[package - 132i386-quarterly][biology/gcta] Failed for gcta-1.26.0_4 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Tue, 10 Oct 2023 05:37:02 UTC
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
Log URL: https://pkg-status.freebsd.org/beefy13/data/132i386-quarterly/32195e384156/logs/gcta-1.26.0_4.log
Build URL: https://pkg-status.freebsd.org/beefy13/build.html?mastername=132i386-quarterly&build=32195e384156
Log:
=>> Building biology/gcta
build started at Tue Oct 10 05:35:51 UTC 2023
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_4
building for: FreeBSD 132i386-quarterly-job-09 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1500000
Jail OSVERSION: 1302001
Job Id: 09
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1302001
UNAME_v=FreeBSD 13.2-RELEASE-p4
UNAME_r=13.2-RELEASE-p4
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
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=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/132i386-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/132i386-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=132i386-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/132i386-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---
---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/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lopenblas -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isys
tem /usr/local/include " 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--
OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gcta" EXAMPLESDIR="share/examples/gcta" DATADIR="share/gcta" WWWDIR="www/gcta" ETCDIR="etc/gcta"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gcta DOCSDIR=/usr/local/share/doc/gcta EXAMPLESDIR=/usr/local/share/examples/gcta WWWDIR=/usr/local/www/gcta ETCDIR=/usr/local/etc/gcta
--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=3
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: i386-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: i386-unknown-freebsd13.2 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_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: i386-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=13.2-RELEASE-p4
OSREL=13.2
OSVERSION=1302001
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.7.pkg
[132i386-quarterly-job-09] Installing pkg-1.20.7...
[132i386-quarterly-job-09] Extracting pkg-1.20.7: .......... done
===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_4 for building
=> SHA256 Checksum OK for gcta_1.26.0_src.zip.
=> SHA256 Checksum OK for eigen-3.3.9.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_4 for building
===> Extracting for gcta-1.26.0_4
=> SHA256 Checksum OK for gcta_1.26.0_src.zip.
=> SHA256 Checksum OK for eigen-3.3.9.tar.gz.
Archive: /portdistfiles/gcta_1.26.0_src.zip
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/bivar_reml.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/cdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Copyright.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/data.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/edata.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ejma.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/est_hsq.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gcta.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/GNU_General_Public_License_v3.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/grm.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gwas_simu.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/HowToCompile.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ipmpar.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/joint_meta.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ld.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Makefile
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mkl.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mlm_assoc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/option.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/popu_genet.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/raw_geno.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/read_imput.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/README.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/reml_within_family.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/sbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/UnusedCode.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.h
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for gcta-1.26.0_4
===> Converting DOS text files to UNIX text files
===> Applying FreeBSD patches for gcta-1.26.0_4 from /usr/ports/biology/gcta/files
===========================================================================
=======================<phase: build-depends >============================
===> gcta-1.26.0_4 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[132i386-quarterly-job-09] Installing gmake-4.3_2...
[132i386-quarterly-job-09] `-- Installing gettext-runtime-0.22_1...
[132i386-quarterly-job-09] | `-- Installing indexinfo-0.3.1...
[132i386-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[132i386-quarterly-job-09] `-- Extracting gettext-runtime-0.22_1: .......... done
[132i386-quarterly-job-09] Extracting gmake-4.3_2: .......... done
===> gcta-1.26.0_4 depends on package: gmake>=4.3 - found
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: lib-depends >============================
===> gcta-1.26.0_4 depends on shared library: libopenblas.so - not found
===> Installing existing package /packages/All/openblas-0.3.24,1.pkg
[132i386-quarterly-job-09] Installing openblas-0.3.24,1...
[132i386-quarterly-job-09] `-- Installing gcc12-12.2.0_6...
[132i386-quarterly-job-09] | `-- Installing binutils-2.40_4,1...
[132i386-quarterly-job-09] | | `-- Installing zstd-1.5.5...
[132i386-quarterly-job-09] | | `-- Installing liblz4-1.9.4,1...
[132i386-quarterly-job-09] | | `-- Extracting liblz4-1.9.4,1: .......... done
[132i386-quarterly-job-09] | | `-- Extracting zstd-1.5.5: .......... done
[132i386-quarterly-job-09] | `-- Extracting binutils-2.40_4,1: .......... done
[132i386-quarterly-job-09] | `-- Installing gmp-6.3.0...
[132i386-quarterly-job-09] | `-- Extracting gmp-6.3.0: .......... done
[132i386-quarterly-job-09] | `-- Installing mpc-1.3.1_1...
[132i386-quarterly-job-09] | | `-- Installing mpfr-4.2.1,1...
[132i386-quarterly-job-09] | | `-- Extracting mpfr-4.2.1,1: .......... done
[132i386-quarterly-job-09] | `-- Extracting mpc-1.3.1_1: ......... done
[132i386-quarterly-job-09] `-- Extracting gcc12-12.2.0_6: .......... done
[132i386-quarterly-job-09] Extracting openblas-0.3.24,1: .......... done
=====
Message from gcc12-12.2.0_6:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> gcta-1.26.0_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: configure >============================
===> Configuring for gcta-1.26.0_4
===========================================================================
=======================<phase: build >============================
===> Building for gcta-1.26.0_4
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0'
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c bivar_reml.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c CommFunc.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c eigen_func.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c data.cpp
bivar_reml.cpp:321:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c dcdflib.cpp
dcdflib.cpp:6027:23: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR");
^
dcdflib.cpp:6403:28: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR");
^
dcdflib.cpp:6784:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM");
^
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c edata.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c ejma.cpp
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c est_hsq.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c grm.cpp
est_hsq.cpp:893:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."};
^
est_hsq.cpp:893:46: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."};
^
est_hsq.cpp:893:68: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."};
^
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c gwas_simu.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c ld.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c joint_meta.cpp
joint_meta.cpp:179:34: warning: implicit conversion of out of range value from 'double' to 'int' is undefined [-Wliteral-conversion]
if (top_SNPs < 0) top_SNPs = 1e30;
~ ^~~~
joint_meta.cpp:218:24: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if (!joint_only && !mld_slct_alg==2) {
^ ~~
joint_meta.cpp:218:24: note: add parentheses after the '!' to evaluate the comparison first
if (!joint_only && !mld_slct_alg==2) {
^
( )
joint_meta.cpp:218:24: note: add parentheses around left hand side expression to silence this warning
if (!joint_only && !mld_slct_alg==2) {
^
( )
joint_meta.cpp:218:37: warning: result of comparison of constant 2 with expression of type 'bool' is always false [-Wtautological-constant-out-of-range-compare]
if (!joint_only && !mld_slct_alg==2) {
~~~~~~~~~~~~~^ ~
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c mlm_assoc.cpp
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c mkl.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c option.cpp
mkl.cpp:360:5: error: no matching function for call to 'dpotrf_'
dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info);
^~~~~~~
/usr/local/include/lapack.h:13624:12: note: candidate function not viable: requires 6 arguments, but 5 were provided
lapack_int LAPACK_dpotrf_base(
^
/usr/local/include/lapack.h:13623:28: note: expanded from macro 'LAPACK_dpotrf_base'
#define LAPACK_dpotrf_base LAPACK_GLOBAL(dpotrf,DPOTRF)
^
/usr/local/include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
^
<scratch space>:357:1: note: expanded from here
dpotrf_
^
mkl.cpp:372:9: error: no matching function for call to 'dpotri_'
dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info);
^~~~~~~
/usr/local/include/lapack.h:13752:6: note: candidate function not viable: requires 6 arguments, but 5 were provided
void LAPACK_dpotri_base(
^
/usr/local/include/lapack.h:13751:28: note: expanded from macro 'LAPACK_dpotri_base'
#define LAPACK_dpotri_base LAPACK_GLOBAL(dpotri,DPOTRI)
^
/usr/local/include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
^
<scratch space>:365:1: note: expanded from here
dpotri_
^
2 errors generated.
gmake[1]: *** [Makefile:72: mkl.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
option.cpp:135:24: warning: ISO C++11 does not allow conversion from string literal to 'std::vector<char *>::value_type' (aka 'char *') [-Wwritable-strings]
argv[option_num] = "gcta";
^
option.cpp:136:28: warning: ISO C++11 does not allow conversion from string literal to 'std::vector<char *>::value_type' (aka 'char *') [-Wwritable-strings]
argv[option_num + 1] = "gcta";
^
2 warnings generated.
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/gcta