############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_3.43.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CGEN.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CGEN.buildbin-libdir CGEN_3.43.0.tar.gz' >>>>>>> * installing *source* package ‘CGEN’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Additive.c -o Additive.o Additive.c:103:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void vecinit(vec, n, c) ^ Additive.c:115:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void vecmove(invec, n, outvec) ^ Additive.c:130:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void vecMultCon(invec, n, c, ret) ^ Additive.c:144:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void rMatMMultVec(mat, nrow, ncol, vec, ret) ^ Additive.c:172:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double mylog(x) ^ Additive.c:187:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double mylog2(x) ^ Additive.c:203:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void compute_g(method, theta, x1cols, x2cols, g11, g12, g21, g22) ^ Additive.c:242:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double add1(theta, op) ^ Additive.c:297:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void getLL_mat(op) ^ Additive.c:344:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void Pdg_xs(eta, op) ^ Additive.c:416:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double add1_indep(theta, op) ^ Additive.c:463:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double negloglike(theta, op) ^ Additive.c:484:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void gradient(eta, op, ret) ^ Additive.c:677:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void getadd1(op, meth) ^ Additive.c:730:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void additive1(theta0, nparms, x1cols, nx1, x2cols, nx2, datX, Xnrow, Xncol, covs, ncovs, y, method,\ ^ Additive.c:784:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void additive1_indep(theta0, nparms, x1cols, nx1, x2cols, nx2, Xnrow, covCols, ncovs, method,\ ^ 16 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CML.c -o CML.o CML.c:147:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void vecinit(vec, n, c) ^ CML.c:159:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void vecmove(invec, n, outvec) ^ CML.c:174:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double vecsum(vec, n) ^ CML.c:191:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void vecMultCon(invec, n, c, ret) ^ CML.c:205:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void rMatMMultVec(mat, nrow, ncol, vec, ret) ^ CML.c:229:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void rmatrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret) ^ CML.c:249:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void Pdg_xs(eta, op) ^ CML.c:407:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void Pd1_xs(op, ret, index) ^ CML.c:427:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void Edg_xs(op, ret, ret2, index) ^ CML.c:461:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void Eg_xs(op, ret, index) ^ CML.c:482:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void getWtYmu(eta, op, ret) ^ CML.c:565:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double fSNP(SNP, gmodel) ^ CML.c:588:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void getLL_mat(op) ^ CML.c:638:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static double negloglike(eta, op) ^ CML.c:666:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void gradient(eta, op, ret) ^ CML.c:697:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void hessian(eta, op, ret) ^ CML.c:895:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void chol(mat, n, ret, retdiag) ^ CML.c:931:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void cholinv(L, diag, n, ret) ^ CML.c:957:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void rmatTranspose(mat, n, ret) ^ CML.c:973:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void symrMatInv(mat, n, ret) ^ CML.c:995:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void getCML(eta, op) ^ CML.c:1044:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void getEB(op) ^ CML.c:1256:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static void check_init(eta, op) ^ CML.c:1318:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void CML_EB(eta0, nparms, nbeta, D, snp, nrow, xMain, nx, xInt, nv, xStrata, nstrata, gmodel, genoBinary,\ ^ 24 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ccl.c -o ccl.o ccl.c:430:16: warning: variable 'det' set but not used [-Wunused-but-set-variable] double temp , det = 1.0 ; ^ 1 warning generated. /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c csclust.f -o csclust.o f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs] csclust.f:72:72: 72 | 10 FLAG(I)=.TRUE. | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1) csclust.f:222:3: 222 | 650 RETURN | 1 Warning: Label 650 at (1) defined but not used [-Wunused-label] clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fsclust.c -o fsclust.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hcl.c -o hcl.o hcl.c:419:16: warning: variable 'det' set but not used [-Wunused-but-set-variable] double temp , det = 1.0 ; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pmatch.c -o pmatch.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c score.c -o score.o score.c:14:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void infoSmallStandard(xmat, pnr, pnc, pphat, infoSum) ^ score.c:48:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void getCOV0(pncinf, phatprod, pn, pinfoprods, retcov) ^ score.c:80:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void getCOV1(pnc, pn, weights, twopmu, pinfob1, pinfoh, pinfohnc, retcov) ^ score.c:133:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void getScore(y, score, pnr, pnc, avgscore0, avgscore1, retcov) ^ score.c:174:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void getScoreEB(y, score1, score2, pnr, pnc1, pnc2, avgscore1_0, avgscore1_1, ^ 5 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/CGEN/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CGEN) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CGEN.buildbin-libdir/CGEN/libs/CGEN.so >>>>>>> >>>>>>> Paths before fix: CGEN.buildbin-libdir/CGEN/libs/CGEN.so: CGEN.so (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so" >>>>>>> Paths after fix: CGEN.buildbin-libdir/CGEN/libs/CGEN.so: CGEN.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)