Date: Thu, 18 Oct 2018 05:40:43 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 112amd64-default][biology/py-orange3-single-cell] Failed for py36-orange3-single-cell-0.8.2 in run-depends Message-ID: <201810180540.w9I5eh4Q064561@beefy9.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: yuri@FreeBSD.org Ident: $FreeBSD: head/biology/py-orange3-single-cell/Makefile 482277 2018-10-17 07:31:34Z yuri $ Log URL: http://beefy9.nyi.freebsd.org/data/112amd64-default/482319/logs/py36-orange3-single-cell-0.8.2.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=112amd64-default&build=482319 Log: =>> Building biology/py-orange3-single-cell build started at Thu Oct 18 05:39:30 UTC 2018 port directory: /usr/ports/biology/py-orange3-single-cell package name: py36-orange3-single-cell-0.8.2 building for: FreeBSD 112amd64-default-job-14 11.2-RELEASE-p4 FreeBSD 11.2-RELEASE-p4 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/py-orange3-single-cell/Makefile 482277 2018-10-17 07:31:34Z yuri $ Poudriere version: 3.2.7-7-gb715fabe Host OSVERSION: 1200084 Jail OSVERSION: 1102000 Job Id: 14 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1102000 UNAME_v=FreeBSD 11.2-RELEASE-p4 UNAME_r=11.2-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.7-7-gb715fabe MASTERMNT=/usr/local/poudriere/data/.m/112amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/112amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=112amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/112amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py36 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py36 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py36-orange3-single-cell-0.8.2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36 HOME=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36 HOME=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-orange3-single-cell/work-py36/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=freebsd11 PYTHON_PYOEXTENSION=opt-1.pyc PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=11.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/orange3-single-cell" EXAMPLESDIR="share/examples/orange3-single-cell" DATADIR="share/orange3-single-cell" WWWDIR="www/orange3-single-cell" ETCDIR="etc/orange3-single-cell" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/orange3-single-cell DOCSDIR=/usr/local/share/doc/orange3-single-cell EXAMPLESDIR=/usr/local/share/examples/orange3-single-cell WWWDIR=/usr/local/www/orange3-single-cell ETCDIR=/usr/local/etc/orange3-single-cell --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: x86_64-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: x86_64-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: x86_64-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=11.2-RELEASE-p4 OSREL=11.2 OSVERSION=1102000 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License AGPLv3+ accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py36-orange3-single-cell-0.8.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [112amd64-default-job-14] Installing pkg-1.10.5_5... [112amd64-default-job-14] Extracting pkg-1.10.5_5: .......... done ===> py36-orange3-single-cell-0.8.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py36-orange3-single-cell-0.8.2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License AGPLv3+ accepted by the user => biolab-orange3-single-cell-0.8.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/biolab/orange3-single-cell/tar.gz/0.8.2?dummy=/biolab-orange3-single-cell-0.8.2_GH0.tar.gz fetch: https://codeload.github.com/biolab/orange3-single-cell/tar.gz/0.8.2?dummy=/biolab-orange3-single-cell-0.8.2_GH0.tar.gz: size unknown fetch: https://codeload.github.com/biolab/orange3-single-cell/tar.gz/0.8.2?dummy=/biolab-orange3-single-cell-0.8.2_GH0.tar.gz: size of remote file is not known biolab-orange3-single-cell-0.8.2_GH0.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by py36-orange3-single-cell-0.8.2 for building =========================================================================== =======================<phase: checksum >============================ ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by py36-orange3-single-cell-0.8.2 for building => SHA256 Checksum OK for biolab-orange3-single-cell-0.8.2_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by py36-orange3-single-cell-0.8.2 for building ===> Extracting for py36-orange3-single-cell-0.8.2 => SHA256 Checksum OK for biolab-orange3-single-cell-0.8.2_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py36-orange3-single-cell-0.8.2 =========================================================================== =======================<phase: build-depends >============================ ===> py36-orange3-single-cell-0.8.2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz [112amd64-default-job-14] Installing gmake-4.2.1_2... [112amd64-default-job-14] `-- Installing gettext-runtime-0.19.8.1_1... [112amd64-default-job-14] | `-- Installing indexinfo-0.3.1... [112amd64-default-job-14] | `-- Extracting indexinfo-0.3.1: .... done <snip> [112amd64-default-job-14] | `-- Extracting qt5-webengine-5.9.5_8: .......... done [112amd64-default-job-14] `-- Extracting py36-qt5-webengine-5.9.2_4: .......... done [112amd64-default-job-14] `-- Installing py36-scikit-learn-0.19.2... [112amd64-default-job-14] | `-- Installing py36-scipy-1.1.0_1... [112amd64-default-job-14] | `-- Extracting py36-scipy-1.1.0_1: .......... done [112amd64-default-job-14] `-- Extracting py36-scikit-learn-0.19.2: .......... done [112amd64-default-job-14] `-- Installing py36-serverfiles-0.2.1... [112amd64-default-job-14] `-- Extracting py36-serverfiles-0.2.1: .......... done [112amd64-default-job-14] `-- Installing py36-xlrd-1.0.0... [112amd64-default-job-14] `-- Extracting py36-xlrd-1.0.0: .......... done [112amd64-default-job-14] Extracting orange3-3.15.0: .......... done Message from freeglut-3.0.0_1: Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. Message from gcc7-7.3.0_5: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc7 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_9: ===> NOTICE: The cblas port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from metis-5.1.0_5: ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from perl5-5.26.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from qtchooser-66: qtchooser is a wrapper that allows selecting whether Qt4 or Qt5 binaries for qmake, moc and other tools will be run when invoking the binaries in $PATH. By default, the Qt5 versions are run. It is possible to change the behavior by setting the QT_SELECT environment variable to "qt4". See qtchooser(1) for more information. Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from trousers-0.3.14_2: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Message from qt5-sql-5.11.2: ====================================================================== To enable Qt database support, install the database plugin ports. The following plugin ports are available: - databases/qt5-sqldrivers-ibase InterBase/Firebird - databases/qt5-sqldrivers-mysql MySQL - databases/qt5-sqldrivers-odbc Open Database Connectivity - databases/qt5-sqldrivers-pgsql PostgreSQL - databases/qt5-sqldrivers-sqlite2 SQLite 2 - databases/qt5-sqldrivers-sqlite3 SQLite 3 - databases/qt5-sqldrivers-tds FreeTDS ====================================================================== Message from opencv-core-3.4.1_8: ===> NOTICE: The opencv-core port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> py36-orange3-single-cell-0.8.2 depends on package: orange3>0 - found ===> Returning to build of py36-orange3-single-cell-0.8.2 ===> py36-orange3-single-cell-0.8.2 depends on package: py36-orange3-bioinformatics>0 - not found ===> Installing existing package /packages/All/py36-orange3-bioinformatics-3.2.2.txz [112amd64-default-job-14] Installing py36-orange3-bioinformatics-3.2.2... [112amd64-default-job-14] `-- Installing py36-Genesis-PyAPI-1.2.1... [112amd64-default-job-14] | `-- Installing py36-slumber-0.7.1... [112amd64-default-job-14] | `-- Extracting py36-slumber-0.7.1: .......... done [112amd64-default-job-14] `-- Extracting py36-Genesis-PyAPI-1.2.1: .......... done [112amd64-default-job-14] `-- Installing py36-requests-cache-0.4.13... [112amd64-default-job-14] `-- Extracting py36-requests-cache-0.4.13: .......... done [112amd64-default-job-14] Extracting py36-orange3-bioinformatics-3.2.2: .......... done ===> py36-orange3-single-cell-0.8.2 depends on package: py36-orange3-bioinformatics>0 - found ===> Returning to build of py36-orange3-single-cell-0.8.2 ===> py36-orange3-single-cell-0.8.2 depends on package: py36-astropy>0 - not found ===> Installing existing package /packages/All/py36-astropy-1.1.2_1.txz [112amd64-default-job-14] Installing py36-astropy-1.1.2_1... [112amd64-default-job-14] Extracting py36-astropy-1.1.2_1: .......... done ===> py36-orange3-single-cell-0.8.2 depends on package: py36-astropy>0 - found ===> Returning to build of py36-orange3-single-cell-0.8.2 ===> py36-orange3-single-cell-0.8.2 depends on package: py36-fastdtw>0 - not found ===> Installing existing package /packages/All/py36-fastdtw-0.3.2.txz [112amd64-default-job-14] Installing py36-fastdtw-0.3.2... [112amd64-default-job-14] Extracting py36-fastdtw-0.3.2: .......... done ===> py36-orange3-single-cell-0.8.2 depends on package: py36-fastdtw>0 - found ===> Returning to build of py36-orange3-single-cell-0.8.2 ===> py36-orange3-single-cell-0.8.2 depends on package: py36-joblib>=0.11 - not found ===> Installing existing package /packages/All/py36-joblib-0.9.4.txz [112amd64-default-job-14] Installing py36-joblib-0.9.4... the most recent version of py36-joblib-0.9.4 is already installed ===> py36-orange3-single-cell-0.8.2 depends on package: py36-joblib>=0.11 - not found *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-orange3-single-cell
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