------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/eigen-3.3.7.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_3,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.10,1.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:36 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gcta-1.26.0_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gcta-1.26.0_1 for building => SHA256 Checksum OK for gcta_1.26.0_src.zip. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gcta-1.26.0_1 for building ===> Extracting for gcta-1.26.0_1 => SHA256 Checksum OK for gcta_1.26.0_src.zip. /usr/bin/unzip -d /construction/biology/gcta/gcta_1.26.0_src /distfiles/gcta_1.26.0_src.zip Archive: /distfiles/gcta_1.26.0_src.zip extracting: /construction/biology/gcta/gcta_1.26.0_src/bivar_reml.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/cdflib.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/CommFunc.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/CommFunc.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/Copyright.txt |  extracting: /construction/biology/gcta/gcta_1.26.0_src/data.cpp | / -  extracting: /construction/biology/gcta/gcta_1.26.0_src/dcdflib.cpp | / - \ | / - \  extracting: /construction/biology/gcta/gcta_1.26.0_src/dcdflib.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/edata.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/eigen_func.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/eigen_func.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/ejma.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/est_hsq.cpp | / -  extracting: /construction/biology/gcta/gcta_1.26.0_src/gbat.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/gcta.h | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/GNU_General_Public_License_v3.txt | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/grm.cpp | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/gwas_simu.cpp | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/HowToCompile.txt |  extracting: /construction/biology/gcta/gcta_1.26.0_src/ipmpar.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/joint_meta.cpp | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/ld.cpp | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/Makefile |  extracting: /construction/biology/gcta/gcta_1.26.0_src/mkl.cpp | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/mlm_assoc.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/option.cpp | / -  extracting: /construction/biology/gcta/gcta_1.26.0_src/popu_genet.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/raw_geno.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/read_imput.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/README.txt |  extracting: /construction/biology/gcta/gcta_1.26.0_src/reml_within_family.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/sbat.cpp | /  extracting: /construction/biology/gcta/gcta_1.26.0_src/StatFunc.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/StatFunc.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/StrFunc.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/StrFunc.h |  extracting: /construction/biology/gcta/gcta_1.26.0_src/UnusedCode.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/zfstream.cpp |  extracting: /construction/biology/gcta/gcta_1.26.0_src/zfstream.h |  Extracted Memory Use: 0.93M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for gcta-1.26.0_1 ===> Converting DOS text files to UNIX text files ===> Applying ports patches for gcta-1.26.0_1 from /xports/biology/gcta/files SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on package: eigen>=3 - found ===> gcta-1.26.0_1 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> gcta-1.26.0_1 depends on package: eigen>=3 - found ===> gcta-1.26.0_1 depends on package: gmake>=4.3 - found ===> gcta-1.26.0_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Configuring for gcta-1.26.0_1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for gcta-1.26.0_1 gmake[1]: Entering directory '/construction/biology/gcta/gcta_1.26.0_src' c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c bivar_reml.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c CommFunc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c eigen_func.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c data.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c dcdflib.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c edata.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c ejma.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c est_hsq.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c grm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c gwas_simu.cpp dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6027:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6403:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6784:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c ld.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c joint_meta.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c mlm_assoc.cpp est_hsq.cpp: In member function 'double gcta::reml_iteration(eigenMatrix&, eigenMatrix&, eigenMatrix&, eigenVector&, eigenVector&, bool, bool, bool)': est_hsq.cpp:893:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."}; ^ est_hsq.cpp:893:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] est_hsq.cpp:893:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c mkl.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c option.cpp joint_meta.cpp: In member function 'void gcta::run_massoc_slct(std::__cxx11::string, int, double, double, int, bool, bool, double, bool, int)': joint_meta.cpp:179:34: warning: overflow in conversion from 'double' to 'int' changes value from '1.0e+30' to '2147483647' [-Woverflow] if (top_SNPs < 0) top_SNPs = 1e30; ^~~~ option.cpp: In function 'void option(int, char**)': option.cpp:135:24: warning: ISO C++ forbids converting a string constant to '__gnu_cxx::__alloc_traits, char*>::value_type' {aka 'char*'} [-Wwrite-strings] argv[option_num] = "gcta"; ^~~~~~ option.cpp:136:28: warning: ISO C++ forbids converting a string constant to '__gnu_cxx::__alloc_traits, char*>::value_type' {aka 'char*'} [-Wwrite-strings] argv[option_num + 1] = "gcta"; ^~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c popu_genet.cpp bivar_reml.cpp: In member function 'bool gcta::calcu_Vi_bivar(eigenMatrix&, eigenVector&, double&, int&)': bivar_reml.cpp:295:21: warning: control reaches end of non-void function [-Wreturn-type] string errmsg = "\nError: the V (variance-covariance) matrix is not invertible."; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c raw_geno.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c sbat.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c StatFunc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c StrFunc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c reml_within_family.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c zfstream.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -o gcta bivar_reml.o CommFunc.o eigen_func.o data.o dcdflib.o edata.o ejma.o est_hsq.o grm.o gwas_simu.o ld.o joint_meta.o mlm_assoc.o mkl.o option.o popu_genet.o raw_geno.o sbat.o StatFunc.o StrFunc.o reml_within_family.o zfstream.o -lopenblas -lz -Wl,--start-group -lpthread -lm -ldl /usr/libexec/binutils227/elf/ld.gold: missing group end /usr/libexec/binutils227/elf/ld.gold: use the --help option for usage information collect2: error: ld returned 1 exit status gmake[1]: *** [Makefile:67: gcta] Error 1 gmake[1]: Leaving directory '/construction/biology/gcta/gcta_1.26.0_src' ===> 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 /xports/biology/gcta FAILED 00:01:31