Install log for 'mvabund'

* installing *source* package ‘mvabund’ ...
** package ‘mvabund’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mvabund/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c Rinterface.cpp -o Rinterface.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c anova.cpp -o anova.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c calctest.cpp -o calctest.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c glm.cpp -o glm.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c glmtest.cpp -o glmtest.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c io.cpp -o io.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c rnd.cpp -o rnd.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c simutility.cpp -o simutility.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include    -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   -c summary.cpp -o summary.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 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o mvabund.so RcppExports.o Rinterface.o anova.o calctest.o glm.o glmtest.o io.o rnd.o simutility.o summary.o -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mvabund/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mvabund/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mvabund/src'
installing to /data/gannet/ripley/R/packages/tests-devel/mvabund.Rcheck/00LOCK-mvabund/00new/mvabund/libs
** R
** data
** 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 (mvabund)