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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CGEN
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CGEN’ ...
** this is package ‘CGEN’ version ‘3.43.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/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;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/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,\
| ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ccl.c -o ccl.o
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]
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fsclust.c -o fsclust.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c hcl.c -o hcl.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pmatch.c -o pmatch.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/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,
| ^~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/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 -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/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)
