* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘vegan’ ...
** package ‘vegan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmKDwZD/R.INSTALL30215e1291b89f/vegan/src'
gcc-14 -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 data2hill.c -o data2hill.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c decorana.f -o decorana.o
gcc-14 -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 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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/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,
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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,
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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"/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 goffactor.c -o goffactor.o
gcc-14 -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
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c monoMDS.f -o monoMDS.o
gcc-14 -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 nestedness.c -o nestedness.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c ordering.f -o ordering.o
gcc-14 -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 pnpoly.c -o pnpoly.o
gcc-14 -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 stepacross.c -o stepacross.o
gcc-14 -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 vegdist.c -o vegdist.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmKDwZD/R.INSTALL30215e1291b89f/vegan/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmKDwZD/R.INSTALL30215e1291b89f/vegan/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmKDwZD/R.INSTALL30215e1291b89f/vegan/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-vegan/00new/vegan/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘vegan’
finding HTML links ... done
BCI html
CCorA html
MDSrotate html
MOStest html
RsquareAdj html
SSarrhenius html
add1.cca html
adipart html
adonis html
anosim html
anova.cca html
avgdist html
beals html
betadisper html
betadiver html
bgdispersal html
bioenv html
biplot.rda html
cascadeKM html
cca html
cca.object html
clamtest html
commsim html
contribdiv html
dbrda html
decorana html
decostand html
designdist html
deviance.cca html
dispindmorisita html
dispweight html
distconnected html
diversity html
dune html
dune.taxon html
eigenvals html
envfit html
eventstar html
fisherfit html
goodness.cca html
goodness.metaMDS html
indpower html
influence.cca html
isomap html
kendall.global html
linestack html
make.cepnames html
mantel html
mantel.correlog html
metaMDS html
mite html
monoMDS html
mrpp html
mso html
multipart html
nestedtemp html
nobs.cca html
nullmodel html
oecosimu html
ordiArrowTextXY html
ordiarrows html
ordihull html
ordilabel html
ordiplot html
ordipointlabel html
ordiresids html
ordistep html
ordisurf html
orditorp html
ordixyplot html
pcnm html
permatfull html
permustats html
permutations html
permutest.betadisper html
plot.cca html
prc html
predict.cca html
procrustes html
pyrifos html
radfit html
rankindex html
rarefy html
raupcrick html
read.cep html
renyi html
reorder.hclust html
scores html
screeplot.cca html
simper html
simulate.rda html
sipoo html
spantree html
specaccum html
specpool html
sppscores html
stepacross html
stressplot.wcmdscale html
taxondive html
tolerance html
treedive html
tsallis html
varechem html
varpart html
vegan-defunct html
vegan-deprecated html
REDIRECT:topic Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-vegan/00new/vegan/help/adonis.html
vegan-internal html
vegan-package html
vegdist html
vegemite html
wascores html
wcmdscale html
** 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)