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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SMAD
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
Warning: SystemRequirements specified C++14: support has been removed
* installing *source* package ‘SMAD’ ...
** this is package ‘SMAD’ version ‘1.27.5’
** using staged installation
** libs
specified C++14
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/api/deprecated.c -o nlopt/api/deprecated.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/api/general.c -o nlopt/api/general.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/api/optimize.c -o nlopt/api/optimize.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/api/options.c -o nlopt/api/options.o
nlopt/api/options.c: In function ‘nlopt_set_min_objective’:
nlopt/api/options.c:235:1: warning: control reaches end of non-void function [-Wreturn-type]
235 | }
| ^
nlopt/api/options.c: In function ‘nlopt_set_max_objective’:
nlopt/api/options.c:257:1: warning: control reaches end of non-void function [-Wreturn-type]
257 | }
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/cobyla/cobyla.c -o nlopt/cobyla/cobyla.o
nlopt/cobyla/cobyla.c: In function ‘trstlp’:
nlopt/cobyla/cobyla.c:1256:7: warning: variable ‘iout’ set but not used [-Wunused-but-set-variable]
1256 | int iout, i__, j, k;
| ^~~~
nlopt/cobyla/cobyla.c: At top level:
nlopt/cobyla/cobyla.c:35:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=]
35 | static char const rcsid[] =
| ^~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/auglag/auglag.c -o nlopt/auglag/auglag.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/bobyqa/bobyqa.c -o nlopt/bobyqa/bobyqa.o
nlopt/bobyqa/bobyqa.c: In function ‘update_’:
nlopt/bobyqa/bobyqa.c:27:20: warning: variable ‘jl’ set but not used [-Wunused-but-set-variable]
27 | int i__, j, k, jl, jp;
| ^~
nlopt/bobyqa/bobyqa.c: In function ‘trsbox_’:
nlopt/bobyqa/bobyqa.c:1182:54: warning: variable ‘sqstp’ set but not used [-Wunused-but-set-variable]
1182 | double resid, delsq, ggsav, tempa, tempb, ratio, sqstp, redmax,
| ^~~~~
nlopt/bobyqa/bobyqa.c:1182:47: warning: variable ‘ratio’ set but not used [-Wunused-but-set-variable]
1182 | double resid, delsq, ggsav, tempa, tempb, ratio, sqstp, redmax,
| ^~~~~
nlopt/bobyqa/bobyqa.c:1627:14: warning: ‘iact’ may be used uninitialized [-Wmaybe-uninitialized]
1627 | if (iact > 0 && isav == iu) {
| ~~~~~^~~
nlopt/bobyqa/bobyqa.c:1177:9: note: ‘iact’ was declared here
1177 | int iact, nact;
| ^~~~
nlopt/bobyqa/bobyqa.c:1629:20: warning: ‘xsav’ may be used uninitialized [-Wmaybe-uninitialized]
1629 | xbdi[iact] = xsav;
| ~~~~~~~~~~~^~~~~~
nlopt/bobyqa/bobyqa.c:1180:24: note: ‘xsav’ was declared here
1180 | double temp, zero, xsav, xsum, angbd, dredg, sredg;
| ^~~~
nlopt/bobyqa/bobyqa.c:1571:23: warning: ‘angbd’ may be used uninitialized [-Wmaybe-uninitialized]
1571 | iu = (int) (angbd * 17. + 3.1);
| ~~~~~~^~~~~
nlopt/bobyqa/bobyqa.c:1180:36: note: ‘angbd’ was declared here
1180 | double temp, zero, xsav, xsum, angbd, dredg, sredg;
| ^~~~~
nlopt/bobyqa/bobyqa.c:1577:30: warning: ‘dredg’ may be used uninitialized [-Wmaybe-uninitialized]
1577 | rednew = sth * (angt * dredg - sredg - half * sth * temp);
| ~~~~~^~~~~~~
nlopt/bobyqa/bobyqa.c:1180:43: note: ‘dredg’ was declared here
1180 | double temp, zero, xsav, xsum, angbd, dredg, sredg;
| ^~~~~
nlopt/bobyqa/bobyqa.c:1577:38: warning: ‘sredg’ may be used uninitialized [-Wmaybe-uninitialized]
1577 | rednew = sth * (angt * dredg - sredg - half * sth * temp);
| ~~~~~~~~~~~~~^~~~~~~
nlopt/bobyqa/bobyqa.c:1180:50: note: ‘sredg’ was declared here
1180 | double temp, zero, xsav, xsum, angbd, dredg, sredg;
| ^~~~~
nlopt/bobyqa/bobyqa.c:1478:19: warning: ‘dredsq’ may be used uninitialized [-Wmaybe-uninitialized]
1478 | temp = gredsq * dredsq - dredg * dredg;
| ~~~~~~~^~~~~~~~
nlopt/bobyqa/bobyqa.c:1183:13: note: ‘dredsq’ was declared here
1183 | dredsq, redsav, onemin, gredsq, rednew;
| ^~~~~~
nlopt/bobyqa/bobyqa.c:1702:8: warning: ‘itcsav’ may be used uninitialized [-Wmaybe-uninitialized]
1702 | if (iterc > itcsav) {
| ^
nlopt/bobyqa/bobyqa.c:1184:9: note: ‘itcsav’ was declared here
1184 | int itcsav;
| ^~~~~~
nlopt/bobyqa/bobyqa.c:1437:14: warning: ‘ggsav’ may be used uninitialized [-Wmaybe-uninitialized]
1437 | beta = gredsq / ggsav;
| ~~~~~^~~~~~~~~~~~~~~~
nlopt/bobyqa/bobyqa.c:1182:26: note: ‘ggsav’ was declared here
1182 | double resid, delsq, ggsav, tempa, tempb, ratio, sqstp, redmax,
| ^~~~~
nlopt/bobyqa/bobyqa.c: In function ‘rescue_.constprop’:
nlopt/bobyqa/bobyqa.c:642:29: warning: ‘xp’ may be used uninitialized [-Wmaybe-uninitialized]
642 | vquad += xp * xq * hq[iw];
| ~~~^~~~
nlopt/bobyqa/bobyqa.c:161:12: note: ‘xp’ was declared here
161 | double xp, xq, den;
| ^~
nlopt/bobyqa/bobyqa.c:15:37: warning: ‘ihp’ may be used uninitialized [-Wmaybe-uninitialized]
15 | #define MAX2(a,b) ((a) >= (b) ? (a) : (b))
| ~~~~~~~~~~~~~~~~~~^~~~~~
nlopt/bobyqa/bobyqa.c:641:22: note: in expansion of macro ‘MAX2’
641 | iw = MAX2(ihp,ihq) - (i__3 = ip - iq, IABS(i__3));
| ^~~~
nlopt/bobyqa/bobyqa.c:162:9: note: ‘ihp’ was declared here
162 | int ihp;
| ^~~
In function ‘prelim_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2077:11,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:1898:36: warning: ‘stepa’ may be used uninitialized [-Wmaybe-uninitialized]
1898 | gopt[nfm] = (f - fbeg) / stepa;
| ~~~~~~~~~~~^~~~~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1732:54: note: ‘stepa’ was declared here
1732 | double two, fbeg, diff, half, temp, zero, recip, stepa, stepb;
| ^~~~~
In function ‘prelim_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2077:11,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:1910:23: warning: ‘stepb’ may be used uninitialized [-Wmaybe-uninitialized]
1910 | if (stepa * stepb < zero) {
| ~~~~~~^~~~~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1732:61: note: ‘stepb’ was declared here
1732 | double two, fbeg, diff, half, temp, zero, recip, stepa, stepb;
| ^~~~~
In function ‘prelim_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2077:11,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:1942:30: warning: ‘ipt’ may be used uninitialized [-Wmaybe-uninitialized]
1942 | hq[ih] = (fbeg - fval[ipt + 1] - fval[jpt + 1] + f) / temp;
| ^
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1731:14: note: ‘ipt’ was declared here
1731 | int nfx, ipt, jpt;
| ^~~
In function ‘prelim_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2077:11,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:1942:46: warning: ‘jpt’ may be used uninitialized [-Wmaybe-uninitialized]
1942 | hq[ih] = (fbeg - fval[ipt + 1] - fval[jpt + 1] + f) / temp;
| ^
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1731:19: note: ‘jpt’ was declared here
1731 | int nfx, ipt, jpt;
| ^~~
In function ‘bobyqb_’,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:15:37: warning: ‘diffc’ may be used uninitialized [-Wmaybe-uninitialized]
15 | #define MAX2(a,b) ((a) >= (b) ? (a) : (b))
| ~~~~~~~~~~~~~~~~~~^~~~~~
nlopt/bobyqa/bobyqa.c:2176:18: note: in expansion of macro ‘MAX2’
2176 | errbig = MAX2(d__1,diffc);
| ^~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1982:50: note: ‘diffc’ was declared here
1982 | double gqsq, dist, sumw, sumz, diffa, diffb, diffc, hdiag;
| ^~~~~
In function ‘altmov_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2383:5,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:886:14: warning: ‘adelt’ may be used uninitialized [-Wmaybe-uninitialized]
886 | subd = *adelt / sqrt(distsq);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1984:26: note: ‘adelt’ was declared here
1984 | double alpha, delta, adelt, denom, fsave, bdtol, delsq;
| ^~~~~
nlopt/bobyqa/bobyqa.c:763:9: warning: ‘ksav’ may be used uninitialized [-Wmaybe-uninitialized]
763 | int ksav;
| ^~~~
In function ‘altmov_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2383:5,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:989:35: warning: ‘stpsav’ may be used uninitialized [-Wmaybe-uninitialized]
989 | temp = xopt[i__] + stpsav * (xpt[ksav + i__ * xpt_dim1] - xopt[i__]);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:768:52: note: ‘stpsav’ was declared here
768 | double dderiv, bigstp, predsq, presav, distsq, stpsav, wfixsq, wsqsav;
| ^~~~~~
In function ‘altmov_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2383:5,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:997:8: warning: ‘ibdsav’ may be used uninitialized [-Wmaybe-uninitialized]
997 | if (ibdsav < 0) {
| ^
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:767:9: note: ‘ibdsav’ was declared here
767 | int ibdsav;
| ^~~~~~
In function ‘altmov_’,
inlined from ‘bobyqb_’ at nlopt/bobyqa/bobyqa.c:2383:5,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:1077:22: warning: ‘step’ may be used uninitialized [-Wmaybe-uninitialized]
1077 | w[i__] = -step * glag[i__];
| ^~~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:764:12: note: ‘step’ was declared here
764 | double step, zero, curv;
| ^~~~
In function ‘bobyqb_’,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:2466:37: warning: ‘alpha’ may be used uninitialized [-Wmaybe-uninitialized]
2466 | denom = d__1 * d__1 + alpha * beta;
| ~~~~~~^~~~~~
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1984:12: note: ‘alpha’ was declared here
1984 | double alpha, delta, adelt, denom, fsave, bdtol, delsq;
| ^~~~~
In function ‘bobyqb_’,
inlined from ‘bobyqa’ at nlopt/bobyqa/bobyqa.c:3253:11:
nlopt/bobyqa/bobyqa.c:2467:12: warning: ‘cauchy’ may be used uninitialized [-Wmaybe-uninitialized]
2467 | if (denom < cauchy && cauchy > zero) {
| ^
nlopt/bobyqa/bobyqa.c: In function ‘bobyqa’:
nlopt/bobyqa/bobyqa.c:1989:20: note: ‘cauchy’ was declared here
1989 | double errbig, cauchy, fracsq, biglsq, densav;
| ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/cdirect/cdirect.c -o nlopt/cdirect/cdirect.o
nlopt/cdirect/cdirect.c: In function ‘cdirect’:
nlopt/cdirect/cdirect.c:593:12: warning: ‘<unknown>’ may be used uninitialized [-Wmaybe-uninitialized]
593 | ret = cdirect_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n, x, minf, stop,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
594 | magic_eps, which_alg);
| ~~~~~~~~~~~~~~~~~~~~~
nlopt/cdirect/cdirect.c:476:14: note: by argument 4 of type ‘const double *’ to ‘cdirect_unscaled’ declared here
476 | nlopt_result cdirect_unscaled(int n, nlopt_func f, void *f_data,
| ^~~~~~~~~~~~~~~~
nlopt/cdirect/cdirect.c:593:12: warning: ‘<unknown>’ may be used uninitialized [-Wmaybe-uninitialized]
593 | ret = cdirect_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n, x, minf, stop,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
594 | magic_eps, which_alg);
| ~~~~~~~~~~~~~~~~~~~~~
nlopt/cdirect/cdirect.c:476:14: note: by argument 5 of type ‘const double *’ to ‘cdirect_unscaled’ declared here
476 | nlopt_result cdirect_unscaled(int n, nlopt_func f, void *f_data,
| ^~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/cdirect/hybrid.c -o nlopt/cdirect/hybrid.o
nlopt/cdirect/hybrid.c: In function ‘cdirect_hybrid’:
nlopt/cdirect/hybrid.c:309:12: warning: ‘<unknown>’ may be used uninitialized [-Wmaybe-uninitialized]
309 | ret = cdirect_hybrid_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
310 | x, minf, stop, local_alg, local_maxeval,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
311 | randomized_div);
| ~~~~~~~~~~~~~~~
nlopt/cdirect/hybrid.c:227:14: note: by argument 4 of type ‘const double *’ to ‘cdirect_hybrid_unscaled’ declared here
227 | nlopt_result cdirect_hybrid_unscaled(int n, nlopt_func f, void *f_data,
| ^~~~~~~~~~~~~~~~~~~~~~~
nlopt/cdirect/hybrid.c:309:12: warning: ‘<unknown>’ may be used uninitialized [-Wmaybe-uninitialized]
309 | ret = cdirect_hybrid_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
310 | x, minf, stop, local_alg, local_maxeval,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
311 | randomized_div);
| ~~~~~~~~~~~~~~~
nlopt/cdirect/hybrid.c:227:14: note: by argument 5 of type ‘const double *’ to ‘cdirect_hybrid_unscaled’ declared here
227 | nlopt_result cdirect_hybrid_unscaled(int n, nlopt_func f, void *f_data,
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/crs/crs.c -o nlopt/crs/crs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/direct/DIRect.c -o nlopt/direct/DIRect.o
nlopt/direct/DIRect.c: In function ‘direct_direct_’:
nlopt/direct/DIRect.c:81:13: warning: variable ‘writed’ set but not used [-Wunused-but-set-variable]
81 | integer writed;
| ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/direct/direct_wrap.c -o nlopt/direct/direct_wrap.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/direct/DIRserial.c -o nlopt/direct/DIRserial.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/direct/DIRsubrout.c -o nlopt/direct/DIRsubrout.o
nlopt/direct/DIRsubrout.c: In function ‘direct_dirinit_’:
nlopt/direct/DIRsubrout.c:1157:16: warning: variable ‘costmin’ set but not used [-Wunused-but-set-variable]
1157 | doublereal costmin;
| ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/isres/isres.c -o nlopt/isres/isres.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/luksan/mssubs.c -o nlopt/luksan/mssubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/luksan/plip.c -o nlopt/luksan/plip.o
nlopt/luksan/plip.c: In function ‘plip_’:
nlopt/luksan/plip.c:142:9: warning: variable ‘meta’ set but not used [-Wunused-but-set-variable]
142 | int meta, mred, nred, iold;
| ^~~~
nlopt/luksan/plip.c:140:21: warning: variable ‘mes3’ set but not used [-Wunused-but-set-variable]
140 | int mes1, mes2, mes3, met3;
| ^~~~
nlopt/luksan/plip.c:140:15: warning: variable ‘mes2’ set but not used [-Wunused-but-set-variable]
140 | int mes1, mes2, mes3, met3;
| ^~~~
nlopt/luksan/plip.c:140:9: warning: variable ‘mes1’ set but not used [-Wunused-but-set-variable]
140 | int mes1, mes2, mes3, met3;
| ^~~~
nlopt/luksan/plip.c:139:24: warning: variable ‘eta0’ set but not used [-Wunused-but-set-variable]
139 | double alf1, alf2, eta0, eta9, par1, par2;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/luksan/plis.c -o nlopt/luksan/plis.o
nlopt/luksan/plis.c: In function ‘plis_’:
nlopt/luksan/plis.c:131:21: warning: variable ‘mes3’ set but not used [-Wunused-but-set-variable]
131 | int mes1, mes2, mes3;
| ^~~~
nlopt/luksan/plis.c:131:15: warning: variable ‘mes2’ set but not used [-Wunused-but-set-variable]
131 | int mes1, mes2, mes3;
| ^~~~
nlopt/luksan/plis.c:131:9: warning: variable ‘mes1’ set but not used [-Wunused-but-set-variable]
131 | int mes1, mes2, mes3;
| ^~~~
nlopt/luksan/plis.c:130:24: warning: variable ‘eta0’ set but not used [-Wunused-but-set-variable]
130 | double alf1, alf2, eta0, eta9, par1, par2;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/luksan/pnet.c -o nlopt/luksan/pnet.o
nlopt/luksan/pnet.c: In function ‘pnet_’:
nlopt/luksan/pnet.c:159:21: warning: variable ‘mes3’ set but not used [-Wunused-but-set-variable]
159 | int mes1, mes2, mes3;
| ^~~~
nlopt/luksan/pnet.c:159:15: warning: variable ‘mes2’ set but not used [-Wunused-but-set-variable]
159 | int mes1, mes2, mes3;
| ^~~~
nlopt/luksan/pnet.c:159:9: warning: variable ‘mes1’ set but not used [-Wunused-but-set-variable]
159 | int mes1, mes2, mes3;
| ^~~~
In function ‘pnet_’,
inlined from ‘luksan_pnet’ at nlopt/luksan/pnet.c:630:6:
nlopt/luksan/pnet.c:443:16: warning: ‘a’ may be used uninitialized [-Wmaybe-uninitialized]
443 | if (a > 0.) {
| ^
nlopt/luksan/pnet.c: In function ‘luksan_pnet’:
nlopt/luksan/pnet.c:147:12: note: ‘a’ was declared here
147 | double a, b;
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/luksan/pssubs.c -o nlopt/luksan/pssubs.o
nlopt/luksan/pssubs.c: In function ‘luksan_pulsp3__’:
nlopt/luksan/pssubs.c:527:18: warning: variable ‘c__’ set but not used [-Wunused-but-set-variable]
527 | double a, b, c__, aa, bb, ah, den, par, pom;
| ^~~
nlopt/luksan/pssubs.c: In function ‘luksan_pulvp3__’:
nlopt/luksan/pssubs.c:656:18: warning: variable ‘c__’ set but not used [-Wunused-but-set-variable]
656 | double a, b, c__, aa, bb, cc, ah, den, par, pom, zet;
| ^~~
nlopt/luksan/pssubs.c: In function ‘luksan_pnint1__’:
nlopt/luksan/pssubs.c:156:21: warning: ‘a’ may be used uninitialized [-Wmaybe-uninitialized]
156 | dis = a * a - b;
| ~~^~~
nlopt/luksan/pssubs.c:99:12: note: ‘a’ was declared here
99 | double a, b, c__, d__, den, dis;
| ^
nlopt/luksan/pssubs.c:156:17: warning: ‘b’ may be used uninitialized [-Wmaybe-uninitialized]
156 | dis = a * a - b;
| ~~~~^~~~~~~~~~~
nlopt/luksan/pssubs.c:99:15: note: ‘b’ was declared here
99 | double a, b, c__, d__, den, dis;
| ^
nlopt/luksan/pssubs.c:168:24: warning: ‘den’ may be used uninitialized [-Wmaybe-uninitialized]
168 | if (*mode == 1 && den > 0. && den < 1.) {
| ~~~~~~~~~~~^~~~~~~~~~~
nlopt/luksan/pssubs.c:99:28: note: ‘den’ was declared here
99 | double a, b, c__, d__, den, dis;
| ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/mlsl/mlsl.c -o nlopt/mlsl/mlsl.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/mma/ccsa_quadratic.c -o nlopt/mma/ccsa_quadratic.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/mma/mma.c -o nlopt/mma/mma.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/neldermead/nldrmd.c -o nlopt/neldermead/nldrmd.o
In file included from /usr/include/string.h:548,
from nlopt/neldermead/nldrmd.c:25:
In function ‘memset’,
inlined from ‘nldrmd_minimize_’ at nlopt/neldermead/nldrmd.c:200:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
59 | return __builtin___memset_chk (__dest, __ch, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
60 | __glibc_objsize0 (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/neldermead/sbplx.c -o nlopt/neldermead/sbplx.o
nlopt/neldermead/sbplx.c: In function ‘sbplx_minimize’:
nlopt/neldermead/sbplx.c:78:13: warning: variable ‘fprev’ set but not used [-Wunused-but-set-variable]
78 | double fprev;
| ^~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/newuoa/newuoa.c -o nlopt/newuoa/newuoa.o
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1799:12: warning: ‘xipt’ may be used uninitialized [-Wmaybe-uninitialized]
1799 | if (xipt < zero) {
| ^
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1596:18: note: ‘xipt’ was declared here
1596 | double zero, xipt, xjpt, sumz, diffa, diffb, diffc, hdiag, alpha,
| ^~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1802:12: warning: ‘xjpt’ may be used uninitialized [-Wmaybe-uninitialized]
1802 | if (xjpt < zero) {
| ^
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1596:24: note: ‘xjpt’ was declared here
1596 | double zero, xipt, xjpt, sumz, diffa, diffb, diffc, hdiag, alpha,
| ^~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:2151:8: warning: ‘rho’ may be used uninitialized [-Wmaybe-uninitialized]
2151 | if (dnorm > rho) {
| ^
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1588:17: note: ‘rho’ was declared here
1588 | double dsq, rho;
| ^~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1798:18: warning: ‘ipt’ may be used uninitialized [-Wmaybe-uninitialized]
1798 | ih = ipt * (ipt - 1) / 2 + jpt;
| ~~~~^~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1589:9: note: ‘ipt’ was declared here
1589 | int ipt, jpt;
| ^~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1798:12: warning: ‘jpt’ may be used uninitialized [-Wmaybe-uninitialized]
1798 | ih = ipt * (ipt - 1) / 2 + jpt;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1589:14: note: ‘jpt’ was declared here
1589 | int ipt, jpt;
| ^~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:2151:8: warning: ‘dnorm’ may be used uninitialized [-Wmaybe-uninitialized]
2151 | if (dnorm > rho) {
| ^
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1599:12: note: ‘dnorm’ was declared here
1599 | double dnorm, ratio, dstep, tenth, vquad;
| ^~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:2333:13: warning: ‘itest’ may be used uninitialized [-Wmaybe-uninitialized]
2333 | ++itest;
| ^~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1602:9: note: ‘itest’ was declared here
1602 | int itest;
| ^~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:2308:13: warning: ‘ratio’ may be used uninitialized [-Wmaybe-uninitialized]
2308 | if (fabs(ratio) > .01) {
| ^~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1599:19: note: ‘ratio’ was declared here
1599 | double dnorm, ratio, dstep, tenth, vquad;
| ^~~~~
In function ‘update_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:2261:5,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1462:29: warning: ‘tempb’ may be used uninitialized [-Wmaybe-uninitialized]
1462 | w[i__] += tempb * zmat[i__ + jl * zmat_dim1];
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1393:48: note: ‘tempb’ was declared here
1393 | double scala, scalb_, alpha, denom, tempa, tempb, tausq;
| ^~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1809:24: warning: ‘fbeg’ may be used uninitialized [-Wmaybe-uninitialized]
1809 | hq[ih] = (fbeg - fval[ipt + 1] - fval[jpt + 1] + f) / (xipt * xjpt);
| ~~~~~^~~~~~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1590:17: note: ‘fbeg’ was declared here
1590 | double sum, fbeg, diff, half, beta;
| ^~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:36:37: warning: ‘diffa’ may be used uninitialized [-Wmaybe-uninitialized]
36 | #define MAX2(a,b) ((a) >= (b) ? (a) : (b))
| ~~~~~~~~~~~~~~~~~~^~~~~~
nlopt/newuoa/newuoa.c:1867:16: note: in expansion of macro ‘MAX2’
1867 | d__1 = MAX2(diffa,diffb);
| ^~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1596:36: note: ‘diffa’ was declared here
1596 | double zero, xipt, xjpt, sumz, diffa, diffb, diffc, hdiag, alpha,
| ^~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:36:37: warning: ‘diffc’ may be used uninitialized [-Wmaybe-uninitialized]
36 | #define MAX2(a,b) ((a) >= (b) ? (a) : (b))
| ~~~~~~~~~~~~~~~~~~^~~~~~
nlopt/newuoa/newuoa.c:1868:21: note: in expansion of macro ‘MAX2’
1868 | if (temp <= MAX2(d__1,diffc)) {
| ^~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1596:50: note: ‘diffc’ was declared here
1596 | double zero, xipt, xjpt, sumz, diffa, diffb, diffc, hdiag, alpha,
| ^~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1862:25: warning: ‘nfsav’ may be used uninitialized [-Wmaybe-uninitialized]
1862 | if (nf <= nfsav + 2) {
| ~~~~~~^~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1598:16: note: ‘nfsav’ was declared here
1598 | int ksave, nfsav, itemp;
| ^~~~~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:266:14: warning: ‘dd’ may be used uninitialized [-Wmaybe-uninitialized]
266 | temp = dhd / dd;
| ~~~~~^~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:111:12: note: ‘dd’ was declared here
111 | double dd, cf, dg, gg;
| ^~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:275:24: warning: ‘gg’ may be used uninitialized [-Wmaybe-uninitialized]
275 | qadd = alpha * (gg - half * alpha * dhd);
| ~~~~^~~~~~~~~~~~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:111:24: note: ‘gg’ was declared here
111 | double dd, cf, dg, gg;
| ^~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:378:10: warning: ‘sg’ may be used uninitialized [-Wmaybe-uninitialized]
378 | qbeg = sg + cf;
| ~~~~~^~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:113:16: note: ‘sg’ was declared here
113 | double ds, sg;
| ^~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:377:22: warning: ‘shs’ may be used uninitialized [-Wmaybe-uninitialized]
377 | cf = half * (shs - dhd);
| ~~~~~^~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:115:36: note: ‘shs’ was declared here
115 | double ss, dhd, dhs, cth, sgk, shs, sth, qadd, half, qbeg, qred, qmin,
| ^~~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:276:10: warning: ‘qred’ may be used uninitialized [-Wmaybe-uninitialized]
276 | qred += qadd;
| ~~~~~^~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:115:64: note: ‘qred’ was declared here
115 | double ss, dhd, dhs, cth, sgk, shs, sth, qadd, half, qbeg, qred, qmin,
| ^~~~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:298:25: warning: ‘ggbeg’ may be used uninitialized [-Wmaybe-uninitialized]
298 | if (gg <= ggbeg * 1e-4) {
| ~~~~~~^~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:116:38: note: ‘ggbeg’ was declared here
116 | temp, qsav, qnew, zero, ggbeg, alpha, angle, reduc;
| ^~~~~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:275:10: warning: ‘bstep’ may be used uninitialized [-Wmaybe-uninitialized]
275 | qadd = alpha * (gg - half * alpha * dhd);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:120:12: note: ‘bstep’ was declared here
120 | double bstep, ratio, twopi;
| ^~~~~
In function ‘trsapp_’,
inlined from ‘newuob_’ at nlopt/newuoa/newuoa.c:1840:11,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:35:37: warning: ‘crvmin’ may be used uninitialized [-Wmaybe-uninitialized]
35 | #define MIN2(a,b) ((a) <= (b) ? (a) : (b))
| ~~~~~~~~~~~~~~~~~~^~~~~~
nlopt/newuoa/newuoa.c:270:19: note: in expansion of macro ‘MIN2’
270 | *crvmin = MIN2(*crvmin,temp);
| ^~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1604:20: note: ‘crvmin’ was declared here
1604 | double detrat, crvmin;
| ^~~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:1878:23: warning: ‘xoptsq’ may be used uninitialized [-Wmaybe-uninitialized]
1878 | if (dsq <= xoptsq * .001) {
| ~~~~~~~^~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1606:12: note: ‘xoptsq’ was declared here
1606 | double xoptsq;
| ^~~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:2073:28: warning: ‘alpha’ may be used uninitialized [-Wmaybe-uninitialized]
2073 | temp = one + alpha * beta / (d__1 * d__1);
| ~~~~~~^~~~~~
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1596:64: note: ‘alpha’ was declared here
1596 | double zero, xipt, xjpt, sumz, diffa, diffb, diffc, hdiag, alpha,
| ^~~~~
In function ‘newuob_’,
inlined from ‘newuoa’ at nlopt/newuoa/newuoa.c:2548:11:
nlopt/newuoa/newuoa.c:2457:8: warning: ‘f’ may be used uninitialized [-Wmaybe-uninitialized]
2457 | if (fopt <= f) {
| ^
nlopt/newuoa/newuoa.c: In function ‘newuoa’:
nlopt/newuoa/newuoa.c:1582:12: note: ‘f’ was declared here
1582 | double f;
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/praxis/praxis.c -o nlopt/praxis/praxis.o
In function ‘minfit_’,
inlined from ‘praxis_’ at nlopt/praxis/praxis.c:530:5:
nlopt/praxis/praxis.c:715:12: warning: ‘f’ may be used uninitialized [-Wmaybe-uninitialized]
715 | if (f >= 0.) {
| ^
nlopt/praxis/praxis.c: In function ‘praxis_’:
nlopt/praxis/praxis.c:625:17: note: ‘f’ was declared here
625 | double c__, f, g, h__;
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/slsqp/slsqp.c -o nlopt/slsqp/slsqp.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/mt19937ar.c -o nlopt/util/mt19937ar.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/qsort_r.c -o nlopt/util/qsort_r.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/redblack.c -o nlopt/util/redblack.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/rescale.c -o nlopt/util/rescale.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/sobolseq.c -o nlopt/util/sobolseq.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/stop.c -o nlopt/util/stop.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fpic -g -O2 -Wall -Werror=format-security -c nlopt/util/timer.c -o nlopt/util/timer.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_common/BaitClass.cpp -o saint_common/BaitClass.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_common/PreyClass.cpp -o saint_common/PreyClass.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_common/InterClass.cpp -o saint_common/InterClass.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_common/UIClass.cpp -o saint_common/UIClass.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_spc/SpcStats.cpp -o saint_spc/SpcStats.o
saint_spc/SpcStats.cpp: In function ‘saint_spc::Model_data saint_spc::statModel(const Options&, const std::vector<std::vector<long unsigned int> >&, const std::vector<std::__cxx11::basic_string<char> >&, const Countmat&, const Countmat&, const std::vector<long unsigned int>&, size_t, size_t)’:
saint_spc/SpcStats.cpp:62:17: warning: label ‘mu_init’ defined but not used [-Wunused-label]
62 | mu_init:
| ^~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_spc/SpcStats_fns.cpp -o saint_spc/SpcStats_fns.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_spc/SpcMapping.cpp -o saint_spc/SpcMapping.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c SpcEntry.cpp -o SpcEntry.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_int/IntStats.cpp -o saint_int/IntStats.o
saint_int/IntStats.cpp: In function ‘saint_int::Model_data saint_int::statModel(const Options&, const std::vector<std::vector<long unsigned int> >&, const std::vector<std::__cxx11::basic_string<char> >&, const Quantmat&, const Quantmat&, const std::vector<long unsigned int>&, size_t, size_t)’:
saint_int/IntStats.cpp:92:13: warning: unused variable ‘L’ [-Wunused-variable]
92 | int L = min<size_t>(n_ctrl_ip, L_user_input);
| ^
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c saint_int/IntMapping.cpp -o saint_int/IntMapping.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c IntEntry.cpp -o IntEntry.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c GetDICE.cpp -o GetDICE.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c GetPPN.cpp -o GetPPN.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o SMAD.so nlopt/api/deprecated.o nlopt/api/general.o nlopt/api/optimize.o nlopt/api/options.o nlopt/cobyla/cobyla.o nlopt/auglag/auglag.o nlopt/bobyqa/bobyqa.o nlopt/cdirect/cdirect.o nlopt/cdirect/hybrid.o nlopt/crs/crs.o nlopt/direct/DIRect.o nlopt/direct/direct_wrap.o nlopt/direct/DIRserial.o nlopt/direct/DIRsubrout.o nlopt/isres/isres.o nlopt/luksan/mssubs.o nlopt/luksan/plip.o nlopt/luksan/plis.o nlopt/luksan/pnet.o nlopt/luksan/pssubs.o nlopt/mlsl/mlsl.o nlopt/mma/ccsa_quadratic.o nlopt/mma/mma.o nlopt/neldermead/nldrmd.o nlopt/neldermead/sbplx.o nlopt/newuoa/newuoa.o nlopt/praxis/praxis.o nlopt/slsqp/slsqp.o nlopt/util/mt19937ar.o nlopt/util/qsort_r.o nlopt/util/redblack.o nlopt/util/rescale.o nlopt/util/sobolseq.o nlopt/util/stop.o nlopt/util/timer.o saint_common/BaitClass.o saint_common/PreyClass.o saint_common/InterClass.o saint_common/UIClass.o saint_spc/SpcStats.o saint_spc/SpcStats_fns.o saint_spc/SpcMapping.o SpcEntry.o saint_int/IntStats.o saint_int/IntMapping.o IntEntry.o GetDICE.o GetPPN.o RcppExports.o -fopenmp -lm -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-SMAD/00new/SMAD/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 (SMAD)
