------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- 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 00:00:21 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building => SHA256 Checksum OK for chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building ===> Extracting for plink-1.90.b6.17_1 => SHA256 Checksum OK for chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz. Extracted Memory Use: 14.32M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for plink-1.90.b6.17_1 ===> Applying ports patches for plink-1.90.b6.17_1 from /xports/biology/plink/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on package: gmake>=4.3 - found ===> plink-1.90.b6.17_1 depends on executable: gfortran8 - found ===> plink-1.90.b6.17_1 depends on file: /usr/local/bin/as - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on package: gmake>=4.3 - found ===> plink-1.90.b6.17_1 depends on executable: gfortran8 - found ===> plink-1.90.b6.17_1 depends on file: /usr/local/bin/as - found ===> plink-1.90.b6.17_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Configuring for plink-1.90.b6.17_1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for plink-1.90.b6.17_1 gmake[1]: Entering directory '/construction/biology/plink/plink-ng-79b2df8c/1.9' c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink.c -o plink.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_assoc.c -o plink_assoc.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_calc.c -o plink_calc.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_cluster.c -o plink_cluster.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_cnv.c -o plink_cnv.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_common.c -o plink_common.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_data.c -o plink_data.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_dosage.c -o plink_dosage.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_family.c -o plink_family.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_filter.c -o plink_filter.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_glm.c -o plink_glm.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_help.c -o plink_help.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_homozyg.c -o plink_homozyg.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_lasso.c -o plink_lasso.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_ld.c -o plink_ld.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_matrix.c -o plink_matrix.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_misc.c -o plink_misc.o plink_glm.c: In function 'int32_t glm_linear_nosnp(pthread**, FILE*, uintptr_t, char*, char*, uint32_t, double, uint32_t, uint32_t, Range_list*, Range_list*, double, double, double, double, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, char*, char*, Chrom_info*, uintptr_t, uintptr_t, uintptr_t*, uint32_t, uint32_t*, uint32_t*, uint32_t, uint32_t, uintptr_t*, double*, uintptr_t, char*, uintptr_t, uintptr_t*, double*, uintptr_t*, uintptr_t*, uint32_t, uint32_t, Set_info*)': plink_glm.c:7845:8: warning: 'void* memcpy(void*, const void*, size_t)' reading 17 bytes from a region of size 16 [-Wstringop-overflow=] memcpy(wptr, ".mperm.dump.all", 17); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plink_glm.c: In function 'int32_t glm_logistic_nosnp(pthread**, FILE*, uintptr_t, char*, char*, uint32_t, double, uint32_t, uint32_t, Range_list*, Range_list*, double, double, double, double, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, char*, char*, Chrom_info*, uintptr_t, uintptr_t, uintptr_t*, uint32_t, uint32_t*, uint32_t*, uint32_t, uint32_t, uintptr_t*, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, double*, uintptr_t*, uintptr_t*, uint32_t, uint32_t, Set_info*)': plink_glm.c:8629:8: warning: 'void* memcpy(void*, const void*, size_t)' reading 17 bytes from a region of size 16 [-Wstringop-overflow=] memcpy(wptr, ".mperm.dump.all", 17); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_perm.c -o plink_perm.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_rserve.c -o plink_rserve.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_set.c -o plink_set.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing plink_stats.c -o plink_stats.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing SFMT.c -o SFMT.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing dcdflib.c -o dcdflib.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing pigz.c -o pigz.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing yarn.c -o yarn.o c++ -x c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing Rconnection.cc -o Rconnection.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing hfile.c -o hfile.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -O2 -fno-strict-aliasing bgzf.c -o bgzf.o plink.c: In function 'int32_t main(int32_t, char**)': plink.c:6853:25: warning: 'int __builtin_memcmp_eq(const void*, const void*, long unsigned int)' reading 22 bytes from a region of size 19 [-Wstringop-overflow=] } else if (!memcmp(argptr2, "lip-scan-window-kb", 22)) { ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plink.c:10750:25: warning: 'int __builtin_memcmp_eq(const void*, const void*, long unsigned int)' reading 19 bytes from a region of size 16 [-Wstringop-overflow=] } else if (!memcmp(argptr2, "ead-genome-list", 19)) { ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_perm.o plink_rserve.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o -lopenblas -lopenblas -lthr -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -B/usr/local/bin -L/usr/local/lib -L. -lz -o plink /usr/local/bin/ld: cannot find -lthr /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) collect2: error: ld returned 1 exit status gmake[1]: *** [Makefile.std:78: plink] Error 1 gmake[1]: Leaving directory '/construction/biology/plink/plink-ng-79b2df8c/1.9' ===> 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/plink FAILED 00:00:45