=> Bootstrap dependency digest>=20211023: found digest-20211023 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for plink-1.07nb1 c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c plink.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c options.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c input.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c binput.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tinput.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genome.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c helper.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c stats.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c filters.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c locus.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c multi.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c crandom.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cluster.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mds.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c output.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c informative.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c assoc.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c epi.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c prephap.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c phase.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c trio.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tdt.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sharing.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genepi.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sets.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c perm.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mh.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genedrop.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c gxe.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c merge.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c hotel.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c multiple.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploCC.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploTDT.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c poo.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c webcheck.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c qfam.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c linear.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c bmerge.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c parse.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mishap.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c legacy.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c homozyg.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c segment.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c model.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c logistic.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c glm.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dcdflib.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:6025:60: 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:6401:59: 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:6782:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c elf.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dfam.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c fisher.cpp fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:501:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1539:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(20, "This should never occur."); ^ c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c linput.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sockets.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lookup.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c proxy.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c pdriver.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploQTL.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haplohelper.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haplowindow.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genogroup.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c nonfounderphasing.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c clumpld.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genoerr.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c em.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c impute.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c metaem.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c profile.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c nlist.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c whap.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c simul.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c gvar.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cnv.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c step.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c greport.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c flip.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c qualscores.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cnvqt.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cfamily.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c setscreen.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c idhelp.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tag.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c hapglm.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lookup2.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c blox.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c zed.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dosage.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c annot.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c metaanal.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c r.cpp In file included from r.cpp:29:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c Rconnection.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c zfstream.cpp c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lapackf.cpp In file included from Rconnection.cpp:30:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ ^~~~~~~~~~~~~~ lapackf.cpp: In function 'bool svd_lapack(int, vector_t&, vector_t&, matrix_t&)': lapackf.cpp:58:104: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] dgesdd_("A", &m, &n, &A[0] , &m, &S[0], &U[0], &m, &tV[0], &n, &optim_lwork, &lwork, &iwork[0], &info); ^ lapackf.cpp:63:100: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] dgesdd_("A", &m, &n, &A[0] , &m, &S[0], &U[0], &m, &tV[0], &n, &work[0], &lwork, &iwork[0], &info); ^ lapackf.cpp: In function 'bool eigen_lapack(int, vector_t&, vector_t&, matrix_t&)': lapackf.cpp:132:10: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] &info ); ^ lapackf.cpp:132:10: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] lapackf.cpp:132:10: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] lapackf.cpp:158:10: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] &info ); ^ lapackf.cpp:158:10: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] lapackf.cpp:158:10: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] c++ -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o lapackf.o -lcrypt -lz -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -llapack -lblas -lf2c