[package - 120powerpc64-quarterly][biology/bolt-lmm] Failed for bolt-lmm-2.3.2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Jul 24 07:42:30 UTC 2019
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: jwb at FreeBSD.org
Ident: $FreeBSD: branches/2019Q3/biology/bolt-lmm/Makefile 502673 2019-05-26 03:36:49Z jwb $
Log URL: http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/507260/logs/bolt-lmm-2.3.2.log
Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=507260
Log:
=>> Building biology/bolt-lmm
build started at Wed Jul 24 07:41:02 UTC 2019
port directory: /usr/ports/biology/bolt-lmm
package name: bolt-lmm-2.3.2
building for: FreeBSD 120powerpc64-quarterly-job-09 12.0-RELEASE-p7 FreeBSD 12.0-RELEASE-p7 1200086 powerpc
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q3/biology/bolt-lmm/Makefile 502673 2019-05-26 03:36:49Z jwb $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300031
Jail OSVERSION: 1200086
Job Id: 09
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---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for bolt-lmm-2.3.2:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bolt-lmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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r/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 " 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"
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_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11"
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11"
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x"
CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11"
CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
_OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bolt-lmm-2.3.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.11.1.txz
[120powerpc64-quarterly-job-09] Installing pkg-1.11.1...
[120powerpc64-quarterly-job-09] Extracting pkg-1.11.1: .......... done
===> bolt-lmm-2.3.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bolt-lmm-2.3.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.2 for building
=> SHA256 Checksum OK for BOLT-LMM_v2.3.2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.2 for building
===> Extracting for bolt-lmm-2.3.2
=> SHA256 Checksum OK for BOLT-LMM_v2.3.2.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bolt-lmm-2.3.2
===> Applying FreeBSD patches for bolt-lmm-2.3.2
===========================================================================
=======================<phase: build-depends >============================
===> bolt-lmm-2.3.2 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[120powerpc64-quarterly-job-09] Installing gmake-4.2.1_3...
[120powerpc64-quarterly-job-09] `-- Installing gettext-runtime-0.20.1...
[120powerpc64-quarterly-job-09] | `-- Installing indexinfo-0.3.1...
[120powerpc64-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[120powerpc64-quarterly-job-09] `-- Extracting gettext-runtime-0.20.1: .......... done
[120powerpc64-quarterly-job-09] Extracting gmake-4.2.1_3: .......... done
===> bolt-lmm-2.3.2 depends on executable: gmake - found
===> Returning to build of bolt-lmm-2.3.2
===> bolt-lmm-2.3.2 depends on executable: gcc8 - not found
<snip>
vector <double> logDeltasLOVCO =
^~~~~~
BoltMain.cpp:318:12: error: expected primary-expression before 'double'
vector <double> h2sLOVCO(VCs);
^~~~~~
BoltMain.cpp:320:6: error: 'h2sLOVCO' was not declared in this scope
h2sLOVCO[v] = std::max(1e-9, 1 / (1 + exp(logDeltasLOVCO[v])));
^~~~~~~~
BoltMain.cpp:320:48: error: 'logDeltasLOVCO' was not declared in this scope
h2sLOVCO[v] = std::max(1e-9, 1 / (1 + exp(logDeltasLOVCO[v])));
^~~~~~~~~~~~~~
BoltMain.cpp:320:48: note: suggested alternative: 'logDeltaEst'
h2sLOVCO[v] = std::max(1e-9, 1 / (1 + exp(logDeltasLOVCO[v])));
^~~~~~~~~~~~~~
logDeltaEst
BoltMain.cpp:323:41: error: 'h2sLOVCO' was not declared in this scope
double h2sLOVCOsum = std::accumulate(h2sLOVCO.begin(), h2sLOVCO.end(), 0.0);
^~~~~~~~
BoltMain.cpp:323:41: note: suggested alternative: 'h2sLOVCOsum'
double h2sLOVCOsum = std::accumulate(h2sLOVCO.begin(), h2sLOVCO.end(), 0.0);
^~~~~~~~
h2sLOVCOsum
BoltMain.cpp:333:6: error: 'h2Guesses' was not declared in this scope
h2Guesses[v] = h2vGuess; //log(h2vGuess/(1-h2all));
^~~~~~~~~
BoltMain.cpp:333:6: note: suggested alternative: 'h2vGuess'
h2Guesses[v] = h2vGuess; //log(h2vGuess/(1-h2all));
^~~~~~~~~
h2vGuess
BoltMain.cpp:337:22: error: 'h2Guesses' was not declared in this scope
Vegs[v+1](d, d) = h2Guesses[v];
^~~~~~~~~
BoltMain.cpp:338:31: error: 'h2Guesses' was not declared in this scope
Vegs[0](d, d) = 1-accumulate(h2Guesses.begin(), h2Guesses.end(), 0.0);
^~~~~~~~~
BoltMain.cpp:341:10: error: expected ';' before 'usePhenoCorrs'
bool usePhenoCorrs = params.remlGuessVegs.empty();
^~~~~~~~~~~~~
BoltMain.cpp:342:23: error: 'usePhenoCorrs' was not declared in this scope
bolt.remlAI(Vegs, usePhenoCorrs, phenoVecsRep, &snpVCnums[0], params.remlMCtrials,
^~~~~~~~~~~~~
BoltMain.cpp:342:38: error: 'phenoVecsRep' was not declared in this scope
bolt.remlAI(Vegs, usePhenoCorrs, phenoVecsRep, &snpVCnums[0], params.remlMCtrials,
^~~~~~~~~~~~
BoltMain.cpp:352:35: error: expected primary-expression before '>' token
vector <Bolt::StatsDataRetroLOCO> retroData;
^
BoltMain.cpp:352:37: error: 'retroData' was not declared in this scope
vector <Bolt::StatsDataRetroLOCO> retroData;
^~~~~~~~~
In file included from /usr/local/lib/gcc8/gcc/powerpc64-portbld-freebsd12.0/8.3.0/include/xmmintrin.h:63,
from MemoryUtils.hpp:34,
from BoltMain.cpp:38:
BoltMain.cpp:353:9: error: '__vector' does not name a type; did you mean 'vector'?
const vector <double> &pheno = phenoVecs[0];
^~~~~~
BoltMain.cpp:358:60: error: 'pheno' was not declared in this scope
Bolt::StatsDataRetroLOCO LINREGdata = bolt.computeLINREG(pheno);
^~~~~
BoltMain.cpp:365:11: error: expected primary-expression before 'double'
vector <double> LDscores, LDscoresChip;
^~~~~~
BoltMain.cpp:392:13: error: expected primary-expression before 'double'
vector <double> sigma2Ks, logDeltas;
^~~~~~
BoltMain.cpp:394:5: error: 'logDeltas' was not declared in this scope
logDeltas = vector <double> (params.numLeaveOutChunks, logDeltaEst);
^~~~~~~~~
BoltMain.cpp:394:5: note: suggested alternative: 'logDeltaEst'
logDeltas = vector <double> (params.numLeaveOutChunks, logDeltaEst);
^~~~~~~~~
logDeltaEst
BoltMain.cpp:394:25: error: expected primary-expression before 'double'
logDeltas = vector <double> (params.numLeaveOutChunks, logDeltaEst);
^~~~~~
BoltMain.cpp:395:5: error: 'sigma2Ks' was not declared in this scope
sigma2Ks = vector <double> (params.numLeaveOutChunks, sigma2Kest);
^~~~~~~~
BoltMain.cpp:395:5: note: suggested alternative: 'sigma2Kest'
sigma2Ks = vector <double> (params.numLeaveOutChunks, sigma2Kest);
^~~~~~~~
sigma2Kest
BoltMain.cpp:395:24: error: expected primary-expression before 'double'
sigma2Ks = vector <double> (params.numLeaveOutChunks, sigma2Kest);
^~~~~~
BoltMain.cpp:426:7: error: 'LDscoresChip' was not declared in this scope
LDscoresChip = snpData.estChipLDscores(sampleSize);
^~~~~~~~~~~~
BoltMain.cpp:440:7: error: 'LDscores' was not declared in this scope
LDscores = vector <double> (snps.size(), NAN); // NAN if missing
^~~~~~~~
BoltMain.cpp:440:26: error: expected primary-expression before 'double'
LDscores = vector <double> (snps.size(), NAN); // NAN if missing
^~~~~~
BoltMain.cpp:444:25: error: 'snps' was not declared in this scope
for (uint64 m = 0; m < snps.size(); m++)
^~~~
BoltMain.cpp:462:18: error: expected primary-expression before '>' token
vector <string> tokens = StringUtils::tokenizeMultipleDelimiters(line, " \t");
^
BoltMain.cpp:462:20: error: 'tokens' was not declared in this scope
vector <string> tokens = StringUtils::tokenizeMultipleDelimiters(line, " \t");
^~~~~~
BoltMain.cpp:462:20: note: suggested alternative: 'popen'
vector <string> tokens = StringUtils::tokenizeMultipleDelimiters(line, " \t");
^~~~~~
popen
BoltMain.cpp:478:25: error: 'snps' was not declared in this scope
for (uint64 m = 0; m < snps.size(); m++)
^~~~
BoltMain.cpp:499:18: error: expected primary-expression before '>' token
vector <string> tokens = StringUtils::tokenizeMultipleDelimiters(line, " \t");
^
BoltMain.cpp:499:20: error: 'tokens' was not declared in this scope
vector <string> tokens = StringUtils::tokenizeMultipleDelimiters(line, " \t");
^~~~~~
BoltMain.cpp:499:20: note: suggested alternative: 'popen'
vector <string> tokens = StringUtils::tokenizeMultipleDelimiters(line, " \t");
^~~~~~
popen
BoltMain.cpp:519:40: error: 'LDscoresChip' was not declared in this scope
LINREGdata.stats, LDscores, LDscoresChip, minMAF,
^~~~~~~~~~~~
BoltMain.cpp:529:7: error: 'LDscores' was not declared in this scope
LDscores = LDscoresChip;
^~~~~~~~
BoltMain.cpp:529:18: error: 'LDscoresChip' was not declared in this scope
LDscores = LDscoresChip;
^~~~~~~~~~~~
BoltMain.cpp:546:7: error: expected ';' before 'useMCMCinCV'
bool useMCMCinCV = false; //params.lmmBayesMCMC;
^~~~~~~~~~~
BoltMain.cpp:549:64: error: 'useMCMCinCV' was not declared in this scope
params.CVfoldsCompute, params.CVnoEarlyExit, predBoostMin, useMCMCinCV,
^~~~~~~~~~~
BoltMain.cpp:574:38: error: 'LDscores' was not declared in this scope
retroData[lmmInfInd].stats, LDscores, LDscoresChip));
^~~~~~~~
BoltMain.cpp:574:48: error: 'LDscoresChip' was not declared in this scope
retroData[lmmInfInd].stats, LDscores, LDscoresChip));
^~~~~~~~~~~~
BoltMain.cpp:614:38: error: 'LDscores' was not declared in this scope
retroData[lmmInfInd].stats, LDscores, LDscoresChip));
^~~~~~~~
BoltMain.cpp:614:48: error: 'LDscoresChip' was not declared in this scope
retroData[lmmInfInd].stats, LDscores, LDscoresChip));
^~~~~~~~~~~~
BoltMain.cpp:640:13: error: expected primary-expression before 'double'
vector <double> sortStats;
^~~~~~
BoltMain.cpp:644:2: error: 'sortStats' was not declared in this scope
sortStats.push_back(retroData[s].stats[m]);
^~~~~~~~~
BoltMain.cpp:644:2: note: suggested alternative: 'totStats'
sortStats.push_back(retroData[s].stats[m]);
^~~~~~~~~
totStats
BoltMain.cpp:647:15: error: 'sortStats' was not declared in this scope
std::sort(sortStats.begin(), sortStats.end());
^~~~~~~~~
BoltMain.cpp:647:15: note: suggested alternative: 'totStats'
std::sort(sortStats.begin(), sortStats.end());
^~~~~~~~~
totStats
BoltMain.cpp:732:10: error: 'LDscoresChip' was not declared in this scope
if (!LDscoresChip.empty()) fout << "\t" << "CHIPLD";
^~~~~~~~~~~~
BoltMain.cpp:733:9: error: 'simPheno' was not declared in this scope
if (simPheno) fout << "\t" << "simBeta" << "\t" << "simRegion";
^~~~~~~~
BoltMain.cpp:733:9: note: suggested alternative: 'fileno'
if (simPheno) fout << "\t" << "simBeta" << "\t" << "simRegion";
^~~~~~~~
fileno
BoltMain.cpp:739:15: error: 'snps' was not declared in this scope
fout << snps[m].ID << "\t" << snps[m].chrom << "\t" << snps[m].physpos << "\t"
^~~~
BoltMain.cpp:741:12: error: 'LDscoresChip' was not declared in this scope
if (!LDscoresChip.empty()) {
^~~~~~~~~~~~
BoltMain.cpp:745:11: error: 'simPheno' was not declared in this scope
if (simPheno) fout << "\t" << simBetas[m] << "\t" << simRegions[m];
^~~~~~~~
BoltMain.cpp:745:11: note: suggested alternative: 'fileno'
if (simPheno) fout << "\t" << simBetas[m] << "\t" << simRegions[m];
^~~~~~~~
fileno
BoltMain.cpp:745:37: error: 'simBetas' was not declared in this scope
if (simPheno) fout << "\t" << simBetas[m] << "\t" << simRegions[m];
^~~~~~~~
BoltMain.cpp:745:37: note: suggested alternative: 'memset_s'
if (simPheno) fout << "\t" << simBetas[m] << "\t" << simRegions[m];
^~~~~~~~
memset_s
gmake[1]: *** [Makefile:116: BoltMain.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.2/src'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bolt-lmm
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