[package - 114i386-default][misc/snakemake] Failed for snakemake-6.2.1 in run-depends
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Apr 29 13:34:23 UTC 2021
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 at FreeBSD.org
Log URL: http://beefy10.nyi.freebsd.org/data/114i386-default/762f9d5a8fbb/logs/snakemake-6.2.1.log
Build URL: http://beefy10.nyi.freebsd.org/build.html?mastername=114i386-default&build=762f9d5a8fbb
Log:
=>> Building misc/snakemake
build started at Thu Apr 29 13:34:17 UTC 2021
port directory: /usr/ports/misc/snakemake
package name: snakemake-6.2.1
building for: FreeBSD 114i386-default-job-08 11.4-RELEASE-p9 FreeBSD 11.4-RELEASE-p9 i386
maintained by: yuri at FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1400008
Jail OSVERSION: 1104001
Job Id: 08
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1104001
UNAME_v=FreeBSD 11.4-RELEASE-p9
UNAME_r=11.4-RELEASE-p9
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=3.2.8-8-gaf08dbda
MASTERMNT=/usr/local/poudriere/data/.m/114i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/114i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=114i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/114i386-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=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/misc/snakemake/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/misc/snakemake/work HOME=/wrkdirs/usr/ports/misc/snakemake/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/misc/snakemake/work/.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/misc/snakemake/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/misc/snakemake/work HOME=/wrkdirs/usr/ports/misc/snakemake/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/misc/snakemake/work/.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-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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--
PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd11 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=11.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/snakemake" EXAMPLESDIR="share/examples/snakemake" DATADIR="share/snakemake" WWWDIR="www/snakemake" ETCDIR="etc/snakemake"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/snakemake DOCSDIR=/usr/local/share/doc/snakemake EXAMPLESDIR=/usr/local/share/examples/snakemake WWWDIR=/usr/local/www/snakemake ETCDIR=/usr/local/etc/snakemake
--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
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git at github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.0 (git at github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd11.4 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" "-m" "elf_i386_fbsd" "-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 10.0.0 (git at github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=11.4-RELEASE-p9
OSREL=11.4
OSVERSION=1104001
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
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) 524288
stack size (kbytes, -s) 65536
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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> snakemake-6.2.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[114i386-default-job-08] Installing pkg-1.16.3...
[114i386-default-job-08] Extracting pkg-1.16.3: .......... done
===> snakemake-6.2.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of snakemake-6.2.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by snakemake-6.2.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by snakemake-6.2.1 for building
=> SHA256 Checksum OK for snakemake-6.2.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by snakemake-6.2.1 for building
===> Extracting for snakemake-6.2.1
=> SHA256 Checksum OK for snakemake-6.2.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for snakemake-6.2.1
===========================================================================
=======================<phase: build-depends >============================
===> snakemake-6.2.1 depends on package: py38-setuptools>0 - not found
===> Installing existing package /packages/All/py38-setuptools-44.0.0_1.txz
[114i386-default-job-08] Installing py38-setuptools-44.0.0_1...
[114i386-default-job-08] `-- Installing python38-3.8.9...
[114i386-default-job-08] | `-- Installing gettext-runtime-0.21...
[114i386-default-job-08] | | `-- Installing indexinfo-0.3.1...
[114i386-default-job-08] | | `-- Extracting indexinfo-0.3.1: .... done
[114i386-default-job-08] | `-- Extracting gettext-runtime-0.21: .......... done
[114i386-default-job-08] | `-- Installing libffi-3.3_1...
[114i386-default-job-08] | `-- Extracting libffi-3.3_1: .......... done
[114i386-default-job-08] | `-- Installing readline-8.1.0...
[114i386-default-job-08] | `-- Extracting readline-8.1.0: .......... done
[114i386-default-job-08] `-- Extracting python38-3.8.9: .......... done
[114i386-default-job-08] Extracting py38-setuptools-44.0.0_1: .......... done
=====
Message from python38-3.8.9:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py38-gdbm databases/py-gdbm at py38
py38-sqlite3 databases/py-sqlite3 at py38
py38-tkinter x11-toolkits/py-tkinter at py38
===> snakemake-6.2.1 depends on package: py38-setuptools>0 - found
===> Returning to build of snakemake-6.2.1
===> snakemake-6.2.1 depends on file: /usr/local/bin/python3.8 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for snakemake-6.2.1
running config
===========================================================================
=======================<phase: build >============================
===> Building for snakemake-6.2.1
running build
running build_py
creating build
creating build/lib
creating build/lib/snakemake
copying snakemake/modules.py -> build/lib/snakemake
copying snakemake/decorators.py -> build/lib/snakemake
copying snakemake/workflow.py -> build/lib/snakemake
copying snakemake/notebook.py -> build/lib/snakemake
copying snakemake/logging.py -> build/lib/snakemake
copying snakemake/shell.py -> build/lib/snakemake
copying snakemake/__main__.py -> build/lib/snakemake
copying snakemake/common.py -> build/lib/snakemake
copying snakemake/__init__.py -> build/lib/snakemake
copying snakemake/stats.py -> build/lib/snakemake
copying snakemake/wrapper.py -> build/lib/snakemake
copying snakemake/rules.py -> build/lib/snakemake
copying snakemake/checkpoints.py -> build/lib/snakemake
copying snakemake/jobs.py -> build/lib/snakemake
copying snakemake/io.py -> build/lib/snakemake
copying snakemake/gui.py -> build/lib/snakemake
copying snakemake/persistence.py -> build/lib/snakemake
copying snakemake/resources.py -> build/lib/snakemake
copying snakemake/benchmark.py -> build/lib/snakemake
copying snakemake/script.py -> build/lib/snakemake
copying snakemake/path_modifier.py -> build/lib/snakemake
copying snakemake/parser.py -> build/lib/snakemake
copying snakemake/ruleinfo.py -> build/lib/snakemake
copying snakemake/utils.py -> build/lib/snakemake
copying snakemake/dag.py -> build/lib/snakemake
copying snakemake/exceptions.py -> build/lib/snakemake
copying snakemake/cwl.py -> build/lib/snakemake
copying snakemake/output_index.py -> build/lib/snakemake
copying snakemake/scheduler.py -> build/lib/snakemake
copying snakemake/sourcecache.py -> build/lib/snakemake
copying snakemake/_version.py -> build/lib/snakemake
creating build/lib/snakemake/remote
copying snakemake/remote/SFTP.py -> build/lib/snakemake/remote
copying snakemake/remote/S3.py -> build/lib/snakemake/remote
copying snakemake/remote/GS.py -> build/lib/snakemake/remote
copying snakemake/remote/gridftp.py -> build/lib/snakemake/remote
copying snakemake/remote/__init__.py -> build/lib/snakemake/remote
copying snakemake/remote/NCBI.py -> build/lib/snakemake/remote
copying snakemake/remote/dropbox.py -> build/lib/snakemake/remote
copying snakemake/remote/HTTP.py -> build/lib/snakemake/remote
copying snakemake/remote/FTP.py -> build/lib/snakemake/remote
copying snakemake/remote/S3Mocked.py -> build/lib/snakemake/remote
copying snakemake/remote/AzBlob.py -> build/lib/snakemake/remote
copying snakemake/remote/EGA.py -> build/lib/snakemake/remote
copying snakemake/remote/webdav.py -> build/lib/snakemake/remote
copying snakemake/remote/XRootD.py -> build/lib/snakemake/remote
copying snakemake/remote/gfal.py -> build/lib/snakemake/remote
copying snakemake/remote/iRODS.py -> build/lib/snakemake/remote
creating build/lib/snakemake/report
copying snakemake/report/__init__.py -> build/lib/snakemake/report
creating build/lib/snakemake/caching
copying snakemake/caching/__init__.py -> build/lib/snakemake/caching
copying snakemake/caching/local.py -> build/lib/snakemake/caching
copying snakemake/caching/remote.py -> build/lib/snakemake/caching
copying snakemake/caching/hash.py -> build/lib/snakemake/caching
creating build/lib/snakemake/deployment
copying snakemake/deployment/containerize.py -> build/lib/snakemake/deployment
copying snakemake/deployment/__init__.py -> build/lib/snakemake/deployment
copying snakemake/deployment/env_modules.py -> build/lib/snakemake/deployment
copying snakemake/deployment/singularity.py -> build/lib/snakemake/deployment
copying snakemake/deployment/conda.py -> build/lib/snakemake/deployment
creating build/lib/snakemake/linting
copying snakemake/linting/__init__.py -> build/lib/snakemake/linting
copying snakemake/linting/rules.py -> build/lib/snakemake/linting
copying snakemake/linting/links.py -> build/lib/snakemake/linting
copying snakemake/linting/snakefiles.py -> build/lib/snakemake/linting
creating build/lib/snakemake/executors
copying snakemake/executors/google_lifesciences.py -> build/lib/snakemake/executors
copying snakemake/executors/__init__.py -> build/lib/snakemake/executors
copying snakemake/executors/google_lifesciences_helper.py -> build/lib/snakemake/executors
copying snakemake/executors/ga4gh_tes.py -> build/lib/snakemake/executors
creating build/lib/snakemake/unit_tests
copying snakemake/unit_tests/__init__.py -> build/lib/snakemake/unit_tests
creating build/lib/snakemake/unit_tests/templates
copying snakemake/unit_tests/templates/__init__.py -> build/lib/snakemake/unit_tests/templates
copying snakemake/report.css -> build/lib/snakemake
copying snakemake/gui.html -> build/lib/snakemake
copying snakemake/report/report.html.jinja2 -> build/lib/snakemake/report
copying snakemake/executors/jobscript.sh -> build/lib/snakemake/executors
copying snakemake/unit_tests/templates/common.py.jinja2 -> build/lib/snakemake/unit_tests/templates
copying snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/lib/snakemake/unit_tests/templates
UPDATING build/lib/snakemake/_version.py
set build/lib/snakemake/_version.py to '6.2.1'
===========================================================================
=======================<phase: run-depends >============================
===> snakemake-6.2.1 depends on package: py38-appdirs>0 - not found
===> Installing existing package /packages/All/py38-appdirs-1.4.4.txz
[114i386-default-job-08] Installing py38-appdirs-1.4.4...
[114i386-default-job-08] Extracting py38-appdirs-1.4.4: .......... done
===> snakemake-6.2.1 depends on package: py38-appdirs>0 - found
===> Returning to build of snakemake-6.2.1
===> snakemake-6.2.1 depends on package: py38-configargparse>0 - not found
===> Installing existing package /packages/All/py38-configargparse-1.2.3.txz
[114i386-default-job-08] Installing py38-configargparse-1.2.3...
[114i386-default-job-08] Extracting py38-configargparse-1.2.3: .......... done
===> snakemake-6.2.1 depends on package: py38-configargparse>0 - found
===> Returning to build of snakemake-6.2.1
===> snakemake-6.2.1 depends on package: py38-datrie>0 - not found
===> Installing existing package /packages/All/py38-datrie-0.8.2.txz
[114i386-default-job-08] Installing py38-datrie-0.8.2...
[114i386-default-job-08] Extracting py38-datrie-0.8.2: ........ done
===> snakemake-6.2.1 depends on package: py38-datrie>0 - found
===> Returning to build of snakemake-6.2.1
===> snakemake-6.2.1 depends on package: py38-docutils>0 - not found
===> Installing existing package /packages/All/py38-docutils-0.17.1.txz
[114i386-default-job-08] Installing py38-docutils-0.17.1...
[114i386-default-job-08] Extracting py38-docutils-0.17.1: .......... done
===> snakemake-6.2.1 depends on package: py38-docutils>0 - found
===> Returning to build of snakemake-6.2.1
===> snakemake-6.2.1 depends on package: py38-filelock>0 - not found
===> Installing existing package /packages/All/py38-filelock-3.0.12.txz
[114i386-default-job-08] Installing py38-filelock-3.0.12...
[114i386-default-job-08] Extracting py38-filelock-3.0.12: .......... done
===> snakemake-6.2.1 depends on package: py38-filelock>0 - found
===> Returning to build of snakemake-6.2.1
===> snakemake-6.2.1 depends on package: py38-GitPython>0 - not found
===> Installing existing package /packages/All/py38-gitpython-3.1.15.txz
[114i386-default-job-08] Installing py38-gitpython-3.1.15...
[114i386-default-job-08] `-- Installing py38-ddt-1.4.1...
[114i386-default-job-08] `-- Extracting py38-ddt-1.4.1: .......... done
[114i386-default-job-08] `-- Installing py38-gitdb2-2.0.6...
[114i386-default-job-08] | `-- Installing py38-smmap2-2.0.5...
[114i386-default-job-08] | `-- Extracting py38-smmap2-2.0.5: .......... done
[114i386-default-job-08] `-- Extracting py38-gitdb2-2.0.6: .......... done
[114i386-default-job-08] Extracting py38-gitpython-3.1.15: .......... done
===> snakemake-6.2.1 depends on package: py38-GitPython>0 - not found
*** Error code 1
Stop.
make: stopped in /usr/ports/misc/snakemake
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