* installing *source* package ‘vegan’ ...
** package ‘vegan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/vegan/src'
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 data2hill.c -o data2hill.o
gfortran-14 -fpic -g -O2 -mtune=native -Wall -pedantic -c decorana.f -o decorana.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 getF.c -o getF.o
getF.c: In function 'do_getF':
getF.c:436:13: warning: 'wperm' may be used uninitialized [-Wmaybe-uninitialized]
436 | wcentre(Xorig, qr, wperm, &nr, &nx);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
getF.c:347:13: note: 'wperm' was declared here
347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7;
| ^~~~~
getF.c:436:13: warning: 'Xorig' may be used uninitialized [-Wmaybe-uninitialized]
436 | wcentre(Xorig, qr, wperm, &nr, &nx);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
getF.c:347:21: note: 'Xorig' was declared here
347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7;
| ^~~~~
getF.c:347:29: warning: 'Zorig' may be used uninitialized [-Wmaybe-uninitialized]
347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7;
| ^~~~~
getF.c:347:37: warning: 'Zperm' may be used uninitialized [-Wmaybe-uninitialized]
347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7;
| ^~~~~
In file included from /data/gannet/ripley/R/R-devel/include/R.h:78,
from getF.c:11:
getF.c:446:22: warning: 'qrwork' may be used uninitialized [-Wmaybe-uninitialized]
446 | F77_CALL(dqrdc2)(qr, &nr, &nr, &nx, &qrtol, &qrank,
| ^
/data/gannet/ripley/R/R-devel/include/R_ext/RS.h:104:25: note: in definition of macro 'F77_CALL'
104 | # define F77_CALL(x) x ## _
| ^
getF.c:347:45: note: 'qrwork' was declared here
347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7;
| ^~~~~~
getF.c:472:22: warning: 'resid' may be used uninitialized [-Wmaybe-uninitialized]
472 | F77_CALL(dqrsl)(qr, &nr, &nr, &qrank, qraux, rY + i*nr, &dummy,
| ^
/data/gannet/ripley/R/R-devel/include/R_ext/RS.h:104:25: note: in definition of macro 'F77_CALL'
104 | # define F77_CALL(x) x ## _
| ^
getF.c:335:13: note: 'resid' was declared here
335 | double *resid;
| ^~~~~
getF.c:370:13: warning: 'transY' may be used uninitialized [-Wmaybe-uninitialized]
370 | double *transY;
| ^~~~~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 goffactor.c -o goffactor.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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
gfortran-14 -fpic -g -O2 -mtune=native -Wall -pedantic -c monoMDS.f -o monoMDS.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 nestedness.c -o nestedness.o
gfortran-14 -fpic -g -O2 -mtune=native -Wall -pedantic -c ordering.f -o ordering.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 pnpoly.c -o pnpoly.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 stepacross.c -o stepacross.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 vegdist.c -o vegdist.o
gcc-14 -shared -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 -fpic -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o vegan.so data2hill.o decorana.o getF.o goffactor.o init.o monoMDS.o nestedness.o ordering.o pnpoly.o stepacross.o vegdist.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/vegan/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/vegan/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/vegan/src'
installing to /data/gannet/ripley/R/packages/tests-devel/vegan.Rcheck/00LOCK-vegan/00new/vegan/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 (vegan)