/pool/main/b/barclay/barclay_5.0.0%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2199 (2.1K) [text/prs.lines.tag] Saving to: ‘barclay_5.0.0+dfsg-1.dsc’ 0K .. 100% 279M=0s 2024-05-15 14:22:17 (279 MB/s) - ‘barclay_5.0.0+dfsg-1.dsc’ saved [2199/2199] Wed May 15 14:22:17 UTC 2024 I: barclay_5.0.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: barclay Binary: libbarclay-java Architecture: all Version: 5.0.0+dfsg-1 Maintainer: Debian Java Maintainers Uploaders: Olivier Sallou , Pierre Gruet Homepage: https://github.com/broadinstitute/barclay Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/java-team/barclay Vcs-Git: https://salsa.debian.org/java-team/barclay.git Build-Depends: default-jdk-headless, debhelper-compat (= 13), javahelper, gradle-debian-helper, maven-repo-helper, libfreemarker-java, libjoptsimple-java, liblog4j2-java, libgoogle-gson-java, libmockito-java, testng, libjacoco-java, default-jdk-doc Package-List: libbarclay-java deb java optional arch=all Checksums-Sha1: afb82bf0d1fce8699b55db8728b16b9112112148 118636 barclay_5.0.0+dfsg.orig.tar.xz 5f1d02f070e965516b4f4e9ebbf2c6dd8b529607 8064 barclay_5.0.0+dfsg-1.debian.tar.xz Checksums-Sha256: fa33e36f1e964a6ac0fe7074d342a1d8e8f5fc0be04dce9a1fd0cda2c4dd0c38 118636 barclay_5.0.0+dfsg.orig.tar.xz 548e04239904d8cfb2589f3295370e8e1ee223944102e250376561b9a4761d4c 8064 barclay_5.0.0+dfsg-1.debian.tar.xz Files: 0d3812cd4d8f6635b069a9d77653236c 118636 barclay_5.0.0+dfsg.orig.tar.xz 5bb67db4618278329180e59ef33b0876 8064 barclay_5.0.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmSRpIQACgkQYAMWptwn dHadMQ//faGwRKKgJBgCy85K3PVfU86a8QtNYvBwkDmZjFpx7qyMs8ZNGwWCXLuw bImSZPcRCA1WGD1BkvyXvNn9Arn1hWETJHyZBvTDI+KSrvdCSHfumvY7X+aRgQdp rCGmVAGI+0Ms2DtosBtK+MFrp2a1lUiPIPrGNwVmTq3SAw/eNcLvcErKBW7x1zLQ OChYDZlRwVbfcnGV+LoCZCMwdJX5QJGUgPXxDuuiF0/gqcJe1LBuqBGHSwDgNKNA dEe+5J7KbuyUOk9ClcN5aJKUPo00Zk+NqbYgBy7kVxZzNuLo17Z9+3GVmW8r3f9l yoasWq2/Y8DdTy/u1UiW/tnMzaFeeqSa1vJcUJqWSQsWo0v34MS1JU2H+8nxkXJr x86ytQygRgF5OOXFmnahN6rAh5xq+psJ1nQSCSc3t54cxuH8gePiO2u/BZUt/vUu gtaM0FVRgNXiXhwkfqhauI7wXmDG1Rs5iIyoeel894nEfsQQ8frr9TLxhs0xbLQk OU6IlasdRKfte9Aa02+CWTnkgI3szmZ3phSgDpNWzmMU23YlvKFNM/DkBFnNae0v e5GiTvHO4OwVYRDDFwVHX/JUAP/uqMXsYOpiD4H7I0r3XH/Y0UEM38y2PsyZJIdX fJMzvJViTteT3cUNIpfPJVERy5pX9Ae8DG3e3Rn/eyWfsGkFvwY= =/C6w -----END PGP SIGNATURE----- Wed May 15 14:22:17 UTC 2024 I: Checking whether the package is not for us Wed May 15 14:22:17 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Wed May 15 14:22:17 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Wed May 15 14:26:10 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 17 08:45:19 -12 2025 I: pbuilder-time-stamp: 1750193119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [barclay_5.0.0+dfsg-1.dsc] I: copying [./barclay_5.0.0+dfsg.orig.tar.xz] I: copying [./barclay_5.0.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jun 20 13:07:16 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./barclay_5.0.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting barclay in barclay-5.0.0+dfsg dpkg-source: info: unpacking barclay_5.0.0+dfsg.orig.tar.xz dpkg-source: info: unpacking barclay_5.0.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_debian_build.patch dpkg-source: info: applying fix_dataprovider.patch dpkg-source: info: applying com_sun_javadoc_removal_in_openjdk17.patch dpkg-source: info: applying ignore_flaky_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3431041/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='813263f45edf4827a7607444755d0cce' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3431041' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/pbuilderrc_9GDQ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/b1 --logfile b1/build.log barclay_5.0.0+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 16 03:14 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3431041/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: default-jdk-headless, debhelper-compat (= 13), javahelper, gradle-debian-helper, maven-repo-helper, libfreemarker-java, libjoptsimple-java, liblog4j2-java, libgoogle-gson-java, libmockito-java, testng, libjacoco-java, default-jdk-doc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on gradle-debian-helper; however: Package gradle-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on maven-repo-helper; however: Package maven-repo-helper is not installed. pbuilder-satisfydepends-dummy depends on libfreemarker-java; however: Package libfreemarker-java is not installed. pbuilder-satisfydepends-dummy depends on libjoptsimple-java; however: Package libjoptsimple-java is not installed. pbuilder-satisfydepends-dummy depends on liblog4j2-java; however: Package liblog4j2-java is not installed. pbuilder-satisfydepends-dummy depends on libgoogle-gson-java; however: Package libgoogle-gson-java is not installed. pbuilder-satisfydepends-dummy depends on libmockito-java; however: Package libmockito-java is not installed. pbuilder-satisfydepends-dummy depends on testng; however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on libjacoco-java; however: Package libjacoco-java is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-doc; however: Package default-jdk-doc is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} antlr{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bnd{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk-doc{a} default-jdk-headless{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} gradle{a} gradle-debian-helper{a} groff-base{a} groovy{a} intltool-debian{a} ivy{a} jarwrapper{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} libantlr-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libasm-java{a} libassuan0{a} libatinject-jsr330-api-java{a} libb-hooks-op-check-perl{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbsf-java{a} libbsh-java{a} libbyte-buddy-java{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libdd-plist-java{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdynaloader-functions-perl{a} libeclipse-jdt-annotation-java{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} liberror-prone-java{a} libexpat1{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfindbugs-java{a} libfreemarker-java{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libhawtjni-runtime-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libjacoco-java{a} libjansi-java{a} libjansi-native-java{a} libjansi1-java{a} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxen-java{a} libjcifs-java{a} libjcip-annotations-java{a} libjcommander-java{a} libjetty9-java{a} libjformatstring-java{a} libjgit-java{a} libjline2-java{a} libjna-java{a} libjna-jni{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjsch-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjzlib-java{a} libkryo-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblightcouch-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libminlog-java{a} libmockito-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libnative-platform-java{a} libnative-platform-jni{a} libnekohtml-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libparams-classify-perl{a} libpcsclite1{a} libpipeline1{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-interpolation-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpolyglot-maven-java{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libreadline8t64{a} libreflectasm-java{a} librhino-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libservlet-api-java{a} libsimple-http-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsub-override-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libxbean-reflect-java{a} libxerces2-java{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{a} libxstream-java{a} libxz-java{a} libyaml-snake-java{a} m4{a} man-db{a} maven-repo-helper{a} media-types{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk-headless{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} testng{a} tzdata{a} unzip{a} wdiff{a} The following packages are RECOMMENDED but will NOT be installed: curl debian-keyring dput dput-ng dupload equivs javascript-common libarchive-cpio-perl libasound2t64 libbindex-java libcups2t64 libdata-dump-perl libdistro-info-perl libfontconfig1 libfreetype6 libgit-wrapper-perl libgitlab-api-v4-perl libgpars-groovy-java libharfbuzz0b libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libreflectasm-java-doc libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget 0 packages upgraded, 249 newly installed, 0 to remove and 0 not upgraded. Need to get 259 MB of archives. After unpacking 826 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B] Get: 29 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 35 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 36 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.14-1 [2162 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.14-1 [455 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libantlr-java all 2.7.7+dfsg-13 [458 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 antlr all 2.7.7+dfsg-13 [8272 B] Get: 40 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.4 [8916 B] Get: 47 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-4 [349 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 52 http://deb.debian.org/debian trixie/main amd64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libjansi1-java all 1.18-3 [66.5 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libjline2-java all 2.14.6-5 [151 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libyaml-snake-java all 1.33-2 [321 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 bnd all 5.0.1-5 [10.1 MB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 71 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 openjdk-17-doc all 17.0.11+9-1 [12.8 MB] Get: 83 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.17-75 [3148 B] Get: 84 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 85 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-3 [565 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-3 [793 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-3 [928 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-3 [950 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-3 [695 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-3 [541 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-3 [532 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-3 [671 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-3 [847 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 104 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 135 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.23.7 [1068 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 ivy all 2.5.2-1 [1295 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7-1 [394 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 151 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libxstream-java all 1.4.20-1 [565 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 groovy all 2.4.21-10 [12.8 MB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libjna-jni amd64 5.14.0-1 [64.0 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libjna-java all 5.14.0-1 [237 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libjzlib-java all 1.1.3-3 [79.4 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libjsch-java all 0.1.55-1 [298 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libminlog-java all 1.3.0-1.1 [7928 B] Get: 178 http://deb.debian.org/debian trixie/main amd64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libkryo-java all 2.20-7 [158 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 liblogback-java all 1:1.2.11-5 [701 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libnative-platform-jni amd64 0.14-6 [11.5 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libnative-platform-java all 0.14-6 [69.8 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libgradle-core-java all 4.4.1-20 [4293 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libbcprov-java all 1.77-1 [5300 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libbcpg-java all 1.77-1 [428 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libbcel-java all 6.5.0-2 [634 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 201 http://deb.debian.org/debian trixie/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libjcifs-java all 1.3.19-2 [394 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.26-2 [25.3 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libjavaewah-java all 1.2.3-1 [159 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libjgit-java all 4.11.9-2 [2534 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 216 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 220 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libgradle-plugins-java all 4.4.1-20 [5206 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 gradle all 4.4.1-20 [398 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 gradle-debian-helper all 2.4 [24.5 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.79 [84.6 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libbyte-buddy-java all 1.14.13-1 [4709 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libjacoco-java all 0.8.12-1 [647 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libmockito-java all 2.23.0-2 [479 kB] Fetched 259 MB in 4s (63.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libicu72:amd64 (72.1-4+b1) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.40-8) ... Setting up java-common (0.75) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libjcip-annotations-java (20060626-6) ... Setting up libobjenesis-java (3.3-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up liblogback-java (1:1.2.11-5) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libminlog-java (1.3.0-1.1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.15.3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libasm-java (9.7-1) ... Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libel-api-java (3.0.0-3) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up file (1:5.45-3) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ... Setting up libfelix-gogo-runtime-java (0.16.2-1.1) ... Setting up libassuan0:amd64 (2.5.6-1+b1) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jun 17 20:48:21 UTC 2025. Universal Time is now: Tue Jun 17 20:48:21 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libjsch-java (0.1.55-1) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libbsf-java (1:2.4.0-8) ... Setting up libosgi-annotation-java (8.1.0-1) ... Setting up libjformatstring-java (0.10~20131207-2.1) ... Setting up libjavaewah-java (1.2.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libkryo-java (2.20-7) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libjna-jni (5.14.0-1) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up dwz (0.15-1+b1) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.22) ... Setting up libjacoco-java (0.8.12-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libjna-java (5.14.0-1) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libnative-platform-jni (0.14-6) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libbcpg-java (1.77-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libantlr-java (2.7.7+dfsg-13) ... Setting up libyaml-snake-java (1.33-2) ... Setting up openssl (3.2.1-3) ... Setting up libcdi-api-java (1.2-3) ... Setting up readline-common (8.2-4) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libnative-platform-java (0.14-6) ... Setting up libosgi-core-java (8.0.0-2) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.20-1) ... Setting up libnekohtml-java (1.9.22.noko2-0.1) ... Setting up gettext (0.21-14+b1) ... Setting up libjetty9-java (9.4.54-1) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libmaven-parent-java (35-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libbcel-java (6.5.0-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up testng (6.9.12-4) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up libjansi-native-java (1.8-2) ... Setting up groff-base (1.23.0-4) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up openjdk-17-doc (17.0.11+9-1) ... Setting up libjansi1-java (1.18-3) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-1) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libjline2-java (2.14.6-5) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up gpg-agent (2.2.40-3) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up default-jdk-doc (2:1.17-75) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-3) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gpg-wks-server (2.2.40-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libjgit-java (4.11.9-2) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up gnupg (2.2.40-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.79) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libbyte-buddy-java (1.14.13-1) ... Setting up libmockito-java (2.23.0-2) ... Processing triggers for libc-bin (2.38-10) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up antlr (2.7.7+dfsg-13) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ivy (2.5.2-1) ... Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up groovy (2.4.21-10) ... update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode Setting up default-jre-headless (2:1.17-75) ... Setting up maven-repo-helper (1.11) ... Setting up ant-optional (1.10.14-1) ... Setting up bnd (5.0.1-5) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up libgradle-core-java (4.4.1-20) ... Setting up libgradle-plugins-java (4.4.1-20) ... Setting up gradle (4.4.1-20) ... Setting up gradle-debian-helper (2.4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/barclay-5.0.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../barclay_5.0.0+dfsg-1_source.changes dpkg-buildpackage: info: source package barclay dpkg-buildpackage: info: source version 5.0.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=gradle --with javahelper,jh_maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/barclay-5.0.0+dfsg' dh_auto_clean sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/reproducible-path/barclay-5.0.0\+dfsg/.gradle /build/reproducible-path/barclay-5.0.0\+dfsg/buildSrc/.gradle .m2 rm debian/pom-barclay.xml rm: cannot remove 'debian/pom-barclay.xml': No such file or directory make[1]: [debian/rules:13: override_dh_auto_clean] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/barclay-5.0.0+dfsg' dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/barclay-5.0.0+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libbarclay-java.substvars debian/files rm -fr -- debian/libbarclay-java/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) rm -f debian/bd-temp-substvars rm -f debian/bd.substvars make[1]: Leaving directory '/build/reproducible-path/barclay-5.0.0+dfsg' debian/rules binary dh binary --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_update_autotools_config -O--buildsystem=gradle dh_autoreconf -O--buildsystem=gradle debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/barclay-5.0.0+dfsg' # As we provide a Debian-made POM file, we have to update the version number # that is inside each time the upstream version changes. This is done # automatically with this tiny hack. sed 's/@VERSION@/5.0.0+dfsg/ ; s/\+dfsg[[:digit:]]*//' debian/pom-barclay.xml.in > debian/pom-barclay.xml dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/barclay-5.0.0+dfsg' jh_linkjars -O--buildsystem=gradle rm -f debian/libbarclay-java.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/barclay-5.0.0+dfsg' dh_auto_build -- jar mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=barclay -Dfile.encoding=UTF-8 --parallel --max-workers=12 jar openjdk version "17.0.11" 2024-04-16 OpenJDK Runtime Environment (build 17.0.11+9-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.11+9-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 0.913 secs. The client will now receive all logging from the daemon (pid: 3480080). The daemon log file: /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/daemon/4.4.1/daemon-3480080.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 12 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@20518a1e Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@20518a1e Creating new cache for fileHashes, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5efb03be Starting Build Compiling initialization script '/build/reproducible-path/barclay-5.0.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3e065e1d Compiling initialization script '/build/reproducible-path/barclay-5.0.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/barclay-5.0.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/barclay-5.0.0+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'barclay' instead of the name of the root directory 'barclay-5.0.0+dfsg' Projects loaded. Root project using build file '/build/reproducible-path/barclay-5.0.0+dfsg/build.gradle'. Included projects: [root project 'barclay'] Keep-alive timer started Adding Debian repository to project 'barclay' Parallel execution is an incubating feature. Evaluating root project 'barclay' using build file '/build/reproducible-path/barclay-5.0.0+dfsg/build.gradle'. Compiling build file '/build/reproducible-path/barclay-5.0.0+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/reproducible-path/barclay-5.0.0+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/barclay-5.0.0+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' Adding Maven pom generation to project 'barclay' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : Creating new cache for annotation-processors, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a682c26 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5efb03be Creating new cache for taskHistory, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@27a1a3c4 Creating new cache for outputFiles, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@3d675dba :compileJava (Thread[Task worker for ':' Thread 3,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.004 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7526eede Loading the Maven rules... Replacing net.sf.jopt-simple:jopt-simple:jar:5.0.3 -> net.sf.jopt-simple:jopt-simple:jar:debian Replacing org.apache.commons:commons-lang3:jar:3.4 -> org.apache.commons:commons-lang3:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing org.apache.logging.log4j:log4j-api:jar:2.17.1 -> org.apache.logging.log4j:log4j-api:jar:debian Passing through org.apache.logging.log4j:log4j:jar:debian Passing through org.apache.logging.log4j:log4j-bom:jar:debian Replacing org.apache.logging.log4j:log4j-core:jar:2.15.0 -> org.apache.logging.log4j:log4j-core:jar:debian Replacing org.freemarker:freemarker:jar:2.3.30 -> org.freemarker:freemarker:jar:debian Replacing com.google.code.gson:gson:jar:2.2.2 -> com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Up-to-date check for task ':compileJava' took 0.814 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. /build/reproducible-path/barclay-5.0.0+dfsg/src/main/java/org/broadinstitute/barclay/utils/Utils.java:173: warning: [deprecation] WordUtils in org.apache.commons.lang3.text has been deprecated .map(line -> WordUtils.wrap(line, width)) ^ 1 warning :compileJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 2.53 secs. :processResources (Thread[Task worker for ':' Thread 3,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Up-to-date check for task ':processResources' took 0.011 secs. It is not up-to-date because: No history is available. :processResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.038 secs. :classes (Thread[Task worker for ':' Thread 3,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. :debianMavenPom (Thread[Task worker for ':' Thread 3,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.001 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/barclay-5.0.0+dfsg/build/debian/barclay.pom :debianMavenPom (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.072 secs. :jar (Thread[Task worker for ':' Thread 3,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.008 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.075 secs. BUILD SUCCESSFUL in 7s 4 actionable tasks: 4 executed make[1]: Leaving directory '/build/reproducible-path/barclay-5.0.0+dfsg' jh_build -O--buildsystem=gradle rm -f debian/libbarclay-java.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/barclay-5.0.0+dfsg' # Tests do not work with locales with a different decimal separator # (for example ',') LC_ALL=C.UTF-8 dh_auto_test mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=barclay -Dfile.encoding=UTF-8 --parallel --max-workers=12 test openjdk version "17.0.11" 2024-04-16 OpenJDK Runtime Environment (build 17.0.11+9-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.11+9-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 0.808 secs. The client will now receive all logging from the daemon (pid: 3485981). The daemon log file: /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/daemon/4.4.1/daemon-3485981.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 12 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@51d297b9 Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@51d297b9 Creating new cache for fileHashes, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a3c1525 Starting Build Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@26063f5d Settings evaluated using settings file '/build/reproducible-path/barclay-5.0.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/barclay-5.0.0+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'barclay' instead of the name of the root directory 'barclay-5.0.0+dfsg' Projects loaded. Root project using build file '/build/reproducible-path/barclay-5.0.0+dfsg/build.gradle'. Included projects: [root project 'barclay'] Keep-alive timer started Adding Debian repository to project 'barclay' Parallel execution is an incubating feature. Evaluating root project 'barclay' using build file '/build/reproducible-path/barclay-5.0.0+dfsg/build.gradle'. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/barclay-5.0.0+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' Adding Maven pom generation to project 'barclay' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : Creating new cache for annotation-processors, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@6c7a2948 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a3c1525 Creating new cache for taskHistory, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d6476ab Creating new cache for outputFiles, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@37b008f9 :compileJava (Thread[Task worker for ':' Thread 5,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.003 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-5.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@25a7ea8c Loading the Maven rules... Replacing net.sf.jopt-simple:jopt-simple:jar:5.0.3 -> net.sf.jopt-simple:jopt-simple:jar:debian Replacing org.apache.commons:commons-lang3:jar:3.4 -> org.apache.commons:commons-lang3:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing org.apache.logging.log4j:log4j-api:jar:2.17.1 -> org.apache.logging.log4j:log4j-api:jar:debian Passing through org.apache.logging.log4j:log4j:jar:debian Passing through org.apache.logging.log4j:log4j-bom:jar:debian Replacing org.apache.logging.log4j:log4j-core:jar:2.15.0 -> org.apache.logging.log4j:log4j-core:jar:debian Replacing org.freemarker:freemarker:jar:2.3.30 -> org.freemarker:freemarker:jar:debian Replacing com.google.code.gson:gson:jar:2.2.2 -> com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Skipping task ':compileJava' as it is up-to-date (took 0.408 secs). :compileJava UP-TO-DATE :compileJava (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.435 secs. :processResources (Thread[Task worker for ':' Thread 5,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Skipping task ':processResources' as it is up-to-date (took 0.01 secs). :processResources UP-TO-DATE :processResources (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.014 secs. :classes (Thread[Task worker for ':' Thread 5,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.0 secs. :compileTestJava (Thread[Task worker for ':' Thread 5,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Replacing commons-io:commons-io:jar:2.11.0 -> commons-io:commons-io:jar:debian Passing through org.testng:testng:jar:debian Replacing org.mockito:mockito-core:jar:4.6.1 -> org.mockito:mockito-core:jar:debian Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Passing through net.bytebuddy:byte-buddy:jar:debian Passing through net.bytebuddy:byte-buddy-parent:jar:debian Passing through net.bytebuddy:byte-buddy-agent:jar:debian Passing through org.objenesis:objenesis:jar:debian Passing through org.objenesis:objenesis-parent:jar:debian Passing through net.bytebuddy:byte-buddy-dep:jar:debian Passing through org.ow2.asm:asm:jar:debian Passing through org.ow2.asm:asm-commons:jar:debian Up-to-date check for task ':compileTestJava' took 1.063 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. :compileTestJava (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 2.877 secs. :processTestResources (Thread[Task worker for ':' Thread 5,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. Up-to-date check for task ':processTestResources' took 0.053 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.101 secs. :testClasses (Thread[Task worker for ':' Thread 5,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.0 secs. :test (Thread[Task worker for ':' Thread 5,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.001 secs. Up-to-date check for task ':test' took 0.484 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/barclay-5.0.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3401301396921206947txt -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. Running Test: Test method testCollectionFromExpansionFile[0](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@41ee7d74, [], /tmp/enabledExpansion8528419544459792976.args, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@498a632f, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[1](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@67c986fa, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion15040787640647994511.args, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@190d6c19, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[2](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@7d5ae70b, [], /tmp/enabledExpansion11654222985576309101.list, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@26c16e06, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[3](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@3b747d48, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion17424727250986654066.list, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@3e0eb0c9, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[4](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@4a48385d, [], /tmp/enabledExpansion629321292270954364.args, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@2de9bbde, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[5](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@160e23af, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion17148976110339057231.args, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@5195b455, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[6](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@3f4bd17b, [], /tmp/enabledExpansion7709111039581623860.list, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@6c0b165f, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[7](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@5a95e96c, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion15025080854556026438.list, [Ljava.lang.String;@264ee966, [Ljava.lang.String;@eaf968, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromListFileMixed[0](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@28b95dc5, [], [Ljava.lang.String;@58da0754, [Ljava.lang.String;@39825915, [Ljava.lang.String;@1653b3a5, [Ljava.lang.String;@74e693df)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromListFileMixed[1](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@16433b5f, [APPEND_TO_COLLECTIONS], [Ljava.lang.String;@58da0754, [Ljava.lang.String;@39825915, [Ljava.lang.String;@3af6e684, [Ljava.lang.String;@37d9c2cd)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionThatCannotBeAutoInitialized(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testGetCommandLineWithExpansionFile(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[0]([Ljava.lang.String;@25302982, [APPEND_TO_COLLECTIONS], [foo, bar, baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[1]([Ljava.lang.String;@25302982, [], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[2]([Ljava.lang.String;@1599df1c, [APPEND_TO_COLLECTIONS], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[3]([Ljava.lang.String;@1599df1c, [], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[4]([Ljava.lang.String;@490606a, [APPEND_TO_COLLECTIONS], [frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[5]([Ljava.lang.String;@490606a, [], [frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[6]([Ljava.lang.String;@6941048e, [APPEND_TO_COLLECTIONS], [foo, bar])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[7]([Ljava.lang.String;@72683b1, [[]], [foo, bar])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testPositionalCollectionFromExpansionFile(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testRejectNonCollectionFileExpansionSuppression(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testUninitializedCollections[0]([Ljava.lang.String;@6e9fe6d2, [], [L1, L2], [S1], [HS1], [P1, P2])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testUninitializedCollections[1]([Ljava.lang.String;@6e9fe6d2, [APPEND_TO_COLLECTIONS], [L1, L2], [S1], [HS1], [P1, P2])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method passingMutexCheck[0](simple mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@771bcdd6, [Ljava.lang.String;@319eb5b1)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method passingMutexCheck[1](collection mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@21cad527, [Ljava.lang.String;@4e4f4e2c)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method passingMutexCheck[2](collection multiple mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@8a577e6, [Ljava.lang.String;@73c54063)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method passingMutexCheck[3](scalar mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@7dfc3bf3, [Ljava.lang.String;@66e47d4f)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testAbbreviationsAreRejected(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testAdvancedArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgCollectionNotInitialized(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgUsage[0](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$FrobnicateArguments@562136e, [--FROBNICATION_FLAVOR , --SHMIGGLE_TYPE , --arguments_file , --FROBNICATION_THRESHOLD,-T , --TRUTHINESS ])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgUsage[1](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$FrobnicateArguments@1641f6f, [--deprecatedString, This argument is DEPRECATED, and will be removed in a future])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgUsage[2](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@6fd26b3, [--collection , --scalar ])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgumentCollection(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgumentNameCollision(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgumentUseClash(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgumentsFile(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgumentsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArrayArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testBadFieldCausesException(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testBadValue(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testBetaExperimentalMutex(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testBetaFeatureUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testCombinationOfFlags(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testDanglingMutex(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testDefault(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testEnsureClusteringDisabled(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testEnumSet(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testEnumSetNegative(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testExperimentalFeatureUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[0](no args, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@64acf662, [Ljava.lang.String;@4f7b5be2)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[1](1 of group required, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@323ff5ee, [Ljava.lang.String;@6646cfa2)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[2](mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@7bd98f0e, [Ljava.lang.String;@2d8b8d9)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[3](mega mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@4e180d6e, [Ljava.lang.String;@6fd9fcbb)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[4](collection and scalar mutex mix, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@6cae195d, [Ljava.lang.String;@184cc20b)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFlagNoArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFlagWithPositionalFollowing(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFlagsWithArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testGatherArgumentValuesOfType[0]([--childSuperTypeTarget, childSuperTypeTargetValue, --childSubTypeTarget, childSubTypeTargetValue, --parentSuperTypeTarget, parentSuperTypeTargetValue, --parentSubTypeTarget, parentSubTypeTargetValue, --childCollectionSuperTypeTarget, childCollectionSuperTypeTargetValue, --childCollectionSubTypeTarget, childCollectionSubTypeTargetValue, --parentCollectionSuperTypeTarget, parentCollectionSuperTypeTargetValue, --parentCollectionSubTypeTarget, parentCollectionSubTypeTargetValue, --childListSuperTypeTarget, childListSuperTypeTargetValue1, --childListSuperTypeTarget, childListSuperTypeTargetValue2, --childListSuperTypeTarget, childListSuperTypeTargetValue3, --childListSubTypeTarget, childListSubTypeTargetValue1, --childListSubTypeTarget, childListSubTypeTargetValue2, --childListSubTypeTarget, childListSubTypeTargetValue3, --parentListSuperTypeTarget, parentListSuperTypeTargetValue1, --parentListSuperTypeTarget, parentListSuperTypeTargetValue2, --parentListSuperTypeTarget, parentListSuperTypeTargetValue3, --parentListSubTypeTarget, parentListSubTypeTargetValue1, --parentListSubTypeTarget, parentListSubTypeTargetValue2, --parentListSubTypeTarget, parentListSubTypeTargetValue3, --childCollectionListSuperTypeTarget, childCollectionListSuperTypeTargetValue1, --childCollectionListSuperTypeTarget, childCollectionListSuperTypeTargetValue2, --childCollectionListSuperTypeTarget, childCollectionListSuperTypeTargetValue3, --childNonTargetArgument, 1, --parentNonTargetArgument, 1, --childCollectionNonTargetArgument, 1, --parentCollectionNonTargetArgument, 1, --childNonTargetListArgument, 1], [(childCollectionListSuperTypeTarget,childCollectionListSuperTypeTargetValue1), (childCollectionListSuperTypeTarget,childCollectionListSuperTypeTargetValue2), (childCollectionListSuperTypeTarget,childCollectionListSuperTypeTargetValue3), (childCollectionSubTypeTarget,childCollectionSubTypeTargetValue), (childCollectionSuperTypeTarget,childCollectionSuperTypeTargetValue), (childListSubTypeTarget,childListSubTypeTargetValue1), (childListSubTypeTarget,childListSubTypeTargetValue2), (childListSubTypeTarget,childListSubTypeTargetValue3), (childListSuperTypeTarget,childListSuperTypeTargetValue1), (childListSuperTypeTarget,childListSuperTypeTargetValue2), (childListSuperTypeTarget,childListSuperTypeTargetValue3), (childSubTypeTarget,childSubTypeTargetValue), (childSuperTypeTarget,childSuperTypeTargetValue), (parentCollectionSubTypeTarget,parentCollectionSubTypeTargetValue), (parentCollectionSuperTypeTarget,parentCollectionSuperTypeTargetValue), (parentListSubTypeTarget,parentListSubTypeTargetValue1), (parentListSubTypeTarget,parentListSubTypeTargetValue2), (parentListSubTypeTarget,parentListSubTypeTargetValue3), (parentListSuperTypeTarget,parentListSuperTypeTargetValue1), (parentListSuperTypeTarget,parentListSuperTypeTargetValue2), (parentListSuperTypeTarget,parentListSuperTypeTargetValue3), (parentSubTypeTarget,parentSubTypeTargetValue), (parentSuperTypeTarget,parentSuperTypeTargetValue), (uninitializedChildCollectionTarget,null), (uninitializedChildListTarget,null), (uninitializedChildTarget,null), (uninitializedParentCollectionTarget,null), (uninitializedParentTarget,null)])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testGatherArgumentValuesOfTypeWithParameterizedType(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testGetCommandLine(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testGetCommandLineWithSensitiveArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: USAGE: BooleanFlags [arguments] Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest.testHelp STANDARD_ERROR USAGE: BooleanFlags [arguments] Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Usage: program [arguments...] Usage: program [arguments...] Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Version:null Version:null Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Optional Arguments: Optional Arguments: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --antiflag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used --antiflag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: in conjunction with argument(s) flag1 in conjunction with argument(s) flag1 Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --arguments_file read one or more arguments files and add them to the command line This argument may be --arguments_file read one or more arguments files and add them to the command line This argument may be Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: specified 0 or more times. Default value: null. specified 0 or more times. Default value: null. Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --flag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used --flag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: in conjunction with argument(s) antiflag1 in conjunction with argument(s) antiflag1 Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --flag2 Undocumented option Default value: true. Possible values: {true, false} --flag2 Undocumented option Default value: true. Possible values: {true, false} Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --flag3 Undocumented option Default value: false. Possible values: {true, false} --flag3 Undocumented option Default value: false. Possible values: {true, false} Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --help,-h display the help message Default value: false. Possible values: {true, false} --help,-h display the help message Default value: false. Possible values: {true, false} Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --version display the version number for this tool Default value: false. Possible values: {true, --version display the version number for this tool Default value: false. Possible values: {true, Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: false} false} Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Advanced Arguments: Advanced Arguments: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --showHidden display hidden arguments Default value: false. Possible values: {true, false} --showHidden display hidden arguments Default value: false. Possible values: {true, false} Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testHiddenArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testHiddenRequiredArgumentThrowException(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testLongPreamble(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testMissingRequiredCollectionArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testNotEnoughOfListArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOnlyPrintNameOnce(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOptionalOnlyUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[0]([Ljava.lang.String;@651a3c45)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[1]([Ljava.lang.String;@5bd098c2)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[2]([Ljava.lang.String;@7e632cb2)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[3]([Ljava.lang.String;@e0e43c6)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[4]([Ljava.lang.String;@7e213c6f)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[5]([Ljava.lang.String;@76488799)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[6]([Ljava.lang.String;@6b673944)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testPositionalDeprecated(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testPositive(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testPrivateArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testRequiredAdvancedNotAllowed(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testRequiredOnlyUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testRequiredOptionalWithDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testRequiredOptionalWithoutDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testSetNonNullableArgumentsToNull[0]([Ljava.lang.String;@7ccb8ac3)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testSetNonNullableArgumentsToNull[1]([Ljava.lang.String;@2f0bf521)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testSetNonNullableArgumentsToNull[2]([Ljava.lang.String;@62f89cb)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testVersionSpecialFlag(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Test: Test method testVersionSpecialFlag(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Version:null Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest.testVersionSpecialFlag STANDARD_ERROR Version:null Running Test: Test method testWithBoundariesArgumentsForNoNumeric(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithDoubleBoundariesArgumentsForInteger(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[0]([Ljava.lang.String;@7d83dc80, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[1]([Ljava.lang.String;@7d33027d, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[2]([Ljava.lang.String;@45a18b00, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[3]([Ljava.lang.String;@7ee24747, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[4]([Ljava.lang.String;@15957338, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[5]([Ljava.lang.String;@48f8bbc0, 1, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[6]([Ljava.lang.String;@5fb9b644, null, 2.0, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[7]([Ljava.lang.String;@49c05880, null, null, somestring)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[8]([Ljava.lang.String;@11b9ba55, 1, 2.0, somestring)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithoutPositionalWithDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithoutPositionalWithoutDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testBasicPlugin[0]([Ljava.lang.String;@6ded58a0, 0)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testBasicPlugin[1]([Ljava.lang.String;@9380700, 1)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testDanglingFilterArguments[0](TestPluginWithRequiredArg, requiredStringArgForPlugin, fakeArgValue)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testDanglingFilterArguments[1](TestPluginWithOptionalArg, optionalStringArgForPlugin, fakeArgValue)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testDefaultIncludePluginClass[0](class org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest$TestPluginBase, true)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testDefaultIncludePluginClass[1](class org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest$TestPluginWithOptionalArg, true)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testDefaultIncludePluginClass[2](class java.lang.Integer, false)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testEnableNonExistentPlugin(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testNoPluginsSpecified(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testAddToDefaultValuesListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testArgumentCollectionFlat(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testArgumentCollectionNested(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testArgumentCollectionNoReferenceProvidedForOptional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'REFERENCE_SEQUENCE' is required. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testArgumentCollectionNoReferenceProvidedForRequired STANDARD_ERROR ERROR: Option 'REFERENCE_SEQUENCE' is required. Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: ToolWithRequiredReference [options] USAGE: ToolWithRequiredReference [options] Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] Usage: program [options...] Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: REFERENCE_SEQUENCE=File A reference is required Required. REFERENCE_SEQUENCE=File A reference is required Required. Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testArgumentCollectionWithReferenceProvidedForOptional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testArgumentCollectionWithReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: 'HiMom' is not a valid value for FrobnicationFlavor. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testBadEnumValue STANDARD_ERROR ERROR: 'HiMom' is not a valid value for FrobnicationFlavor. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Problem constructing Integer from the string 'ABC'. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testBadValue STANDARD_ERROR ERROR: Problem constructing Integer from the string 'ABC'. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testBetaExperimentalMutex(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testBetaFeatureUsage(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testClearDefaultValuesFromListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testClearDefaultValuesFromListOptionAndAddNew(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testCollectionThatCannotBeAutoInitialized(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testDefault(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testExperimentalFeatureUsage(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testForIdenticalShortName(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[0](hello, hello)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[1](, )(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[2](hibye, hi bye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[3](hibye, hibye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[4](hi
  • bye, hi - bye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[5](hibye, hibye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[6](
    , 

)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
Running Test: Test method testHTMLConverter[7]( string,  string (http://go.here.org))(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
Running Test: Test method testHTMLConverter[8]( string,  string (http://go.here.org))(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
Running Test: Test method testHTMLConverter[9](< a href="http://go.here.org"> string,  string (http://go.here.org))(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
Running Test: Test method testHTMLConverter[10](hi
    • bye, hi bye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHTMLConverter[11](Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina).

    Usage example:

        java -jar picard.jar CollectAlignmentSummaryMetrics \
              R=reference_sequence.fasta \
              I=input.bam \
              O=output.txt
    Please see     the AlignmentSummaryMetrics documentation for detailed explanations of each metric.

    Additional information about Illumina's quality filters can be found in the following documents on the Illumina website:
    , Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina). Usage example: java -jar picard.jar CollectAlignmentSummaryMetrics \ R=reference_sequence.fasta \ I=input.bam \ O=output.txt Please see the AlignmentSummaryMetrics documentation (http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics) for detailed explanations of each metric. Additional information about Illumina's quality filters can be found in the following documents on the Illumina website: - hiseq-x-percent-pf-technical-note (http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf) - hiseq-x-system-guide (http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseqx/hiseq-x-system-guide-15050091-d.pdf) )(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHtmlUnescape[0](<, <)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHtmlUnescape[1](x)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testHtmlUnescape[4]( x y< x , x<y y< x )(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[0](-15)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[1](-5)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[2](-2)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[3](1)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[4](0)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[5](2)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[6](5)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testIgnoringBoundaries[7](10)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testLongPreamble(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'FROBNICATION_FLAVOR' is required. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMissingRequiredArgument STANDARD_ERROR ERROR: Option 'FROBNICATION_FLAVOR' is required. Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[0](pass, [Ljava.lang.String;@7218703d, true)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'A' is required unless any of [Y, Z, M, N] are specified. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false) STANDARD_ERROR ERROR: Option 'A' is required unless any of [Y, Z, M, N] are specified. Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] USAGE: MutexOptions [options] Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] Usage: program [options...] Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[1](no args, [Ljava.lang.String;@14a4adc5, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'B' is required unless any of [Y, Z, M, N] are specified. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false) STANDARD_ERROR ERROR: Option 'B' is required unless any of [Y, Z, M, N] are specified. Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] USAGE: MutexOptions [options] Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] Usage: program [options...] Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3e1f9cf3, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'A' cannot be used in conjunction with option(s) Y Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[3](mutex, [Ljava.lang.String;@31daa293, false) STANDARD_ERROR ERROR: Option 'A' cannot be used in conjunction with option(s) Y Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] USAGE: MutexOptions [options] Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] Usage: program [options...] Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[3](mutex, [Ljava.lang.String;@31daa293, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'A' cannot be used in conjunction with option(s) Y Z M N Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false) STANDARD_ERROR ERROR: Option 'A' cannot be used in conjunction with option(s) Y Z M N Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] USAGE: MutexOptions [options] Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] Usage: program [options...] Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@335ba389, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testNonASCIIAccept(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testNonASCIIReject(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testNonAsciiAssertion(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testNonAsciiConverted(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'SHMIGGLE_TYPE' must be specified at least 1 times. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testNotEnoughOfListOption STANDARD_ERROR ERROR: Option 'SHMIGGLE_TYPE' must be specified at least 1 times. Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: At least 2 positional arguments must be specified. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testNotEnoughPositional STANDARD_ERROR ERROR: At least 2 positional arguments must be specified. Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testNullValue STANDARD_ERROR ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptionsWithNullList [options] USAGE: FrobnicateOptionsWithNullList [options] Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Required. T=Integer Frobnication threshold setting. Required. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Default value: BAR. This option can be set to 'null' to clear the Undocumented option Default value: BAR. This option can be set to 'null' to clear the Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {FOO, BAR, BAZ} default value. Possible values: {FOO, BAR, BAZ} Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptionsWithNullList [options] USAGE: FrobnicateOptionsWithNullList [options] Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Required. T=Integer Frobnication threshold setting. Required. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Default value: BAR. This option can be set to 'null' to clear the Undocumented option Default value: BAR. This option can be set to 'null' to clear the Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {FOO, BAR, BAZ} default value. Possible values: {FOO, BAR, BAZ} Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testOptionDefinitionCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'FROBNICATION_FLAVOR' cannot be specified more than once. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testOptionUseCaseClash STANDARD_ERROR ERROR: Option 'FROBNICATION_FLAVOR' cannot be specified more than once. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testOptionsFile(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'T' cannot be specified more than once. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testOptionsFileWithDisallowedOverride STANDARD_ERROR ERROR: Option 'T' cannot be specified more than once. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testPositive(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testPositiveTerminalEqualSign(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testPositiveWithSpaces(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testPositiveWithoutPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'SHMIGGLE_TYPE' cannot be used more than 3 times. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testTooManyListOption STANDARD_ERROR ERROR: Option 'SHMIGGLE_TYPE' cannot be used more than 3 times. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: No more than 2 positional arguments may be specified on the command line. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testTooManyPositional STANDARD_ERROR ERROR: No more than 2 positional arguments may be specified on the command line. Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] USAGE: FrobnicateOptions [options] Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file Usage: frobnicate [options] input-file output-file Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file Read input-file, frobnicate it, and write frobnicated results to output-file Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Invalid argument 'positional'. Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testUnexpectedPositional STANDARD_ERROR ERROR: Invalid argument 'positional'. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: OptionsWithoutPositional [options] USAGE: OptionsWithoutPositional [options] Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: framistat [options] Usage: framistat [options] Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Compute the plebnick of the freebozzle. Compute the plebnick of the freebozzle. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer FROBNICATION_THRESHOLD=Integer Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor FROBNICATION_FLAVOR=FrobnicationFlavor Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} Undocumented option Required. Possible values: {FOO, BAR, BAZ} Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. times. Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testUninitializedCollections(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testUsage(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testUsageWithDefault(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testUsageWithoutPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testUsageWithoutPositionalWithDefault(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testDefaultValueAsString[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$1@7a5770, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$2@65c4bcd9, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$3@175743d1, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$4@28279194, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[4](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$5@628e1884, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[5](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$6@3063dc18, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[6](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$7@39d1d7b1, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[7](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$8@5177efa0, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[8](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$9@401aaf, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[9](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$10@42a8cd39, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[10](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$11@2cb57e38, arg, true, [stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[11](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$12@651ec593, arg, true, [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@78db6a9c, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@606ff903, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@3bf2d4a6, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@52240bed, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@117be44a, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@4c64f43e, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@34408a0e, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@e897466, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@7f7a2caa, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@62a5d81f, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@552a683c, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@6bad6d00, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$1@4edc6912, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$2@48fd77b8, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$3@212c2dfd, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$4@ccf0326, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[4](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$5@6a73e9ac, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[5](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$6@563bb669, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[6](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$7@aff080d, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[7](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$8@69346c03, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[8](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$9@41115abd, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[9](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$10@51546655, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[10](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$11@4d4d10c8, arg, true, [stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[11](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$12@76704cb0, arg, true, [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetCommandLineDisplayString[0]([Ljava.lang.String;@651b2ca1, )(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testGetCommandLineDisplayString[1]([Ljava.lang.String;@407a7404, arg1)(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testGetCommandLineDisplayString[2]([Ljava.lang.String;@3acf016e, arg1 arg2)(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testMaxElements(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testMinElements(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testMinElementsGreaterThanMaxElements(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testNonCollection(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method recognizedValues(org.broadinstitute.barclay.argparser.StrictBooleanConverterTest) Running Test: Test method unrecognizedValues(org.broadinstitute.barclay.argparser.StrictBooleanConverterTest) Running Test: Test method testBadTaggedArguments[0]([Ljava.lang.String;@6883795a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[1]([Ljava.lang.String;@7f0c680c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[2]([Ljava.lang.String;@1fc8ec0a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[3]([Ljava.lang.String;@7a486e42)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[4]([Ljava.lang.String;@442e2ca7)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[5]([Ljava.lang.String;@3b2cb4af)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[6]([Ljava.lang.String;@633d1fd0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[7]([Ljava.lang.String;@40be3c8f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[8]([Ljava.lang.String;@72cede2)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[9]([Ljava.lang.String;@4a66622b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[10]([Ljava.lang.String;@43e31d93)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[11]([Ljava.lang.String;@3e07a4ce)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[12]([Ljava.lang.String;@19093790)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[13]([Ljava.lang.String;@4a514ad3)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[14]([Ljava.lang.String;@35e8730f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[15]([Ljava.lang.String;@213ff6e5)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[16]([Ljava.lang.String;@27a6eb83)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[17]([Ljava.lang.String;@621201ba)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[18]([Ljava.lang.String;@ee0f1dd)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[19]([Ljava.lang.String;@f47baa2)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[20]([Ljava.lang.String;@4fb88ea2)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[21]([Ljava.lang.String;@5347d916)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[22]([Ljava.lang.String;@616a56a3)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[23]([Ljava.lang.String;@5258c859)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[24]([Ljava.lang.String;@6bd46a6a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[25]([Ljava.lang.String;@11c0b810)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[26]([Ljava.lang.String;@462cda44)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[27]([Ljava.lang.String;@2291172b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[28]([Ljava.lang.String;@170f6253)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[29]([Ljava.lang.String;@22597c2f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[30]([Ljava.lang.String;@724585c4)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[31]([Ljava.lang.String;@7690550a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[32]([Ljava.lang.String;@6c3977d3)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[33]([Ljava.lang.String;@75e664fb)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[34]([Ljava.lang.String;@208aeb0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[35]([Ljava.lang.String;@528cdcbb)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[36]([Ljava.lang.String;@6df13c2a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[37]([Ljava.lang.String;@12cdf73a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[38]([Ljava.lang.String;@2e538998)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[39]([Ljava.lang.String;@7f7d14eb)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[40]([Ljava.lang.String;@5d2b1e6e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[41]([Ljava.lang.String;@3bb81531)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[42]([Ljava.lang.String;@3b02fdf5)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[43]([Ljava.lang.String;@a2f3422)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[44]([Ljava.lang.String;@607290e0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[45]([Ljava.lang.String;@15cc1618)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[46]([Ljava.lang.String;@63034d7b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[47]([Ljava.lang.String;@33630255)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[48]([Ljava.lang.String;@51000689)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[49]([Ljava.lang.String;@17d4f16c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[50]([Ljava.lang.String;@6afd86b6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[51]([Ljava.lang.String;@207f2d60)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[52]([Ljava.lang.String;@6c80b0e6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[53]([Ljava.lang.String;@22461ecc)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[54]([Ljava.lang.String;@71899803)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[55]([Ljava.lang.String;@7ed901a6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[56]([Ljava.lang.String;@7a7bf853)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[57]([Ljava.lang.String;@42880482)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[58]([Ljava.lang.String;@4aab7dcf)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[59]([Ljava.lang.String;@6b30f808)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGetCommandLineTagged[0]([Ljava.lang.String;@284924e4, TaggableArguments --tFullName:tumor gcs://my/tumor.bam --tScalar:taggableArgScalar foo --scalarArg 17)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGetCommandLineTagged[1]([Ljava.lang.String;@784e09f7, TaggableArguments --tFullName:tumor,training=true,truth=false tumor.bam --tFullName:normal,training=false,truth=true normal.bam --tScalar:taggableArgScalar foo --scalarArg 17)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[0]([Ljava.lang.String;@1e57e243, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@64bfbc58, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@a25eede)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[1]([Ljava.lang.String;@1d08cab8, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7cbbeb9c, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2ef7542c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[2]([Ljava.lang.String;@306aece9, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@53c2a5cc, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@48bc34a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[3]([Ljava.lang.String;@3e31fe04, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@6c4d56b9, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@62292ce3)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[4]([Ljava.lang.String;@3e3d6f29, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@ae6e7, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@110471f7)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[5]([Ljava.lang.String;@30e3ea4d, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@19b7a884, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7d57d607)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[6]([Ljava.lang.String;@1ca5cc27, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3cd980b5, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@215b012d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[7]([Ljava.lang.String;@41826177, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7cdc79d3, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@721b47ef)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[8]([Ljava.lang.String;@a5a630, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5679326a, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@22667ae9)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[9]([Ljava.lang.String;@5554105, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@77ea887, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4c875985)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[10]([Ljava.lang.String;@2b46edb6, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@61964380, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@11f1df75)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[11]([Ljava.lang.String;@1dc86a8f, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3a0c983, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@76628b2a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[12]([Ljava.lang.String;@4a65dcf7, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2d31b4a6, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@175dbd70)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[13]([Ljava.lang.String;@16087d8e, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@30c6a382, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@76ffa65a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[14]([Ljava.lang.String;@ab4056, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2f9a64af, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@606bb0a8)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[15]([Ljava.lang.String;@339a273f, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@50f66a28, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@ade8ec9)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[16]([Ljava.lang.String;@c35bea, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@8460d59, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@36398177)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[17]([Ljava.lang.String;@54eee638, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@28916e44, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7b5d952a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testMixedTagCollectionArgument(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testMixedTaggedExpansionFile(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testTaggedScalarArgument(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testNonNullDoesNotThrow(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testNonNullThrows(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testNonNullWithMessageReturn(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testNonNullWithMessageThrows(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[0](hello hello hello hello hello, hello hello hello hello hello, 12)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[1](hello hello hello hello hello, hello hello hello hello hello, 11)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[2](hello hello hello hello hello, hello hello hello hello hello, 10)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[3](hello hello hello hello hello, hello hello hello hello hello, 10)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[4](hello hello hello hello hello, hello hello hello hello hello, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[5](hello hello hello hello hello , hello hello hello hello hello , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[6](hello hello hello hello hello , hello hello hello hello hello , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[7](, , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[8]( , , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[9]( , , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[10](null, null, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[11](hello, hello, 0)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[12](hello, hello, -1)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[13](a b c d e f g, a b c d e f g, 1)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[14](a b c d e f g, a b c d e f g, 0)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[15](a b c d e f g, a b c d e f g, -1)(org.broadinstitute.barclay.utils.UtilsUnitTest) Running Test: Test method testWrapParagraph[16](a b c d e f g, a b c d e f g, -1000)(org.broadinstitute.barclay.utils.UtilsUnitTest) Gradle Test Executor 1 finished executing tests. WARNING: A terminally deprecated method in java.lang.System has been called WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar) WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release Results: SUCCESS (337 tests, 337 successes, 0 failures, 0 skipped) Finished generating test XML results (0.053 secs) into: /build/reproducible-path/barclay-5.0.0+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.037 secs) into: /build/reproducible-path/barclay-5.0.0+dfsg/build/reports/tests/test :test (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 3.043 secs. BUILD SUCCESSFUL in 10s 5 actionable tasks: 3 executed, 2 up-to-date rm -fr -- /tmp/dh-xdg-rundir-4HGbNi3c make[1]: Leaving directory '/build/reproducible-path/barclay-5.0.0+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=gradle dh_prep -O--buildsystem=gradle rm -f -- debian/libbarclay-java.substvars rm -fr -- debian/.debhelper/generated/libbarclay-java/ debian/libbarclay-java/ debian/tmp/ dh_auto_install --destdir=debian/libbarclay-java/ -O--buildsystem=gradle install -m0755 -d /build/reproducible-path/barclay-5.0.0\+dfsg/debian/libbarclay-java jh_installjavadoc -O--buildsystem=gradle dh_installdocs -O--buildsystem=gradle install -m0755 -d debian/libbarclay-java/usr/share/doc/libbarclay-java install -p -m0644 debian/copyright debian/libbarclay-java/usr/share/doc/libbarclay-java/copyright dh_installchangelogs -O--buildsystem=gradle install -m0755 -d debian/libbarclay-java/usr/share/doc/libbarclay-java install -p -m0644 debian/.debhelper/generated/libbarclay-java/dh_installchangelogs.dch.trimmed debian/libbarclay-java/usr/share/doc/libbarclay-java/changelog.Debian dh_installsystemduser -O--buildsystem=gradle dh_perl -O--buildsystem=gradle dh_link -O--buildsystem=gradle jh_installlibs -O--buildsystem=gradle install -m0755 -d debian/libbarclay-java/usr/share/java install -p -m0644 ./build/libs/barclay-5.0.0.jar debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar rm -f debian/libbarclay-java/usr/share/java/barclay.jar ln -s barclay-5.0.0.jar debian/libbarclay-java/usr/share/java/barclay.jar jh_classpath -O--buildsystem=gradle jh_manifest -plibbarclay-java "--classpath=/usr/share/java/commons-lang3.jar /usr/share/java/freemarker.jar /usr/share/java/gson.jar /usr/share/java/joptsimple.jar /usr/share/java/log4j-api.jar" debian/libbarclay-java/usr/share/java/barclay.jar Updating symlinked /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar (via debian/libbarclay-java/usr/share/java/barclay.jar) Reading manifest from /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar Updating manifest in /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar jh_manifest -O--buildsystem=gradle find debian/libbarclay-java -name '*.jar' Found symlink usr/share/java/barclay.jar Found usr/share/java/barclay-5.0.0.jar Reading manifest from debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar No update of debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar required. jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle Searching /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java for libbarclay-java Searching /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar Found Jars: /usr/share/java/commons-lang3.jar /usr/share/java/freemarker.jar /usr/share/java/gson.jar /usr/share/java/joptsimple.jar /usr/share/java/log4j-api.jar Checking: /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/commons-lang3-3.14.0.jar Checking: /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/freemarker-17.jar Checking: /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/gson-2.10.1.jar Checking: /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/joptsimple.jar Checking: /build/reproducible-path/barclay-5.0.0+dfsg/debian/libbarclay-java/usr/share/java/log4j-api.jar Found Debs: libcommons-lang3-java libfreemarker-java libgoogle-gson-java libjoptsimple-java liblog4j2-java Adding substvars: java:Depends=libcommons-lang3-java, libfreemarker-java, libgoogle-gson-java, libjoptsimple-java, liblog4j2-java java:Recommends= mh_installpoms -O--buildsystem=gradle mh_installpom --package=libbarclay-java --usj-name=barclay debian/pom-barclay.xml mh_cleanpom --package=libbarclay-java --rules=debian/maven.rules debian/pom-barclay.xml debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/pom.properties mv debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/barclay-debian.pom install -m 644 -D debian/.debhelper/.mh/barclay-5.0.0.pom debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/5.0.0/barclay-5.0.0.pom install -m 644 -D debian/.debhelper/.mh/barclay-debian.pom debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.pom mh_linkjars --skip-clean-poms -O--buildsystem=gradle mh_linkjar --package=libbarclay-java --skip-clean-pom debian/pom-barclay.xml /usr/share/java/barclay.jar dh_link -plibbarclay-java /usr/share/javabarclay.jar usr/share/maven-repo/org/broadinstitute/barclay/5.0.0/barclay-5.0.0.jar rm -f debian/libbarclay-java/usr/share/java/barclay.jar ln -s barclay-5.0.0.jar debian/libbarclay-java/usr/share/java/barclay.jar install -m0755 -d debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/5.0.0 rm -f debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/5.0.0/barclay-5.0.0.jar ln -s ../../../../../java/barclay.jar debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/5.0.0/barclay-5.0.0.jar dh_link -plibbarclay-java /usr/share/javabarclay.jar usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.jar rm -f debian/libbarclay-java/usr/share/java/barclay.jar ln -s barclay-5.0.0.jar debian/libbarclay-java/usr/share/java/barclay.jar rm -f debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/5.0.0/barclay-5.0.0.jar ln -s ../../../../../java/barclay.jar debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/5.0.0/barclay-5.0.0.jar install -m0755 -d debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/debian rm -f debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.jar ln -s ../../../../../java/barclay.jar debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.jar dh_strip_nondeterminism -O--buildsystem=gradle Using 1686519130 as canonical time Normalizing debian/libbarclay-java/usr/share/java/barclay-5.0.0.jar using File::StripNondeterminism::handlers::jar dh_compress -O--buildsystem=gradle cd debian/libbarclay-java chmod a-x usr/share/doc/libbarclay-java/changelog.Debian gzip -9nf usr/share/doc/libbarclay-java/changelog.Debian cd '/build/reproducible-path/barclay-5.0.0+dfsg' dh_fixperms -O--buildsystem=gradle find debian/libbarclay-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libbarclay-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libbarclay-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libbarclay-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libbarclay-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--buildsystem=gradle dh_installdeb -O--buildsystem=gradle install -m0755 -d debian/libbarclay-java/DEBIAN rm -f debian/libbarclay-java.debhelper.log debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/barclay-5.0.0+dfsg' cat debian/control \ | sed -e '/^Build-.*Depends:/,/^[^[:space:]#]/{s/^Build-.*Depends:/ /;p};d' \ | grep '^[[:space:]]' \ | tr ',' '\n' \ > debian/bd-temp-substvars echo -n "bd:barclay-java=" > debian/bd.substvars grep 'libbarclay-java ' debian/bd-temp-substvars \ | tr "\n" "," \ | sed -e 's/[[:space:]]\+/ /g;s/,$/\n/' \ >> debian/bd.substvars dh_gencontrol -O--buildsystem=gradle -- -Tdebian/bd.substvars install -m0755 -d debian/libbarclay-java/DEBIAN echo misc:Depends= >> debian/libbarclay-java.substvars echo misc:Pre-Depends= >> debian/libbarclay-java.substvars dpkg-gencontrol -plibbarclay-java -ldebian/changelog -Tdebian/libbarclay-java.substvars -cdebian/control -Pdebian/libbarclay-java -Tdebian/bd.substvars chmod 0644 -- debian/libbarclay-java/DEBIAN/control make[1]: Leaving directory '/build/reproducible-path/barclay-5.0.0+dfsg' dh_md5sums -O--buildsystem=gradle install -m0755 -d debian/libbarclay-java/DEBIAN cd debian/libbarclay-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libbarclay-java/DEBIAN/md5sums dh_builddeb -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/libbarclay-java .. dpkg-deb: building package 'libbarclay-java' in '../libbarclay-java_5.0.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../barclay_5.0.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../barclay_5.0.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3431041 and its subdirectories I: Current time: Tue Jun 17 08:49:09 -12 2025 I: pbuilder-time-stamp: 1750193349 Wed May 15 14:26:11 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Wed May 15 14:26:11 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Wed May 15 14:30:27 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Wed May 15 14:30:27 UTC 2024 I: barclay_5.0.0+dfsg-1_amd64.changes: Format: 1.8 Date: Sun, 11 Jun 2023 23:32:10 +0200 Source: barclay Binary: libbarclay-java Architecture: all Version: 5.0.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Java Maintainers Changed-By: Pierre Gruet Description: libbarclay-java - Java library to parse command line Changes: barclay (5.0.0+dfsg-1) unstable; urgency=medium . * New upstream version 5.0.0+dfsg * Refreshing patches * Raising Standards version to 4.6.2 (no change) * Reworking build.gradle for a Debian build * Removing more classes due to com.sun.javadoc removal in OpenJDK17 Checksums-Sha1: 85c66ae1eb6fb009787feea73b0a53613c10c208 12394 barclay_5.0.0+dfsg-1_amd64.buildinfo 763ebf2e6b9741645d70de9c9041c85706208f19 108428 libbarclay-java_5.0.0+dfsg-1_all.deb Checksums-Sha256: 4eb5aab4972589bc531375838fcae6c37779a519866a95ab80abf6d844799943 12394 barclay_5.0.0+dfsg-1_amd64.buildinfo c625a8e331bf2c20d27bbb9e9ca9c70eda5caef687f68b66203baf4f63b3c5c8 108428 libbarclay-java_5.0.0+dfsg-1_all.deb Files: 945501e364d368d06ba80633e76ade95 12394 java optional barclay_5.0.0+dfsg-1_amd64.buildinfo 1876c19f068a4e149f1bc3f0d5e0b71c 108428 java optional libbarclay-java_5.0.0+dfsg-1_all.deb Wed May 15 14:30:29 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-11929.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/barclay_5.0.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/barclay_5.0.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/barclay_5.0.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/b1/barclay_5.0.0+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yhiYSipm/b2/barclay_5.0.0+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.360s) 0.360s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.015s) 0.015s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 690ms CPU time consumed: 691ms Wed May 15 14:30:30 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Wed May 15 14:30:30 UTC 2024 I: barclay from trixie built successfully and reproducibly on amd64. Wed May 15 14:30:31 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 15 14:30:31 UTC 2024 I: Submitting 16K b1/barclay_5.0.0+dfsg-1_amd64.buildinfo.asc Wed May 15 14:30:32 UTC 2024 I: Submitting 16K b2/barclay_5.0.0+dfsg-1_amd64.buildinfo.asc Wed May 15 14:30:33 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 15 14:30:33 UTC 2024 I: Done submitting .buildinfo files. Wed May 15 14:30:33 UTC 2024 I: Removing signed barclay_5.0.0+dfsg-1_amd64.buildinfo.asc files: removed './b1/barclay_5.0.0+dfsg-1_amd64.buildinfo.asc' removed './b2/barclay_5.0.0+dfsg-1_amd64.buildinfo.asc'