Date: Sun, 4 Aug 2019 03:26:10 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120powerpc64-quarterly][biology/bolt-lmm] Failed for bolt-lmm-2.3.2 in build Message-ID: <201908040326.x743QAKh062199@pylon.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: jwb@FreeBSD.org Last committer: jwb@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/507990/logs/bolt-lmm-2.3.2.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=507990 Log: =>> Building biology/bolt-lmm build started at Sun Aug 4 03:24:35 UTC 2019 port directory: /usr/ports/biology/bolt-lmm package name: bolt-lmm-2.3.2 building for: FreeBSD 120powerpc64-quarterly-job-15 12.0-RELEASE-p8 FreeBSD 12.0-RELEASE-p8 1200086 powerpc maintained by: jwb@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: 1300037 Jail OSVERSION: 1200086 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p8 1200086 UNAME_r=12.0-RELEASE-p8 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/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--- ===> 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@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 --End CONFIGURE_ENV-- --MAKE_ENV-- 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 NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc8" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/us 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" --End MAKE_ENV-- --PLIST_SUB-- PORTEXAMPLES="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bolt-lmm" EXAMPLESDIR="share/examples/bolt-lmm" DATADIR="share/bolt-lmm" WWWDIR="www/bolt-lmm" ETCDIR="etc/bolt-lmm" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bolt-lmm DOCSDIR=/usr/local/share/doc/bolt-lmm EXAMPLESDIR=/usr/local/share/examples/bolt-lmm WWWDIR=/usr/local/www/bolt-lmm ETCDIR=/usr/local/etc/bolt-lmm --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=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. _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. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p8 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local 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 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-15] Installing pkg-1.11.1... [120powerpc64-quarterly-job-15] 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-15] Installing gmake-4.2.1_3... [120powerpc64-quarterly-job-15] `-- Installing gettext-runtime-0.20.1... [120powerpc64-quarterly-job-15] | `-- Installing indexinfo-0.3.1... [120powerpc64-quarterly-job-15] | `-- Extracting indexinfo-0.3.1: .... done [120powerpc64-quarterly-job-15] `-- Extracting gettext-runtime-0.20.1: .......... done [120powerpc64-quarterly-job-15] 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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