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Date:      Tue, 6 Aug 2019 02:09:21 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:  <201908060209.x7629LHi034525@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/508200/logs/bolt-lmm-2.3.2.log
Build URL:      http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=508200
Log:

=>> Building biology/bolt-lmm
build started at Tue Aug  6 02:07:56 UTC 2019
port directory: /usr/ports/biology/bolt-lmm
package name: bolt-lmm-2.3.2
building for: FreeBSD 120powerpc64-quarterly-job-16 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: 16

---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-16] Installing pkg-1.11.1...
[120powerpc64-quarterly-job-16] 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-16] Installing gmake-4.2.1_3...
[120powerpc64-quarterly-job-16] `-- Installing gettext-runtime-0.20.1...
[120powerpc64-quarterly-job-16] |   `-- Installing indexinfo-0.3.1...
[120powerpc64-quarterly-job-16] |   `-- Extracting indexinfo-0.3.1: .... done
[120powerpc64-quarterly-job-16] `-- Extracting gettext-runtime-0.20.1: .......... done
[120powerpc64-quarterly-job-16] 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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