* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘gremlin’ ...
** package ‘gremlin’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp6KJOxo/R.INSTALL29bf4419428a27/gremlin/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ai.cc -o ai.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_cbind.c -o cs_cbind.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_chol2inv_ii.c -o cs_chol2inv_ii.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_cov2cor.c -o cs_cov2cor.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_directsum.c -o cs_directsum.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_directsumupdate.c -o cs_directsumupdate.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cs_droprowcol.cc -o cs_droprowcol.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_kroneckerA.c -o cs_kroneckerA.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_kroneckerAupdate.c -o cs_kroneckerAupdate.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_kroneckerI.c -o cs_kroneckerI.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_kroneckerIupdate.c -o cs_kroneckerIupdate.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_omega.c -o cs_omega.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_omegaupdate.c -o cs_omegaupdate.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_schur.c -o cs_schur.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gradFun.cc -o gradFun.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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*, double*, double*, double*, double*, int*, int*, int*)’:
gremlin.cc:516:28: warning: ‘KRinv’ may be used uninitialized [-Wmaybe-uninitialized]
516 | cs_kroneckerIupdate(Rinv, dimZWG[2], KRinv);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
gremlin.cc:97:22: note: ‘KRinv’ was declared here
97 | *R, *Rinv, *KRinv, *tyRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~~
gremlin.cc:520:17: warning: ‘tyRinv’ may be used uninitialized [-Wmaybe-uninitialized]
520 | cs_gaxpy(KRinv, y, tyRinv->x); // y = A*x+y XXX my `y` is cs_gaxpy's `x`
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
gremlin.cc:97:30: note: ‘tyRinv’ was declared here
97 | *R, *Rinv, *KRinv, *tyRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~~~
gremlin.cc:560:19: warning: ‘Ctmp’ may be used uninitialized [-Wmaybe-uninitialized]
560 | C = cs_add(tWKRinvW, Ctmp, 1.0, 1.0);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
gremlin.cc:98:11: note: ‘Ctmp’ was declared here
98 | *Ctmp, *C,
| ^~~~
gremlin.cc:1192:15: warning: ‘tWKRinv’ may be used uninitialized [-Wmaybe-uninitialized]
1192 | if(cs_ai(AI, BLUXs, Ginv, R, KRinv, tWKRinv,
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1193 | res, W, tW, ny[0], p[0], nG, rfxlvls, nffx, Lc->L, sLc->pinv,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1194 | nG, 1.0) == 0){
| ~~~~~~~~
gremlin.cc:97:39: note: ‘tWKRinv’ was declared here
97 | *R, *Rinv, *KRinv, *tyRinv, *tWKRinv, *tWKRinvW, *ttWKRinvW,
| ^~~~~~~
gremlin.cc:1168:22: warning: ‘Lc’ may be used uninitialized [-Wmaybe-uninitialized]
1168 | cs_chol2inv_ii(Lc->L, sLc->pinv, Cinv_ii, 0);
| ~~~~^
gremlin.cc:103:11: note: ‘Lc’ was declared here
103 | csn *Lc;
| ^~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c qNewtRhap.cc -o qNewtRhap.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tugug_trace.cc -o tugug_trace.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o gremlin.so ai.o cs.o cs_cbind.o cs_chol2inv_ii.o cs_cov2cor.o cs_directsum.o cs_directsumupdate.o cs_droprowcol.o cs_inv.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 tugug_trace.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp6KJOxo/R.INSTALL29bf4419428a27/gremlin/src'
make[1]: Entering directory '/tmp/Rtmp6KJOxo/R.INSTALL29bf4419428a27/gremlin/src'
make[1]: Leaving directory '/tmp/Rtmp6KJOxo/R.INSTALL29bf4419428a27/gremlin/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-gremlin/00new/gremlin/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘gremlin’
finding HTML links ... done
Mrode11 html
anova.gremlin html
covFun html
deltaSE html
fixef.gremlin html
gremlin-package html
gremlin html
gremlinControl html
logLik.gremlin html
nobs.gremlin html
reml html
remlIt html
residuals.gremlin html
runtime html
summary.gremlin html
tr html
** 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)