[package - 121arm64-quarterly][biology/bowtie2] Failed for bowtie2-2.4.1_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Apr 9 04:24:39 UTC 2020
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: jwb at FreeBSD.org
Last committer: martymac at FreeBSD.org
Ident: $FreeBSD: branches/2020Q2/biology/bowtie2/Makefile 530219 2020-04-01 14:14:51Z martymac $
Log URL: http://thunderx1.nyi.freebsd.org/data/121arm64-quarterly/530537/logs/bowtie2-2.4.1_1.log
Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=530537
Log:
=>> Building biology/bowtie2
build started at Thu Apr 9 04:22:34 UTC 2020
port directory: /usr/ports/biology/bowtie2
package name: bowtie2-2.4.1_1
building for: FreeBSD 121arm64-quarterly-job-23 12.1-RELEASE-p3 FreeBSD 12.1-RELEASE-p3 1201000 arm64
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q2/biology/bowtie2/Makefile 530219 2020-04-01 14:14:51Z martymac $
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===> The following configuration options are available for bowtie2-2.4.1_1:
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EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
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jwb at FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3+ accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bowtie2-2.4.1_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.13.2.txz
[121arm64-quarterly-job-23] Installing pkg-1.13.2...
[121arm64-quarterly-job-23] Extracting pkg-1.13.2: .......... done
===> bowtie2-2.4.1_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bowtie2-2.4.1_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3+ accepted by the user
=> BenLangmead-bowtie2-v2.4.1_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.4.1?dummy=/BenLangmead-bowtie2-v2.4.1_GH0.tar.gz
fetch: https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.4.1?dummy=/BenLangmead-bowtie2-v2.4.1_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.4.1?dummy=/BenLangmead-bowtie2-v2.4.1_GH0.tar.gz: size of remote file is not known
BenLangmead-bowtie2-v2.4.1_GH0.tar.gz 10 MB 8302 kBps 01s
===> Fetching all distfiles required by bowtie2-2.4.1_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3+ accepted by the user
===> Fetching all distfiles required by bowtie2-2.4.1_1 for building
=> SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3+ accepted by the user
===> Fetching all distfiles required by bowtie2-2.4.1_1 for building
===> Extracting for bowtie2-2.4.1_1
=> SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bowtie2-2.4.1_1
===> Applying FreeBSD patches for bowtie2-2.4.1_1
===========================================================================
=======================<phase: build-depends >============================
===> bowtie2-2.4.1_1 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[121arm64-quarterly-job-23] Installing gmake-4.2.1_3...
[121arm64-quarterly-job-23] `-- Installing gettext-runtime-0.20.1...
[121arm64-quarterly-job-23] | `-- Installing indexinfo-0.3.1...
[121arm64-quarterly-job-23] | `-- Extracting indexinfo-0.3.1: .... done
[121arm64-quarterly-job-23] `-- Extracting gettext-runtime-0.20.1: .......... done
[121arm64-quarterly-job-23] Extracting gmake-4.2.1_3: .......... done
===> bowtie2-2.4.1_1 depends on executable: gmake - found
===> Returning to build of bowtie2-2.4.1_1
===> bowtie2-2.4.1_1 depends on file: /usr/local/bin/python3.7 - not found
===> Installing existing package /packages/All/python37-3.7.7.txz
[121arm64-quarterly-job-23] Installing python37-3.7.7...
[121arm64-quarterly-job-23] `-- Installing libffi-3.2.1_3...
[121arm64-quarterly-job-23] `-- Extracting libffi-3.2.1_3: .......... done
[121arm64-quarterly-job-23] `-- Installing readline-8.0.4...
[121arm64-quarterly-job-23] `-- Extracting readline-8.0.4: .......... done
[121arm64-quarterly-job-23] Extracting python37-3.7.7: .......... done
=====
Message from python37-3.7.7:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py37-gdbm databases/py-gdbm at py37
py37-sqlite3 databases/py-sqlite3 at py37
py37-tkinter x11-toolkits/py-tkinter at py37
===> bowtie2-2.4.1_1 depends on file: /usr/local/bin/python3.7 - found
===> Returning to build of bowtie2-2.4.1_1
===========================================================================
=======================<phase: lib-depends >============================
===> bowtie2-2.4.1_1 depends on shared library: libtbb.so - not found
===> Installing existing package /packages/All/tbb-2020.2.txz
[121arm64-quarterly-job-23] Installing tbb-2020.2...
[121arm64-quarterly-job-23] Extracting tbb-2020.2: .......... done
===> bowtie2-2.4.1_1 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so)
===> Returning to build of bowtie2-2.4.1_1
===========================================================================
=======================<phase: configure >============================
===> Configuring for bowtie2-2.4.1_1
===========================================================================
=======================<phase: build >============================
===> Building for bowtie2-2.4.1_1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.4.1'
usage: dirname string [...]
c++ -DCOMPILER_OPTIONS="\" -fopenmp-simd\"" -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-Ithird_party/simde \
-o bowtie2-build-s bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
-fstack-protector-strong -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc
ld: error: undefined symbol: tthread::thread::join()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<SString<char> >::~KarkkainenBlockwiseSA())
ld: error: undefined symbol: tthread::thread::~thread()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<SString<char> >::~KarkkainenBlockwiseSA())
ld: error: undefined symbol: tthread::thread::thread(void (*)(void*), void*)
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<SString<char> >::nextSuffix())
ld: error: undefined symbol: tthread::thread::thread(void (*)(void*), void*)
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(DifferenceCoverSample<SString<char> >::build(int))
ld: error: undefined symbol: tthread::thread::join()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(DifferenceCoverSample<SString<char> >::build(int))
ld: error: undefined symbol: tthread::thread::thread(void (*)(void*), void*)
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<SString<char> >::buildSamples())
ld: error: undefined symbol: tthread::thread::join()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<SString<char> >::buildSamples())
ld: error: undefined symbol: tthread::thread::join()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<S2bDnaString>::~KarkkainenBlockwiseSA())
ld: error: undefined symbol: tthread::thread::~thread()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<S2bDnaString>::~KarkkainenBlockwiseSA())
ld: error: undefined symbol: tthread::thread::thread(void (*)(void*), void*)
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<S2bDnaString>::nextSuffix())
ld: error: undefined symbol: tthread::thread::thread(void (*)(void*), void*)
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(DifferenceCoverSample<S2bDnaString>::build(int))
ld: error: undefined symbol: tthread::thread::join()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(DifferenceCoverSample<S2bDnaString>::build(int))
ld: error: undefined symbol: tthread::thread::thread(void (*)(void*), void*)
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<S2bDnaString>::buildSamples())
ld: error: undefined symbol: tthread::thread::join()
>>> referenced by bt2_build.cpp
>>> /tmp/bt2_build-0bc4fe.o:(KarkkainenBlockwiseSA<S2bDnaString>::buildSamples())
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [Makefile:345: bowtie2-build-s] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.4.1'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bowtie2
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