Mon Aug 25 14:32:21 UTC 2025 I: starting to build barclay/forky/arm64 on jenkins on '2025-08-25 14:32' Mon Aug 25 14:32:21 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/84807/console.log Mon Aug 25 14:32:21 UTC 2025 I: Downloading source for forky/barclay=6.0.0+dfsg-1 --2025-08-25 14:32:21-- http://deb.debian.org/debian/pool/main/b/barclay/barclay_6.0.0%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_6.0.0+dfsg-1.dsc’ 0K .. 100% 262M=0s 2025-08-25 14:32:21 (262 MB/s) - ‘barclay_6.0.0+dfsg-1.dsc’ saved [2199/2199] Mon Aug 25 14:32:21 UTC 2025 I: barclay_6.0.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: barclay Binary: libbarclay-java Architecture: all Version: 6.0.0+dfsg-1 Maintainer: Debian Java Maintainers Uploaders: Olivier Sallou , Pierre Gruet Homepage: https://github.com/broadinstitute/barclay Standards-Version: 4.7.2 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: b5dfb1499920d8a4e3f77e41a386a22261eaa05d 119628 barclay_6.0.0+dfsg.orig.tar.xz d6f522f572f6ba8443913802eba87d52d7cdc2f7 8288 barclay_6.0.0+dfsg-1.debian.tar.xz Checksums-Sha256: 8c897b900841007e28c096e2838c3b6dfd70e5e869bc212c72972a244add9300 119628 barclay_6.0.0+dfsg.orig.tar.xz 77fee9ddd2b7b53d70a078af759776ab6ed864671c8ad2cb83e87bc7f8dc3a5f 8288 barclay_6.0.0+dfsg-1.debian.tar.xz Files: ae072ca1e6ad0cfd9d8707334f976d3f 119628 barclay_6.0.0+dfsg.orig.tar.xz 3e03ce47882b27e6747217d5069f2a69 8288 barclay_6.0.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmikqnUACgkQYAMWptwn dHbutRAAisjtONkC2n9dPqHBeIE/jINLKW/MtBwFt3iCuZcD3uVlbOKBQg1WeFsI jgNy++lqRvPHy06+wZ6NfoI2YNDJsrCBWyH6SHCMCygV3tYDMv3lpEvXV2QE8ND5 4oAp5hiR5Kn+V8dA3xHLtb0UUuCbwwE27RXmbZTRWc+Y4suxaVtBbyhnI3/wpBG7 gRho4F4YMG9X8z2hpKGKp47+HJB8U5ABL/S0fFB3onRmlazdpXzPYXkW1mWitL8l rHrk+9kFVZDaQ0AzPBEaEpf6576i5LxBd2T/ttWPA5y3axRD0Fm+JzUYPQeuDpUk UwbmH4K193Rlh+rY2Np83B3Bq5mbW8eGgA4br+ZzIum0g+MlcHtPQ+EVxhw6HE90 lyGiHG3Ol13EePyZ4WCkwENsL5u5odva/kBTz0ds2jD/GCqFf4b16k3MY1dtT6FT GKWpzcQayD4jXaArFKepDrQYKdZam6/l+ua5Jm6/50UpQF+s5RIOKgXF+6o3DcfT YPom8/NPwZtw644bXaTgCZiHn4gQYh+KKKz+0+XZfLGInFMVbDsZtZ7RoNlbcoNG fubVHDkhOw0M7wDiDbfoo0rw+w9cJZJN2yKMifvf3tl1skPX8XLCFyQ1HND2tHgC w5yH9vXtnTc6xbJ4EHM6L68bhuTjdmDleDeXvSsKBON/iPorj+g= =OMkM -----END PGP SIGNATURE----- Mon Aug 25 14:32:21 UTC 2025 I: Checking whether the package is not for us Mon Aug 25 14:32:21 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Mon Aug 25 14:32:21 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Mon Aug 25 14:33:43 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 25 02:32:23 -12 2025 I: pbuilder-time-stamp: 1756132343 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_6.0.0+dfsg-1.dsc] I: copying [./barclay_6.0.0+dfsg.orig.tar.xz] I: copying [./barclay_6.0.0+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./barclay_6.0.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting barclay in barclay-6.0.0+dfsg dpkg-source: info: unpacking barclay_6.0.0+dfsg.orig.tar.xz dpkg-source: info: unpacking barclay_6.0.0+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/3261747/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='849e3a66bc6a470485c5b81244c8c9d5' 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='3261747' 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.ZQ16DSNB/pbuilderrc_kcWk --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZQ16DSNB/b1 --logfile b1/build.log barclay_6.0.0+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3261747/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: arm64 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 ... 19969 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} dwz{a} fastjar{a} file{a} gettext{a} gettext-base{a} gpg{a} gpg-agent{a} gpgconf{a} gpgv{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} libassuan9{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} libffi8{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} libgcrypt20{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgoogle-gson-java{a} libgpg-error0{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} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-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} libjunixsocket-java{a} libjunixsocket-jni{a} libjzlib-java{a} libkryo-java{a} libksba8{a} liblcms2-2{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} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox-java{a} libreadline8t64{a} libreflectasm-java{a} librhino-java{a} librole-tiny-perl{a} libservlet-api-java{a} libsimple-http-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{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} libxml2-16{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-21-doc{a} openjdk-21-jdk-headless{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sopv-gpgv{a} testng{a} tzdata{a} unzip{a} wdiff{a} The following packages are RECOMMENDED but will NOT be installed: curl debian-keyring debian-tag2upload-keyring dput dput-ng dupload equivs git-debpush gnupg javascript-common libarchive-cpio-perl libasound2t64 libbindex-java libcups2t64 libdata-dump-perl libdistro-info-perl libfontconfig1 libfreetype6 libgitlab-api-v4-perl libgpars-groovy-java libgpg-error-l10n libharfbuzz0b libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmetacpan-client-perl libnamespace-clean-perl liboss4-salsa-asound2 libreflectasm-java-doc libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx lzip pristine-tar python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg sopv-doc strace wget 0 packages upgraded, 244 newly installed, 0 to remove and 0 not upgraded. Need to get 255 MB of archives. After unpacking 831 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.1-2 [93.3 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.6-1 [857 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.6-1 [2005 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.5-1 [27.2 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.6-1 [1897 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.6-1 [761 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.5-1 [10.2 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.5-1 [28.2 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 openssl arm64 3.5.2-1 [1457 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 ca-certificates all 20250419 [162 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.1-1 [93.8 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 java-common all 0.76 [6776 B] Get: 30 http://deb.debian.org/debian forky/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libnss3 arm64 2:3.114-1 [1299 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libpcsclite1 arm64 2.3.3-1 [55.0 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 openjdk-21-jre-headless arm64 21.0.8+9-1 [40.7 MB] Get: 36 http://deb.debian.org/debian forky/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 37 http://deb.debian.org/debian forky/main arm64 ant all 1.10.15-1 [2163 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 ant-optional all 1.10.15-1 [456 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 libantlr-java all 2.7.7+dfsg-14 [458 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 antlr all 2.7.7+dfsg-14 [8376 B] Get: 41 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 unzip arm64 6.0-29 [163 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 java-wrappers all 0.5 [8848 B] Get: 48 http://deb.debian.org/debian forky/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libfelix-framework-java all 4.6.1-3 [577 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libfelix-gogo-runtime-java all 0.16.2-2 [117 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 53 http://deb.debian.org/debian forky/main arm64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libjansi1-java all 1.18-3.1 [66.6 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libjline2-java all 2.14.6-6 [154 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libslf4j-java all 1.7.32-2 [142 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libxz-java all 1.9-1 [143 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libyaml-snake-java all 2.0+ds+really1.33-1 [324 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 bnd all 5.0.1-5 [10.1 MB] Get: 64 http://deb.debian.org/debian forky/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.25 [91.6 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-4 [539 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 71 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.1 [583 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 debhelper all 13.25 [937 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 openjdk-21-doc all 21.0.8+9-1 [13.2 MB] Get: 83 http://deb.debian.org/debian forky/main arm64 default-jdk-doc arm64 2:1.21-76 [3264 B] Get: 84 http://deb.debian.org/debian forky/main arm64 openjdk-21-jdk-headless arm64 21.0.8+9-1 [81.9 MB] Get: 85 http://deb.debian.org/debian forky/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 86 http://deb.debian.org/debian forky/main arm64 libgpg-error0 arm64 1.55-2 [83.9 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libgcrypt20 arm64 1.11.2-2 [772 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 gpgconf arm64 2.4.8-2 [121 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 gpg arm64 2.4.8-2 [578 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 pinentry-curses arm64 1.3.2-3 [85.0 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 gpg-agent arm64 2.4.8-2 [248 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 96 http://deb.debian.org/debian forky/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 99 http://deb.debian.org/debian forky/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libdevel-callchecker-perl arm64 0.009-2 [15.7 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 126 http://deb.debian.org/debian forky/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 libio-socket-ssl-perl all 2.095-1 [226 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 libwww-perl all 6.78-1 [183 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 gpgv arm64 2.4.8-2 [220 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 sopv-gpgv all 0.1.4-1 [11.3 kB] Get: 136 http://deb.debian.org/debian forky/main arm64 wdiff arm64 1.2.2-9 [122 kB] Get: 137 http://deb.debian.org/debian forky/main arm64 devscripts all 2.25.19 [1047 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 139 http://deb.debian.org/debian forky/main arm64 ivy all 2.5.3-1 [1299 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 libasm-java all 9.8-1 [392 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 143 http://deb.debian.org/debian forky/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 144 http://deb.debian.org/debian forky/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 145 http://deb.debian.org/debian forky/main arm64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 148 http://deb.debian.org/debian forky/main arm64 libqdox-java all 1.12.1-4 [173 kB] Get: 149 http://deb.debian.org/debian forky/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 libxpp3-java all 1.1.4c-4 [294 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 libxstream-java all 1.4.21-1 [567 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 groovy all 2.4.21-10 [12.8 MB] Get: 153 http://deb.debian.org/debian forky/main arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 154 http://deb.debian.org/debian forky/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 156 http://deb.debian.org/debian forky/main arm64 libcommons-io-java all 2.19.0-1 [524 kB] Get: 157 http://deb.debian.org/debian forky/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 158 http://deb.debian.org/debian forky/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 159 http://deb.debian.org/debian forky/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 160 http://deb.debian.org/debian forky/main arm64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 161 http://deb.debian.org/debian forky/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 162 http://deb.debian.org/debian forky/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 163 http://deb.debian.org/debian forky/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 164 http://deb.debian.org/debian forky/main arm64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 165 http://deb.debian.org/debian forky/main arm64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 166 http://deb.debian.org/debian forky/main arm64 libjna-jni arm64 5.15.0-1 [62.4 kB] Get: 167 http://deb.debian.org/debian forky/main arm64 libjna-java all 5.15.0-1 [238 kB] Get: 168 http://deb.debian.org/debian forky/main arm64 libbcprov-java all 1.80-3 [5543 kB] Get: 169 http://deb.debian.org/debian forky/main arm64 libjunixsocket-jni arm64 2.6.1-1+b1 [18.3 kB] Get: 170 http://deb.debian.org/debian forky/main arm64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.29-2 [25.5 kB] Get: 171 http://deb.debian.org/debian forky/main arm64 libjunixsocket-java all 2.6.1-1 [264 kB] Get: 172 http://deb.debian.org/debian forky/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 173 http://deb.debian.org/debian forky/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 174 http://deb.debian.org/debian forky/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 175 http://deb.debian.org/debian forky/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 176 http://deb.debian.org/debian forky/main arm64 libjzlib-java all 1.1.3-3 [79.4 kB] Get: 177 http://deb.debian.org/debian forky/main arm64 libjsch-java all 0.2.19-1 [513 kB] Get: 178 http://deb.debian.org/debian forky/main arm64 libminlog-java all 1.3.1-1 [7808 B] Get: 179 http://deb.debian.org/debian forky/main arm64 libobjenesis-java all 3.4-2 [41.3 kB] Get: 180 http://deb.debian.org/debian forky/main arm64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 181 http://deb.debian.org/debian forky/main arm64 libkryo-java all 2.20-8 [161 kB] Get: 182 http://deb.debian.org/debian forky/main arm64 liblogback-java all 1:1.2.11-6 [701 kB] Get: 183 http://deb.debian.org/debian forky/main arm64 libnative-platform-jni arm64 0.14-6+b1 [11.7 kB] Get: 184 http://deb.debian.org/debian forky/main arm64 libnative-platform-java all 0.14-6 [69.8 kB] Get: 185 http://deb.debian.org/debian forky/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 186 http://deb.debian.org/debian forky/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 187 http://deb.debian.org/debian forky/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 188 http://deb.debian.org/debian forky/main arm64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 189 http://deb.debian.org/debian forky/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 190 http://deb.debian.org/debian forky/main arm64 libgradle-core-java all 4.4.1-22 [4318 kB] Get: 191 http://deb.debian.org/debian forky/main arm64 libbcpg-java all 1.80-3 [516 kB] Get: 192 http://deb.debian.org/debian forky/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 193 http://deb.debian.org/debian forky/main arm64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 194 http://deb.debian.org/debian forky/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 195 http://deb.debian.org/debian forky/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 196 http://deb.debian.org/debian forky/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 197 http://deb.debian.org/debian forky/main arm64 libbcel-java all 6.10.0-1 [674 kB] Get: 198 http://deb.debian.org/debian forky/main arm64 libjformatstring-java all 0.10~20131207-3 [34.8 kB] Get: 199 http://deb.debian.org/debian forky/main arm64 libfindbugs-java all 3.1.0~preview2-4 [3535 kB] Get: 200 http://deb.debian.org/debian forky/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 201 http://deb.debian.org/debian forky/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 202 http://deb.debian.org/debian forky/main arm64 libjatl-java all 0.2.3-2 [30.1 kB] Get: 203 http://deb.debian.org/debian forky/main arm64 libjcifs-java all 1.3.19+dfsg-1 [414 kB] Get: 204 http://deb.debian.org/debian forky/main arm64 libjavaewah-java all 1.2.3-2 [160 kB] Get: 205 http://deb.debian.org/debian forky/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 206 http://deb.debian.org/debian forky/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 207 http://deb.debian.org/debian forky/main arm64 libjetty9-java all 9.4.57-1 [2965 kB] Get: 208 http://deb.debian.org/debian forky/main arm64 libjgit-java all 6.7.0-2 [3152 kB] Get: 209 http://deb.debian.org/debian forky/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 210 http://deb.debian.org/debian forky/main arm64 libwagon-provider-api-java all 3.5.3-2 [48.3 kB] Get: 211 http://deb.debian.org/debian forky/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 212 http://deb.debian.org/debian forky/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 213 http://deb.debian.org/debian forky/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 214 http://deb.debian.org/debian forky/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 215 http://deb.debian.org/debian forky/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 216 http://deb.debian.org/debian forky/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 217 http://deb.debian.org/debian forky/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 218 http://deb.debian.org/debian forky/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 219 http://deb.debian.org/debian forky/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 220 http://deb.debian.org/debian forky/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 221 http://deb.debian.org/debian forky/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 222 http://deb.debian.org/debian forky/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 223 http://deb.debian.org/debian forky/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 224 http://deb.debian.org/debian forky/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 225 http://deb.debian.org/debian forky/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 226 http://deb.debian.org/debian forky/main arm64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 227 http://deb.debian.org/debian forky/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 228 http://deb.debian.org/debian forky/main arm64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 229 http://deb.debian.org/debian forky/main arm64 libwagon-file-java all 3.5.3-2 [8452 B] Get: 230 http://deb.debian.org/debian forky/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 231 http://deb.debian.org/debian forky/main arm64 libwagon-http-java all 3.5.3-2 [49.6 kB] Get: 232 http://deb.debian.org/debian forky/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 233 http://deb.debian.org/debian forky/main arm64 testng all 6.9.12-4 [795 kB] Get: 234 http://deb.debian.org/debian forky/main arm64 libgradle-plugins-java all 4.4.1-22 [5245 kB] Get: 235 http://deb.debian.org/debian forky/main arm64 gradle all 4.4.1-22 [400 kB] Get: 236 http://deb.debian.org/debian forky/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 237 http://deb.debian.org/debian forky/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 238 http://deb.debian.org/debian forky/main arm64 jarwrapper all 0.80 [9692 B] Get: 239 http://deb.debian.org/debian forky/main arm64 javahelper all 0.80 [80.4 kB] Get: 240 http://deb.debian.org/debian forky/main arm64 libbyte-buddy-java all 1.14.19-1 [4756 kB] Get: 241 http://deb.debian.org/debian forky/main arm64 libfreemarker-java all 2.3.32-2.1 [1525 kB] Get: 242 http://deb.debian.org/debian forky/main arm64 libjacoco-java all 0.8.12-1 [647 kB] Get: 243 http://deb.debian.org/debian forky/main arm64 libjoptsimple-java all 5.0.4-7 [73.7 kB] Get: 244 http://deb.debian.org/debian forky/main arm64 libmockito-java all 3.3.0-2 [510 kB] Fetched 255 MB in 1s (205 MB/s) Preconfiguring packages ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.6-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.6-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.6-1_arm64.deb ... Unpacking python3.13 (3.13.6-1) ... 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Setting up libfile-which-perl (1.27-2) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:arm64 (1.8-3) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libqdox-java (1.12.1-4) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.41.1-1) ... Setting up libgpg-error0:arm64 (1.55-2) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libjcip-annotations-java (20060626-6) ... Setting up libobjenesis-java (3.4-2) ... 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 libmagic-mgc (1:5.46-5) ... Setting up liblogback-java (1:1.2.11-6) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libminlog-java (1.3.1-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up unzip (6.0-29) ... Setting up libdebhelper-perl (13.25) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libasm-java (9.8-1) ... Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:arm64 (1.11.2-2) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up file (1:5.46-5) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ... Setting up libfelix-gogo-runtime-java (0.16.2-2) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Aug 25 14:32:54 UTC 2025. Universal Time is now: Mon Aug 25 14:32:54 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 (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up libio-string-perl (1.08-4) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20240727.1) ... Setting up libbsf-java (1:2.4.0-8) ... Setting up libosgi-annotation-java (8.1.0-1) ... Setting up libjformatstring-java (0.10~20131207-3) ... Setting up libjavaewah-java (1.2.3-2) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-4) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.29-2) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libxpp3-java (1.1.4c-4) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libkryo-java (2.20-8) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-2) ... Setting up binfmt-support (2.2.2-7+b1) ... 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:arm64 (0.22-3+b2) ... Setting up libjunixsocket-jni (2.6.1-1+b1) ... Setting up libfelix-framework-java (4.6.1-3) ... Setting up libpcsclite1:arm64 (2.3.3-1) ... 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 autoconf (2.72-3.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up libfreemarker-java (2.3.32-2.1) ... Setting up sensible-utils (0.0.26) ... Setting up libjacoco-java (0.8.12-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up gpgv (2.4.8-2) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.2-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up netbase (6.5) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libnative-platform-jni (0.14-6+b1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-7) ... Setting up libbcpg-java (1.80-3) ... 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-14) ... Setting up libyaml-snake-java (2.0+ds+really1.33-1) ... Setting up openssl (3.5.2-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up readline-common (8.2-6) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up liburi-perl (5.30-1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libjatl-java (0.2.3-2) ... Setting up libnet-ssleay-perl:arm64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.2-3) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libwagon-provider-api-java (3.5.3-2) ... 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 (1.4.21-1) ... Setting up libnekohtml-java (1.9.22.noko2-0.1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libjetty9-java (9.4.57-1) ... Setting up java-wrappers (0.5) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-4) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libnss3:arm64 (2:3.114-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjunixsocket-java (2.6.1-1) ... 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+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up testng (6.9.12-4) ... Setting up libjna-jni (5.15.0-1) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... 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 (1.23.0-9) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up libjna-java (5.15.0-1) ... Setting up gpgconf (2.4.8-2) ... Setting up libjansi1-java (1.18-3.1) ... 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 (3.5.3-2) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libjline2-java (2.14.6-6) ... Setting up libpython3.13-stdlib:arm64 (3.13.6-1) ... Setting up libio-socket-ssl-perl (2.095-1) ... Setting up gpg (2.4.8-2) ... Setting up libpython3-stdlib:arm64 (3.13.5-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.4.8-2) ... Setting up openjdk-21-jre-headless:arm64 (21.0.8+9-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.6-1) ... Setting up libcommons-io-java (2.19.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up python3 (3.13.5-1) ... Setting up sopv-gpgv (0.1.4-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up openjdk-21-doc (21.0.8+9-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up libbcel-java (6.10.0-1) ... Setting up libmodule-runtime-perl (0.018-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfindbugs-java (3.1.0~preview2-4) ... Setting up libcommons-compress-java (1.27.1-2) ... 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 (13.25) ... Setting up default-jdk-doc (2:1.21-76) ... Setting up libjsch-java (0.2.19-1) ... Setting up libjgit-java (6.7.0-2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.78-1) ... Setting up devscripts (2.25.19) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.80) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libbyte-buddy-java (1.14.19-1) ... Setting up libmockito-java (3.3.0-2) ... Processing triggers for libc-bin (2.41-12) ... 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_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.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_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.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: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: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_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.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-14) ... Setting up ivy (2.5.3-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... 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 openjdk-21-jdk-headless:arm64 (21.0.8+9-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up maven-repo-helper (1.11) ... Setting up ant-optional (1.10.15-1) ... Setting up bnd (5.0.1-5) ... Setting up default-jdk-headless (2:1.21-76) ... Setting up libgradle-core-java (4.4.1-22) ... Setting up libgradle-plugins-java (4.4.1-22) ... Setting up gradle (4.4.1-22) ... Setting up gradle-debian-helper (2.4) ... Processing triggers for ca-certificates (20250419) ... 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-6.0.0+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_6.0.0+dfsg-1_source.changes dpkg-buildpackage: info: source package barclay dpkg-buildpackage: info: source version 6.0.0+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 arm64 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-6.0.0+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-6.0.0\+dfsg/.gradle /build/reproducible-path/barclay-6.0.0\+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-6.0.0+dfsg' dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* Duplicate specification "unlink|u" for option "u" Duplicate specification "unlink|u" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/barclay-6.0.0+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-6.0.0+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-6.0.0+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@/6.0.0+dfsg/ ; s/\+dfsg[[:digit:]]*//' debian/pom-barclay.xml.in > debian/pom-barclay.xml dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/barclay-6.0.0+dfsg' jh_linkjars -O--buildsystem=gradle Duplicate specification "u=s" for option "u" Duplicate specification "unlink|u" for option "u" rm -f debian/libbarclay-java.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/barclay-6.0.0+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 "21.0.8" 2025-07-15 OpenJDK Runtime Environment (build 21.0.8+9-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.8+9-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/barclay-6.0.0+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-6.0.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-arm64/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 0.869 secs. The client will now receive all logging from the daemon (pid: 3276905). The daemon log file: /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/daemon/4.4.1/daemon-3276905.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-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@39f8b4db Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@39f8b4db Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@74698245 Starting Build Compiling initialization script '/build/reproducible-path/barclay-6.0.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@6add0443 Compiling initialization script '/build/reproducible-path/barclay-6.0.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'barclay' instead of the name of the root directory 'barclay-6.0.0+dfsg' Projects loaded. Root project using build file '/build/reproducible-path/barclay-6.0.0+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-6.0.0+dfsg/build.gradle'. Compiling build file '/build/reproducible-path/barclay-6.0.0+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/reproducible-path/barclay-6.0.0+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/barclay-6.0.0+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-6.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@73f9a007 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@74698245 Creating new cache for taskHistory, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@558fdd78 Creating new cache for outputFiles, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@6d60382 :compileJava (Thread[#56,Task worker for ':' Thread 2,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.005 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@425b88be Loading the Maven rules... Replacing net.sf.jopt-simple:jopt-simple:jar:5.0.3 -> net.sf.jopt-simple:jopt-simple:jar:debian Replacing com.google.code.gson:gson:jar:2.8.9 -> com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Replacing org.freemarker:freemarker:jar:2.3.30 -> org.freemarker:freemarker: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 Up-to-date check for task ':compileJava' took 0.594 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-6.0.0+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[#56,Task worker for ':' Thread 2,5,main]) completed. Took 2.592 secs. :processResources (Thread[#63,Task worker for ':' Thread 9,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Up-to-date check for task ':processResources' took 0.007 secs. It is not up-to-date because: No history is available. :processResources (Thread[#63,Task worker for ':' Thread 9,5,main]) completed. Took 0.035 secs. :classes (Thread[#63,Task worker for ':' Thread 9,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[#63,Task worker for ':' Thread 9,5,main]) completed. Took 0.0 secs. :debianMavenPom (Thread[#61,Task worker for ':' Thread 7,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/barclay-6.0.0+dfsg/build/debian/barclay.pom :debianMavenPom (Thread[#61,Task worker for ':' Thread 7,5,main]) completed. Took 0.065 secs. :jar (Thread[#61,Task worker for ':' Thread 7,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.007 secs. It is not up-to-date because: No history is available. :jar (Thread[#61,Task worker for ':' Thread 7,5,main]) completed. Took 0.056 secs. BUILD SUCCESSFUL in 7s 4 actionable tasks: 4 executed make[1]: Leaving directory '/build/reproducible-path/barclay-6.0.0+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-6.0.0+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 "21.0.8" 2025-07-15 OpenJDK Runtime Environment (build 21.0.8+9-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.8+9-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/barclay-6.0.0+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-6.0.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-arm64/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 0.863 secs. The client will now receive all logging from the daemon (pid: 3280280). The daemon log file: /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/daemon/4.4.1/daemon-3280280.out.log Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Daemon will be stopped at the end of the build stopping after processing Using 12 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f46ce12 Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f46ce12 Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@264ccec0 Starting Build Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@622e7fad Settings evaluated using settings file '/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'barclay' instead of the name of the root directory 'barclay-6.0.0+dfsg' Projects loaded. Root project using build file '/build/reproducible-path/barclay-6.0.0+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-6.0.0+dfsg/build.gradle'. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/barclay-6.0.0+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-6.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@560bfb24 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-6.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@264ccec0 Creating new cache for taskHistory, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@52e09c5 Creating new cache for outputFiles, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@23c26116 :compileJava (Thread[#56,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.01 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@55e3dfe0 Loading the Maven rules... Replacing net.sf.jopt-simple:jopt-simple:jar:5.0.3 -> net.sf.jopt-simple:jopt-simple:jar:debian Replacing com.google.code.gson:gson:jar:2.8.9 -> com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Replacing org.freemarker:freemarker:jar:2.3.30 -> org.freemarker:freemarker: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 Skipping task ':compileJava' as it is up-to-date (took 0.777 secs). :compileJava UP-TO-DATE :compileJava (Thread[#56,Task worker for ':',5,main]) completed. Took 0.844 secs. :processResources (Thread[#56,Task worker for ':',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 0.035 secs). :processResources UP-TO-DATE :processResources (Thread[#56,Task worker for ':',5,main]) completed. Took 0.044 secs. :classes (Thread[#56,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[#56,Task worker for ':',5,main]) completed. Took 0.0 secs. :compileTestJava (Thread[#56,Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Malformed class file [Pair.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82) at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234) at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185) at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53) at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38) at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331) at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154) at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61) at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114) at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201) at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86) at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53) at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54) at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60) at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97) at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87) at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52) at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52) at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54) at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98) at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626) at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) 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 2.18 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[#56,Task worker for ':',5,main]) completed. Took 6.967 secs. :processTestResources (Thread[#56,Task worker for ':',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 0.063 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[#56,Task worker for ':',5,main]) completed. Took 0.161 secs. :testClasses (Thread[#56,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[#56,Task worker for ':',5,main]) completed. Took 0.0 secs. :test (Thread[#56,Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.001 secs. Replacing org.apache.logging.log4j:log4j-core:jar:2.17.1 -> org.apache.logging.log4j:log4j-core:jar:debian Up-to-date check for task ':test' took 0.909 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/barclay-6.0.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17088410508379954926txt -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@15900423, [], /tmp/enabledExpansion13945949190114033152.args, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@21a1b303, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[1](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@7afceccb, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion11418950234467378218.args, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@4f85cc52, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[2](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@4108b6a8, [], /tmp/enabledExpansion11126868340705646063.list, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@709dc6, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[3](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@1404682a, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion7803277815896072323.list, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@1d9f85ff, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[4](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@2ccb9676, [], /tmp/enabledExpansion12617047942510719503.args, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@3bad075b, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[5](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@164787b5, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion18402503433026506540.args, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@415f5318, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[6](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@5a381d83, [], /tmp/enabledExpansion9770168333968798931.list, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@3e28b54a, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromExpansionFile[7](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@127cbe2c, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion15722790906299128193.list, [Ljava.lang.String;@5d4832e0, [Ljava.lang.String;@68ff7411, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromListFileMixed[0](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@68ef74d8, [], [Ljava.lang.String;@1cd85c2, [Ljava.lang.String;@4df7ec38, [Ljava.lang.String;@7747b69f, [Ljava.lang.String;@641d451b)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testCollectionFromListFileMixed[1](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@292105b2, [APPEND_TO_COLLECTIONS], [Ljava.lang.String;@1cd85c2, [Ljava.lang.String;@4df7ec38, [Ljava.lang.String;@121b9c1d, [Ljava.lang.String;@48e2ad34)(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;@573bf109, [APPEND_TO_COLLECTIONS], [foo, bar, baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[1]([Ljava.lang.String;@573bf109, [], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[2]([Ljava.lang.String;@582d78e8, [APPEND_TO_COLLECTIONS], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[3]([Ljava.lang.String;@582d78e8, [], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[4]([Ljava.lang.String;@456b1d49, [APPEND_TO_COLLECTIONS], [frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[5]([Ljava.lang.String;@456b1d49, [], [frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[6]([Ljava.lang.String;@1b0bbe54, [APPEND_TO_COLLECTIONS], [foo, bar])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testInitializedCollections[7]([Ljava.lang.String;@5a1d6a5a, [[]], [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;@7d1a6ac0, [], [L1, L2], [S1], [HS1], [P1, P2])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) Running Test: Test method testUninitializedCollections[1]([Ljava.lang.String;@7d1a6ac0, [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@4009d97b, [Ljava.lang.String;@391de386)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method passingMutexCheck[1](collection mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@764cd093, [Ljava.lang.String;@21ecfe00)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method passingMutexCheck[2](collection multiple mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@3da07c4a, [Ljava.lang.String;@6e6f186b)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method passingMutexCheck[3](scalar mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@1cb8020f, [Ljava.lang.String;@e178630)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testAbbreviationsAreRejected(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testAdvancedArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgCollectionNotInitialized(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgUsage[0](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$FrobnicateArguments@42a2a771, [--FROBNICATION_FLAVOR , --SHMIGGLE_TYPE , --arguments-file,-arguments_file , --FROBNICATION_THRESHOLD,-T , --TRUTHINESS ])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgUsage[1](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$FrobnicateArguments@324bd845, [--deprecatedString, This argument is DEPRECATED, and will be removed in a future])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testArgUsage[2](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@fb62351, [--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$MutexArguments@5f01028d, [Ljava.lang.String;@13ee5cd3)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[1](1 of group required, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@56b87b5b, [Ljava.lang.String;@4ec61382)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[2](mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@1b096342, [Ljava.lang.String;@67d634b0)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[3](mega mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@2ce83856, [Ljava.lang.String;@5a5ae66)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testFailingMutex[4](collection and scalar mutex mix, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@eea7c72, [Ljava.lang.String;@95cb420)(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], [Pair[left=childCollectionListSuperTypeTarget, right=childCollectionListSuperTypeTargetValue1], Pair[left=childCollectionListSuperTypeTarget, right=childCollectionListSuperTypeTargetValue2], Pair[left=childCollectionListSuperTypeTarget, right=childCollectionListSuperTypeTargetValue3], Pair[left=childCollectionSubTypeTarget, right=childCollectionSubTypeTargetValue], Pair[left=childCollectionSuperTypeTarget, right=childCollectionSuperTypeTargetValue], Pair[left=childListSubTypeTarget, right=childListSubTypeTargetValue1], Pair[left=childListSubTypeTarget, right=childListSubTypeTargetValue2], Pair[left=childListSubTypeTarget, right=childListSubTypeTargetValue3], Pair[left=childListSuperTypeTarget, right=childListSuperTypeTargetValue1], Pair[left=childListSuperTypeTarget, right=childListSuperTypeTargetValue2], Pair[left=childListSuperTypeTarget, right=childListSuperTypeTargetValue3], Pair[left=childSubTypeTarget, right=childSubTypeTargetValue], Pair[left=childSuperTypeTarget, right=childSuperTypeTargetValue], Pair[left=parentCollectionSubTypeTarget, right=parentCollectionSubTypeTargetValue], Pair[left=parentCollectionSuperTypeTarget, right=parentCollectionSuperTypeTargetValue], Pair[left=parentListSubTypeTarget, right=parentListSubTypeTargetValue1], Pair[left=parentListSubTypeTarget, right=parentListSubTypeTargetValue2], Pair[left=parentListSubTypeTarget, right=parentListSubTypeTargetValue3], Pair[left=parentListSuperTypeTarget, right=parentListSuperTypeTargetValue1], Pair[left=parentListSuperTypeTarget, right=parentListSuperTypeTargetValue2], Pair[left=parentListSuperTypeTarget, right=parentListSuperTypeTargetValue3], Pair[left=parentSubTypeTarget, right=parentSubTypeTargetValue], Pair[left=parentSuperTypeTarget, right=parentSuperTypeTargetValue], Pair[left=uninitializedChildCollectionTarget, right=null], Pair[left=uninitializedChildListTarget, right=null], Pair[left=uninitializedChildTarget, right=null], Pair[left=uninitializedParentCollectionTarget, right=null], Pair[left=uninitializedParentTarget, right=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,-arguments_file --arguments-file,-arguments_file Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: read one or more arguments files and add them to the command line This argument may be 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: --show-hidden,-showHidden --show-hidden,-showHidden Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: display hidden arguments Default value: false. Possible values: {true, false} 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;@1c65934d)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[1]([Ljava.lang.String;@4ace3ac0)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[2]([Ljava.lang.String;@ec4b62e)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[3]([Ljava.lang.String;@6dc61d31)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[4]([Ljava.lang.String;@21b7eb86)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[5]([Ljava.lang.String;@158db8e0)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testOutOfRangesArguments[6]([Ljava.lang.String;@58030cb5)(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;@6c17df11)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testSetNonNullableArgumentsToNull[1]([Ljava.lang.String;@6538fda7)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testSetNonNullableArgumentsToNull[2]([Ljava.lang.String;@196e1f47)(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;@5430b0c0, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[1]([Ljava.lang.String;@fbe2c4, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[2]([Ljava.lang.String;@5f00b124, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[3]([Ljava.lang.String;@e3e0ef6, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[4]([Ljava.lang.String;@56dd6680, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[5]([Ljava.lang.String;@636168b4, 1, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[6]([Ljava.lang.String;@6ec3e5fd, null, 2.0, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[7]([Ljava.lang.String;@163ffd02, null, null, somestring)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) Running Test: Test method testWithinBoundariesArguments[8]([Ljava.lang.String;@189bf108, 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;@434d6cf4, 0)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) Running Test: Test method testBasicPlugin[1]([Ljava.lang.String;@257fe42c, 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;@7b591bf, true)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Running Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[1](no args, [Ljava.lang.String;@169b5979, 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;@169b5979, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@3c1c682d, 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;@3c1c682d, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false) STANDARD_ERROR ERROR: Option 'A' cannot be used in conjunction with option(s) Y Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[3](mutex, [Ljava.lang.String;@263a2744, 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;@263a2744, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Running Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null Version: null Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: Options: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help --help Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. tools. Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@bed4180, 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;@bed4180, 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@fadb8e5, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$2@70822da9, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$3@1e6f28c6, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$4@26356190, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[4](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$5@61270ded, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[5](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$6@742d5b9b, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[6](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$7@62fd3dd9, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[7](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$8@49d8e275, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[8](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$9@194e2d63, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[9](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$10@7c831064, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[10](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$11@30f46bd1, arg, true, [stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testDefaultValueAsString[11](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$12@1268ea4e, arg, true, [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@e829675, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@3a6ad577, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@60790655, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliasDisplayString[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@2494cdee, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@7b4796b4, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@7a43ce8b, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@4d6bc810, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetArgumentAliases[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@51007b8, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@6c628e25, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@15213e88, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@45ac82d3, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetLongName[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@7057a79, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$1@22daeaa0, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$2@738638cb, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$3@fe40fe1, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$4@70185435, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[4](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$5@56944db9, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[5](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$6@5f2029a, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[6](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$7@ed3243e, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[7](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$8@6629dada, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[8](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$9@79a0967b, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[9](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$10@750e02e5, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[10](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$11@4b0c0d91, arg, true, [stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testIsOptional[11](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$12@5cbf9d89, arg, true, [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[0](required, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[1](optional, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[2](defaultedRequired, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[3](defaultedOptional, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[4](required, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[5](optional, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[6](defaultedRequired, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[7](defaultedOptional, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[8](required, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[9](optional, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[10](defaultedRequired, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[11](defaultedOptional, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[12](optional, [], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[13](defaultedOptional, [], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[14](required, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[15](optional, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[16](defaultedRequired, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [default, stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[17](defaultedOptional, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [default, stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[18](required, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[19](optional, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[20](defaultedRequired, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[21](defaultedOptional, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[22](required, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[23](optional, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[24](defaultedRequired, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[25](defaultedOptional, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[26](optional, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollections[27](defaultedOptional, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollectionsFailures[0](required, [], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollectionsFailures[1](defaultedRequired, [], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollectionsFailures[2](required, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testSetArgumentValuesCollectionsFailures[3](defaultedRequired, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) Running Test: Test method testGetCommandLineDisplayString[0]([Ljava.lang.String;@5f47bfae, )(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testGetCommandLineDisplayString[1]([Ljava.lang.String;@7cd40150, arg1)(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) Running Test: Test method testGetCommandLineDisplayString[2]([Ljava.lang.String;@561e15fa, 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;@34408a8b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[1]([Ljava.lang.String;@3cc763c8)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[2]([Ljava.lang.String;@5892b66f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[3]([Ljava.lang.String;@3112d87d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[4]([Ljava.lang.String;@64613501)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[5]([Ljava.lang.String;@7eda4494)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[6]([Ljava.lang.String;@54c89e08)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[7]([Ljava.lang.String;@44fd9646)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[8]([Ljava.lang.String;@e8bda67)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[9]([Ljava.lang.String;@3501c782)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[10]([Ljava.lang.String;@722c017b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[11]([Ljava.lang.String;@67d0fbaa)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[12]([Ljava.lang.String;@6eef1ded)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[13]([Ljava.lang.String;@101d84e9)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[14]([Ljava.lang.String;@2d9c941b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[15]([Ljava.lang.String;@203cf768)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[16]([Ljava.lang.String;@5184121)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[17]([Ljava.lang.String;@4ef85632)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[18]([Ljava.lang.String;@2c21c060)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[19]([Ljava.lang.String;@6aa8e720)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[20]([Ljava.lang.String;@1fa36622)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[21]([Ljava.lang.String;@3f5f7068)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[22]([Ljava.lang.String;@1a52198a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[23]([Ljava.lang.String;@5484ac64)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[24]([Ljava.lang.String;@671d06de)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[25]([Ljava.lang.String;@6474c4ec)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[26]([Ljava.lang.String;@481f4d2d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[27]([Ljava.lang.String;@a81d8b1)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[28]([Ljava.lang.String;@2322ec3f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[29]([Ljava.lang.String;@6e0c3866)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[30]([Ljava.lang.String;@7e5100b6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[31]([Ljava.lang.String;@1d41e765)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[32]([Ljava.lang.String;@32643d43)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[33]([Ljava.lang.String;@2f79397a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[34]([Ljava.lang.String;@2a7765bc)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[35]([Ljava.lang.String;@1acf688a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[36]([Ljava.lang.String;@3c2c8ee2)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[37]([Ljava.lang.String;@6dae30ca)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[38]([Ljava.lang.String;@723d5bec)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[39]([Ljava.lang.String;@67fef74c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[40]([Ljava.lang.String;@511d9e81)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[41]([Ljava.lang.String;@2fc26b20)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[42]([Ljava.lang.String;@3003aed6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[43]([Ljava.lang.String;@45fe5172)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[44]([Ljava.lang.String;@43d3de7e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[45]([Ljava.lang.String;@2ce847a6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[46]([Ljava.lang.String;@60aa927e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[47]([Ljava.lang.String;@6d1755fb)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[48]([Ljava.lang.String;@2e09016f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[49]([Ljava.lang.String;@6691f337)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[50]([Ljava.lang.String;@48d51dc4)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[51]([Ljava.lang.String;@2d7b49fe)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[52]([Ljava.lang.String;@61de9467)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[53]([Ljava.lang.String;@2830b38)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[54]([Ljava.lang.String;@4ba11ca5)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[55]([Ljava.lang.String;@2fb62bf)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[56]([Ljava.lang.String;@18e54e78)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[57]([Ljava.lang.String;@1d63f094)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[58]([Ljava.lang.String;@e0909b0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testBadTaggedArguments[59]([Ljava.lang.String;@38765bdb)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGetCommandLineTagged[0]([Ljava.lang.String;@776983a5, 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;@721aefa0, 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;@4e9c21a4, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4968d3a5, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@66a7b10e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[1]([Ljava.lang.String;@51c82eca, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5d4d5af3, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@1510cd49)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[2]([Ljava.lang.String;@1c75b424, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@6c352300, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@18a471cc)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[3]([Ljava.lang.String;@33ff84c9, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@124108ab, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@14877689)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[4]([Ljava.lang.String;@7eca3993, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@1bf3c25f, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@274760b5)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[5]([Ljava.lang.String;@4634fc59, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5042e72, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@1186bd43)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[6]([Ljava.lang.String;@7f2ab9d9, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@30520657, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@790ce573)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[7]([Ljava.lang.String;@710c1e1f, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@49858ec8, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@1f107825)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[8]([Ljava.lang.String;@b65a841, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4ec1440a, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@1ad107e1)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[9]([Ljava.lang.String;@5b1160c3, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@6c208f1c, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4cf01633)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[10]([Ljava.lang.String;@1a621ced, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5351f7bf, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5261157d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[11]([Ljava.lang.String;@4007c894, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2d1a978d, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@1563e522)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[12]([Ljava.lang.String;@21d9eb2e, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@56e4c8c0, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@69f3d94e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[13]([Ljava.lang.String;@3d0f85a8, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4eaddb22, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@41557c10)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[14]([Ljava.lang.String;@2a27461b, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@552b2fb3, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3a7da805)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[15]([Ljava.lang.String;@106b382f, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@49d869a5, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@723e753f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[16]([Ljava.lang.String;@3947998c, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@78bc06a9, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4888e6be)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) Running Test: Test method testGoodTaggedArguments[17]([Ljava.lang.String;@28acf994, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7a1bc674, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@6c4ef81a)(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. Results: SUCCESS (369 tests, 369 successes, 0 failures, 0 skipped) Finished generating test XML results (0.04 secs) into: /build/reproducible-path/barclay-6.0.0+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.093 secs) into: /build/reproducible-path/barclay-6.0.0+dfsg/build/reports/tests/test :test (Thread[#56,Task worker for ':',5,main]) completed. Took 7.104 secs. BUILD SUCCESSFUL in 22s 5 actionable tasks: 3 executed, 2 up-to-date rm -fr -- /tmp/dh-xdg-rundir-CASr1AWx make[1]: Leaving directory '/build/reproducible-path/barclay-6.0.0+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-6.0.0\+dfsg/debian/libbarclay-java jh_installjavadoc -O--buildsystem=gradle Duplicate specification "author|A=s" for option "A" Duplicate specification "author|A=s" for option "A" 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-6.0.0.jar debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar rm -f debian/libbarclay-java/usr/share/java/barclay.jar ln -s barclay-6.0.0.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 Duplicate specification "version|V" for option "V" Duplicate specification "version|V" for option "V" Updating symlinked /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar (via debian/libbarclay-java/usr/share/java/barclay.jar) Reading manifest from /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar Updating manifest in /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar jh_manifest -O--buildsystem=gradle Duplicate specification "V:s" for option "V" Duplicate specification "version|V" for option "V" find debian/libbarclay-java -name '*.jar' Found usr/share/java/barclay-6.0.0.jar Found symlink usr/share/java/barclay.jar Reading manifest from debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar No update of debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar required. jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle Searching /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java for libbarclay-java Searching /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.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-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/commons-lang3-3.17.0.jar Checking: /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/freemarker-17.jar Checking: /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/gson-2.10.1.jar Checking: /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/joptsimple-5.0.4.jar Checking: /build/reproducible-path/barclay-6.0.0+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-6.0.0.pom debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/6.0.0/barclay-6.0.0.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/6.0.0/barclay-6.0.0.jar rm -f debian/libbarclay-java/usr/share/java/barclay.jar ln -s barclay-6.0.0.jar debian/libbarclay-java/usr/share/java/barclay.jar install -m0755 -d debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/6.0.0 rm -f debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/6.0.0/barclay-6.0.0.jar ln -s ../../../../../java/barclay.jar debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/6.0.0/barclay-6.0.0.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-6.0.0.jar debian/libbarclay-java/usr/share/java/barclay.jar rm -f debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/6.0.0/barclay-6.0.0.jar ln -s ../../../../../java/barclay.jar debian/libbarclay-java/usr/share/maven-repo/org/broadinstitute/barclay/6.0.0/barclay-6.0.0.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 1755621973 as canonical time Normalizing debian/libbarclay-java/usr/share/java/barclay-6.0.0.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-6.0.0+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-6.0.0+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-6.0.0+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_6.0.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../barclay_6.0.0+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../barclay_6.0.0+dfsg-1_arm64.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/3261747 and its subdirectories I: Current time: Mon Aug 25 02:33:43 -12 2025 I: pbuilder-time-stamp: 1756132423 Mon Aug 25 14:33:44 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Mon Aug 25 14:33:44 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Mon Aug 25 14:34:47 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Mon Aug 25 14:34:48 UTC 2025 I: barclay_6.0.0+dfsg-1_arm64.changes: Format: 1.8 Date: Tue, 19 Aug 2025 18:46:13 +0200 Source: barclay Binary: libbarclay-java Architecture: all Version: 6.0.0+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 (6.0.0+dfsg-1) unstable; urgency=medium . * New upstream version 6.0.0+dfsg * Refreshing patches * Raising Standards version to 4.7.2 (no change) * Reworking build.gradle for a Debian build Checksums-Sha1: 736a2128a6bcc8988fc859325b4129fba01effef 11626 barclay_6.0.0+dfsg-1_arm64.buildinfo d0b8291ddf0ce4231b32d838afe807f5283f58e2 110268 libbarclay-java_6.0.0+dfsg-1_all.deb Checksums-Sha256: 576de496db3cf5060b97720e4f9f48541bdc41263a249caf6603b7aec1b0a452 11626 barclay_6.0.0+dfsg-1_arm64.buildinfo 485b7c88f94aa25cb412200db3c7ebef41cbf0249488a7be204a118b9ccb9370 110268 libbarclay-java_6.0.0+dfsg-1_all.deb Files: 8b9ec081ef8270df8279120eafc83053 11626 java optional barclay_6.0.0+dfsg-1_arm64.buildinfo 581ac213fcaf8fb44b784897fdf6e2de 110268 java optional libbarclay-java_6.0.0+dfsg-1_all.deb Mon Aug 25 14:34:48 UTC 2025 I: diffoscope 305 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_8-84807.service; invocation ID: 5efeb917960b415c9cc59fb8c83942b9 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ZQ16DSNB/barclay_6.0.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ZQ16DSNB/barclay_6.0.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ZQ16DSNB/barclay_6.0.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ZQ16DSNB/b1/barclay_6.0.0+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ZQ16DSNB/b2/barclay_6.0.0+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 222ms CPU time consumed: 194ms Memory peak: 17.3M (swap: 0B) Mon Aug 25 14:34:49 UTC 2025 I: diffoscope 305 found no differences in the changes files, and a .buildinfo file also exists. Mon Aug 25 14:34:49 UTC 2025 I: barclay from forky built successfully and reproducibly on arm64. Mon Aug 25 14:34:50 UTC 2025 I: Removing signed barclay_6.0.0+dfsg-1_arm64.buildinfo.asc files: removed './b1/barclay_6.0.0+dfsg-1_arm64.buildinfo.asc' removed './b2/barclay_6.0.0+dfsg-1_arm64.buildinfo.asc'