* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mvabund’ ...
** package ‘mvabund’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/Rtmpj8UW2P/R.INSTALL10234f56c7864c/mvabund/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rinterface.cpp -o Rinterface.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c anova.cpp -o anova.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calctest.cpp -o calctest.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glm.cpp -o glm.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glmtest.cpp -o glmtest.o
glmtest.cpp: In member function ‘int GlmTest::resampNonCase(glm*, gsl_matrix*, unsigned int)’:
glmtest.cpp:849:23: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized]
849 | gsl_sort_index(permid, tmp, 1, nRows);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from resampTest.h:26,
from glmtest.cpp:5:
/usr/include/gsl/gsl_sort_double.h:41:6: note: by argument 2 of type ‘const double*’ to ‘void gsl_sort_index(size_t*, const double*, size_t, size_t)’ declared here
41 | void gsl_sort_index (size_t * p, const double * data, const size_t stride, const size_t n);
| ^~~~~~~~~~~~~~
glmtest.cpp:876:23: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized]
876 | gsl_sort_index(permid, tmp, 1, nRows);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/gsl/gsl_sort_double.h:41:6: note: by argument 2 of type ‘const double*’ to ‘void gsl_sort_index(size_t*, const double*, size_t, size_t)’ declared here
41 | void gsl_sort_index (size_t * p, const double * data, const size_t stride, const size_t n);
| ^~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c io.cpp -o io.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rnd.cpp -o rnd.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simutility.cpp -o simutility.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c summary.cpp -o summary.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o mvabund.so RcppExports.o Rinterface.o anova.o calctest.o glm.o glmtest.o io.o rnd.o simutility.o summary.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpj8UW2P/R.INSTALL10234f56c7864c/mvabund/src'
make[1]: Entering directory '/tmp/Rtmpj8UW2P/R.INSTALL10234f56c7864c/mvabund/src'
make[1]: Leaving directory '/tmp/Rtmpj8UW2P/R.INSTALL10234f56c7864c/mvabund/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mvabund/00new/mvabund/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘mvabund’
finding HTML links ... done
Tasmania html
anova.manyany html
anova.manyglm html
anova.manylm html
anova.traitglm html
antTraits html
best.r.sq html
boxplot.mvabund html
coefplot.manyglm html
cv.glm1path html
deviance.manylm html
extend.x.formula html
formulaUnimva html
glm1 html
glm1path html
logLik.manylm html
manyany html
manyglm html
manylm html
manylm.fit html
meanvar.plot html
mvabund-internal html
mvabund-package html
mvabund html
mvformula html
plot.manyany html
plot.manylm html
plot.mvabund html
plotMvaFactor html
predict.manyglm html
predict.manylm html
predict.traitglm html
residuals.manyglm html
ridgeParamEst html
shiftpoints html
solberg html
spider html
summary.manyglm html
summary.manylm html
tikus html
traitglm html
unabund 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 (mvabund)