############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CGEN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘CGEN’ ... ** this is package ‘CGEN’ version ‘3.43.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Additive.c -o Additive.o Additive.c: In function ‘vecinit’: Additive.c:103:13: warning: old-style function definition [-Wold-style-definition] 103 | static void vecinit(vec, n, c) | ^~~~~~~ Additive.c: In function ‘vecmove’: Additive.c:115:13: warning: old-style function definition [-Wold-style-definition] 115 | static void vecmove(invec, n, outvec) | ^~~~~~~ Additive.c: In function ‘vecMultCon’: Additive.c:130:13: warning: old-style function definition [-Wold-style-definition] 130 | static void vecMultCon(invec, n, c, ret) | ^~~~~~~~~~ Additive.c: In function ‘rMatMMultVec’: Additive.c:144:13: warning: old-style function definition [-Wold-style-definition] 144 | static void rMatMMultVec(mat, nrow, ncol, vec, ret) | ^~~~~~~~~~~~ Additive.c: In function ‘mylog’: Additive.c:172:15: warning: old-style function definition [-Wold-style-definition] 172 | static double mylog(x) | ^~~~~ Additive.c: In function ‘mylog2’: Additive.c:187:15: warning: old-style function definition [-Wold-style-definition] 187 | static double mylog2(x) | ^~~~~~ Additive.c: In function ‘compute_g’: Additive.c:203:13: warning: old-style function definition [-Wold-style-definition] 203 | static void compute_g(method, theta, x1cols, x2cols, g11, g12, g21, g22) | ^~~~~~~~~ Additive.c: In function ‘add1’: Additive.c:242:15: warning: old-style function definition [-Wold-style-definition] 242 | static double add1(theta, op) | ^~~~ Additive.c: In function ‘getLL_mat’: Additive.c:297:13: warning: old-style function definition [-Wold-style-definition] 297 | static void getLL_mat(op) | ^~~~~~~~~ Additive.c: In function ‘Pdg_xs’: Additive.c:344:13: warning: old-style function definition [-Wold-style-definition] 344 | static void Pdg_xs(eta, op) | ^~~~~~ Additive.c: In function ‘add1_indep’: Additive.c:416:15: warning: old-style function definition [-Wold-style-definition] 416 | static double add1_indep(theta, op) | ^~~~~~~~~~ Additive.c: In function ‘negloglike’: Additive.c:463:15: warning: old-style function definition [-Wold-style-definition] 463 | static double negloglike(theta, op) | ^~~~~~~~~~ Additive.c: In function ‘gradient’: Additive.c:484:13: warning: old-style function definition [-Wold-style-definition] 484 | static void gradient(eta, op, ret) | ^~~~~~~~ Additive.c: In function ‘getadd1’: Additive.c:677:13: warning: old-style function definition [-Wold-style-definition] 677 | static void getadd1(op, meth) | ^~~~~~~ Additive.c: In function ‘additive1’: Additive.c:730:6: warning: old-style function definition [-Wold-style-definition] 730 | void additive1(theta0, nparms, x1cols, nx1, x2cols, nx2, datX, Xnrow, Xncol, covs, ncovs, y, method,\ | ^~~~~~~~~ Additive.c: In function ‘additive1_indep’: Additive.c:784:6: warning: old-style function definition [-Wold-style-definition] 784 | void additive1_indep(theta0, nparms, x1cols, nx1, x2cols, nx2, Xnrow, covCols, ncovs, method,\ | ^~~~~~~~~~~~~~~ Additive.c: In function ‘compute_g’: Additive.c:235:25: warning: ‘t22’ may be used uninitialized [-Wmaybe-uninitialized] 235 | *g22 = logx - t12 - t22; | ~~~~~~~~~~~^~~~~ Additive.c:207:25: note: ‘t22’ was declared here 207 | double t11, t12, t21, t22, x, et11, et12, et21, et22, logx; | ^~~ Additive.c:233:19: warning: ‘et22’ may be used uninitialized [-Wmaybe-uninitialized] 233 | x = et12 + et22 - 1; | ~~~~~^~~~~~ Additive.c:207:51: note: ‘et22’ was declared here 207 | double t11, t12, t21, t22, x, et11, et12, et21, et22, logx; | ^~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c CML.c -o CML.o CML.c: In function ‘vecinit’: CML.c:147:13: warning: old-style function definition [-Wold-style-definition] 147 | static void vecinit(vec, n, c) | ^~~~~~~ CML.c: In function ‘vecmove’: CML.c:159:13: warning: old-style function definition [-Wold-style-definition] 159 | static void vecmove(invec, n, outvec) | ^~~~~~~ CML.c: In function ‘vecsum’: CML.c:174:15: warning: old-style function definition [-Wold-style-definition] 174 | static double vecsum(vec, n) | ^~~~~~ CML.c: In function ‘vecMultCon’: CML.c:191:13: warning: old-style function definition [-Wold-style-definition] 191 | static void vecMultCon(invec, n, c, ret) | ^~~~~~~~~~ CML.c: In function ‘rMatMMultVec’: CML.c:205:13: warning: old-style function definition [-Wold-style-definition] 205 | static void rMatMMultVec(mat, nrow, ncol, vec, ret) | ^~~~~~~~~~~~ CML.c: In function ‘rmatrixMult’: CML.c:229:13: warning: old-style function definition [-Wold-style-definition] 229 | static void rmatrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret) | ^~~~~~~~~~~ CML.c: In function ‘Pdg_xs’: CML.c:249:13: warning: old-style function definition [-Wold-style-definition] 249 | static void Pdg_xs(eta, op) | ^~~~~~ CML.c: In function ‘Pd1_xs’: CML.c:407:13: warning: old-style function definition [-Wold-style-definition] 407 | static void Pd1_xs(op, ret, index) | ^~~~~~ CML.c: In function ‘Edg_xs’: CML.c:427:13: warning: old-style function definition [-Wold-style-definition] 427 | static void Edg_xs(op, ret, ret2, index) | ^~~~~~ CML.c: In function ‘Eg_xs’: CML.c:461:13: warning: old-style function definition [-Wold-style-definition] 461 | static void Eg_xs(op, ret, index) | ^~~~~ CML.c: In function ‘getWtYmu’: CML.c:482:13: warning: old-style function definition [-Wold-style-definition] 482 | static void getWtYmu(eta, op, ret) | ^~~~~~~~ CML.c: In function ‘fSNP’: CML.c:565:15: warning: old-style function definition [-Wold-style-definition] 565 | static double fSNP(SNP, gmodel) | ^~~~ CML.c: In function ‘getLL_mat’: CML.c:588:13: warning: old-style function definition [-Wold-style-definition] 588 | static void getLL_mat(op) | ^~~~~~~~~ CML.c: In function ‘negloglike’: CML.c:638:15: warning: old-style function definition [-Wold-style-definition] 638 | static double negloglike(eta, op) | ^~~~~~~~~~ CML.c: In function ‘gradient’: CML.c:666:13: warning: old-style function definition [-Wold-style-definition] 666 | static void gradient(eta, op, ret) | ^~~~~~~~ CML.c: In function ‘hessian’: CML.c:697:13: warning: old-style function definition [-Wold-style-definition] 697 | static void hessian(eta, op, ret) | ^~~~~~~ CML.c: In function ‘chol’: CML.c:895:13: warning: old-style function definition [-Wold-style-definition] 895 | static void chol(mat, n, ret, retdiag) | ^~~~ CML.c: In function ‘cholinv’: CML.c:931:13: warning: old-style function definition [-Wold-style-definition] 931 | static void cholinv(L, diag, n, ret) | ^~~~~~~ CML.c: In function ‘rmatTranspose’: CML.c:957:13: warning: old-style function definition [-Wold-style-definition] 957 | static void rmatTranspose(mat, n, ret) | ^~~~~~~~~~~~~ CML.c: In function ‘symrMatInv’: CML.c:973:13: warning: old-style function definition [-Wold-style-definition] 973 | static void symrMatInv(mat, n, ret) | ^~~~~~~~~~ CML.c: In function ‘getCML’: CML.c:995:13: warning: old-style function definition [-Wold-style-definition] 995 | static void getCML(eta, op) | ^~~~~~ CML.c: In function ‘getEB’: CML.c:1044:13: warning: old-style function definition [-Wold-style-definition] 1044 | static void getEB(op) | ^~~~~ CML.c: In function ‘check_init’: CML.c:1256:13: warning: old-style function definition [-Wold-style-definition] 1256 | static void check_init(eta, op) | ^~~~~~~~~~ CML.c: In function ‘CML_EB’: CML.c:1318:6: warning: old-style function definition [-Wold-style-definition] 1318 | void CML_EB(eta0, nparms, nbeta, D, snp, nrow, xMain, nx, xInt, nv, xStrata, nstrata, gmodel, genoBinary,\ | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ccl.c -o ccl.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c csclust.f -o csclust.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran 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] /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fsclust.c -o fsclust.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c hcl.c -o hcl.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pmatch.c -o pmatch.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c score.c -o score.o score.c: In function ‘infoSmallStandard’: score.c:14:6: warning: old-style function definition [-Wold-style-definition] 14 | void infoSmallStandard(xmat, pnr, pnc, pphat, infoSum) | ^~~~~~~~~~~~~~~~~ score.c: In function ‘getCOV0’: score.c:48:6: warning: old-style function definition [-Wold-style-definition] 48 | void getCOV0(pncinf, phatprod, pn, pinfoprods, retcov) | ^~~~~~~ score.c: In function ‘getCOV1’: score.c:80:6: warning: old-style function definition [-Wold-style-definition] 80 | void getCOV1(pnc, pn, weights, twopmu, pinfob1, pinfoh, pinfohnc, retcov) | ^~~~~~~ score.c: In function ‘getScore’: score.c:133:6: warning: old-style function definition [-Wold-style-definition] 133 | void getScore(y, score, pnr, pnc, avgscore0, avgscore1, retcov) | ^~~~~~~~ score.c: In function ‘getScoreEB’: score.c:174:6: warning: old-style function definition [-Wold-style-definition] 174 | void getScoreEB(y, score1, score2, pnr, pnc1, pnc2, avgscore1_0, avgscore1_1, | ^~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/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)