* installing *source* package ‘gremlin’ ...
** package ‘gremlin’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gremlin/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c ai.cc -o ai.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c chol2inv_ii.c -o chol2inv_ii.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs.c -o cs.o
cs.c: In function 'cs_realloc':
cs.c:1199:26: warning: pointer 'p' may be used after 'realloc' [-Wuse-after-free]
1199 | return ((*ok) ? pnew : p) ; /* return original p if failure */
| ~~~~~~~~~~~~~~^~~~
cs.c:1197:12: note: call to 'realloc' here
1197 | pnew = realloc (p, CS_MAX (n,1) * size) ; /* realloc the block */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_cov2cor.c -o cs_cov2cor.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_directsum.c -o cs_directsum.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_directsumupdate.c -o cs_directsumupdate.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c cs_droprowcol.cc -o cs_droprowcol.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_inv.c -o cs_inv.o
cs_inv.c: In function 'cs_inv':
cs_inv.c:52:10: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized]
52 | if (irow != icol) {
| ^
cs_inv.c:7:15: note: 'icol' was declared here
7 | int n, i, icol,irow,j,k,l,ll;
| ^~~~
cs_inv.c:52:10: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized]
52 | if (irow != icol) {
| ^
cs_inv.c:7:20: note: 'irow' was declared here
7 | int n, i, icol,irow,j,k,l,ll;
| ^~~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_inv_withDiagMod.c -o cs_inv_withDiagMod.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerA.c -o cs_kroneckerA.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerAupdate.c -o cs_kroneckerAupdate.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerI.c -o cs_kroneckerI.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerIupdate.c -o cs_kroneckerIupdate.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_omega.c -o cs_omega.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_omegaupdate.c -o cs_omegaupdate.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_schur.c -o cs_schur.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c gradFun.cc -o gradFun.o
gradFun.cc: In function 'int gradFun_fd(double*, int, double, double*, double, int*, double*, int, int, int*, int, int, double*, cs*, cs*, cs*, int*, double, int*, cs**, cs*, cs*, cs*, cs*, cs*, css*, double, int, int*, int*, int*, int)':
gradFun.cc:230:22: warning: 'tWKRinv' may be used uninitialized [-Wmaybe-uninitialized]
230 | Lc = reml(n, dimZWG, nG, p, y,
| ~~~~^~~~~~~~~~~~~~~~~~~~~
231 | Bpinv, W, tW, rfxlvls, rfxlL,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | R, Rinv, G, Ginv, ndgeninv, geninv,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | KRinv, KGinv, tWKRinv, tWKRinvW, Ctmp,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | RHS, tmpBLUXs, BLUXs, r,
| ~~~~~~~~~~~~~~~~~~~~~~~~
235 | sLc,
| ~~~~
236 | &tyPy, &logDetC, &sigma2e,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
237 | tyRinvy,
| ~~~~~~~~
238 | nminffx,
| ~~~~~~~~
239 | &loglik,
| ~~~~~~~~
240 | 1, 0, 0, lmbda);
| ~~~~~~~~~~~~~~~
gradFun.cc:106:23: note: 'tWKRinv' was declared here
106 | cs *R, *Rinv, *tWKRinv, *tWKRinvW, *ttWKRinvW;
| ^~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c gremlin.cc -o gremlin.o
gremlin.cc: In function 'void ugremlin(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, int*, int*, int*, int*, int*, int*, int*, double*, int*, double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, double*, double*, double*, double*, int*, int*, double*, int*)':
gremlin.cc:439:14: warning: 'KRinv' may be used uninitialized [-Wmaybe-uninitialized]
439 | Lc = reml(ny[0], dimZWG, nG, p[0], y,
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | Bpinv, W, tW, rfxlvls, rfxlL[0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | R, Rinv, G, Ginv, ndgeninv, geninv,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | KRinv, KGinv, tWKRinv, tWKRinvW, Ctmp,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | RHS, tmpBLUXs, BLUXs, res,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | sLc,
| ~~~~
445 | &tyPy, &logDetC, &sigma2e,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
446 | tyRinvy,
| ~~~~~~~~
447 | nminffx[0],
| ~~~~~~~~~~~
448 | &loglik,
| ~~~~~~~~
449 | i, v[0], vitout, lambda[0]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
gremlin.cc:99:22: note: 'KRinv' was declared here
99 | *R, *Rinv, *KRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~~
gremlin.cc:439:14: warning: 'tWKRinv' may be used uninitialized [-Wmaybe-uninitialized]
439 | Lc = reml(ny[0], dimZWG, nG, p[0], y,
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | Bpinv, W, tW, rfxlvls, rfxlL[0],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | R, Rinv, G, Ginv, ndgeninv, geninv,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | KRinv, KGinv, tWKRinv, tWKRinvW, Ctmp,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | RHS, tmpBLUXs, BLUXs, res,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | sLc,
| ~~~~
445 | &tyPy, &logDetC, &sigma2e,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
446 | tyRinvy,
| ~~~~~~~~
447 | nminffx[0],
| ~~~~~~~~~~~
448 | &loglik,
| ~~~~~~~~
449 | i, v[0], vitout, lambda[0]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
gremlin.cc:99:30: note: 'tWKRinv' was declared here
99 | *R, *Rinv, *KRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~~~~
gremlin.cc:380:29: warning: 'tWKRinvW' may be used uninitialized [-Wmaybe-uninitialized]
380 | ttWKRinvW = cs_transpose(tWKRinvW, true);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~
gremlin.cc:99:40: note: 'tWKRinvW' was declared here
99 | *R, *Rinv, *KRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~~~~~
gremlin.cc:1064:18: warning: 'R' may be used uninitialized [-Wmaybe-uninitialized]
1064 | AI = ai(BLUXs, Ginv, R, KRinv, tWKRinv,
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1065 | res, W, tW, ny[0], p[0], nG, rfxlvls, nffx, Lc->L, sLc->pinv,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1066 | nG, 1.0);
| ~~~~~~~~
gremlin.cc:99:11: note: 'R' was declared here
99 | *R, *Rinv, *KRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^
gremlin.cc:1036:24: warning: 'prtCinv' may be used uninitialized [-Wmaybe-uninitialized]
1036 | CinvX = chol2inv_ii(Lc->L, sLc->pinv, prtCinv, Zdiagp, Cinv_ii, CinvX);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gremlin.cc:100:22: note: 'prtCinv' was declared here
100 | *Ctmp, *C, *prtCinv,
| ^~~~~~~
gremlin.cc:1036:37: warning: 'sLc' may be used uninitialized [-Wmaybe-uninitialized]
1036 | CinvX = chol2inv_ii(Lc->L, sLc->pinv, prtCinv, Zdiagp, Cinv_ii, CinvX);
| ~~~~~^~~~
gremlin.cc:105:11: note: 'sLc' was declared here
105 | css *sLc;
| ^~~
gremlin.cc:1036:29: warning: 'Lc' may be used uninitialized [-Wmaybe-uninitialized]
1036 | CinvX = chol2inv_ii(Lc->L, sLc->pinv, prtCinv, Zdiagp, Cinv_ii, CinvX);
| ~~~~^
gremlin.cc:106:11: note: 'Lc' was declared here
106 | csn *Lc;
| ^~
gremlin.cc:1136:12: warning: 'Ctmp' may be used uninitialized [-Wmaybe-uninitialized]
1136 | cs_spfree(Ctmp); cs_spfree(prtCinv);
| ~~~~~~~~~^~~~~~
gremlin.cc:100:11: note: 'Ctmp' was declared here
100 | *Ctmp, *C, *prtCinv,
| ^~~~
gremlin.cc:1129:26: warning: 'Rinv' may be used uninitialized [-Wmaybe-uninitialized]
1129 | cs_spfree(R); cs_spfree(Rinv);
| ~~~~~~~~~^~~~~~
gremlin.cc:99:15: note: 'Rinv' was declared here
99 | *R, *Rinv, *KRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c qNewtRhap.cc -o qNewtRhap.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c reml.cc -o reml.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c tugug_trace.cc -o tugug_trace.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o gremlin.so ai.o chol2inv_ii.o cs.o cs_cov2cor.o cs_directsum.o cs_directsumupdate.o cs_droprowcol.o cs_inv.o cs_inv_withDiagMod.o cs_kroneckerA.o cs_kroneckerAupdate.o cs_kroneckerI.o cs_kroneckerIupdate.o cs_omega.o cs_omegaupdate.o cs_schur.o gradFun.o gremlin.o init.o qNewtRhap.o reml.o tugug_trace.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gremlin/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gremlin/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gremlin/src'
installing to /data/gannet/ripley/R/packages/tests-devel/gremlin.Rcheck/00LOCK-gremlin/00new/gremlin/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (gremlin)