* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ape/src'
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 BIONJ.c -o BIONJ.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 NNI.c -o NNI.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/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
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 SPR.c -o SPR.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 additive.c -o additive.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 ape.c -o ape.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 bNNI.c -o bNNI.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 bionjs.c -o bionjs.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 bipartition.c -o bipartition.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 bitsplits.c -o bitsplits.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 delta_plot.c -o delta_plot.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 dist_dna.c -o dist_dna.o
dist_dna.c: In function 'distDNA_LogDet':
dist_dna.c:822:17: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
  822 |     case 40 : m += 8; break;\
      |               ~~^~~~
dist_dna.c:860:17: note: in expansion of macro 'DO_CONTINGENCY_NUCLEOTIDES'
  860 |                 DO_CONTINGENCY_NUCLEOTIDES
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:850:20: note: 'm' was declared here
  850 |     int i1, i2, k, m, s1, s2, target, L, Ntab[16], ndim = 4, info, ipiv[16];
      |                    ^
dist_dna.c: In function 'distDNA_LogDet_pairdel':
dist_dna.c:822:17: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
  822 |     case 40 : m += 8; break;\
      |               ~~^~~~
dist_dna.c:881:17: note: in expansion of macro 'DO_CONTINGENCY_NUCLEOTIDES'
  881 |                 DO_CONTINGENCY_NUCLEOTIDES
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:871:20: note: 'm' was declared here
  871 |     int i1, i2, k, m, s1, s2, target, L, Ntab[16], ndim = 4, info, ipiv[16];
      |                    ^
dist_dna.c: In function 'distDNA_BH87':
dist_dna.c:822:17: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
  822 |     case 40 : m += 8; break;\
      |               ~~^~~~
dist_dna.c:903:17: note: in expansion of macro 'DO_CONTINGENCY_NUCLEOTIDES'
  903 |                 DO_CONTINGENCY_NUCLEOTIDES
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:896:32: note: 'm' was declared here
  896 |     int i1, i2, k, kb, s1, s2, m, Ntab[16], ROWsums[4];
      |                                ^
dist_dna.c: In function 'distDNA_ParaLin':
dist_dna.c:822:17: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
  822 |     case 40 : m += 8; break;\
      |               ~~^~~~
dist_dna.c:1001:17: note: in expansion of macro 'DO_CONTINGENCY_NUCLEOTIDES'
 1001 |                 DO_CONTINGENCY_NUCLEOTIDES
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:973:28: note: 'm' was declared here
  973 |     int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16];
      |                            ^
dist_dna.c: In function 'distDNA_ParaLin_pairdel':
dist_dna.c:822:17: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
  822 |     case 40 : m += 8; break;\
      |               ~~^~~~
dist_dna.c:1046:17: note: in expansion of macro 'DO_CONTINGENCY_NUCLEOTIDES'
 1046 |                 DO_CONTINGENCY_NUCLEOTIDES
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:1012:28: note: 'm' was declared here
 1012 |     int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16];
      |                            ^
dist_dna.c: In function 'dist_dna':
dist_dna.c:1342:13: warning: 'var' may be used uninitialized [-Wmaybe-uninitialized]
 1342 |             distDNA_ParaLin(x, n, s, d, variance, var);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:1233:29: note: 'var' was declared here
 1233 |     double *BF, alpha, *d, *var;
      |                             ^~~
dist_dna.c:1318:13: warning: 'alpha' may be used uninitialized [-Wmaybe-uninitialized]
 1318 |             distDNA_TN93(x, n, s, d, BF, variance, var, gamma, alpha);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dist_dna.c:1233:17: note: 'alpha' was declared here
 1233 |     double *BF, alpha, *d, *var;
      |                 ^~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 dist_nodes.c -o dist_nodes.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 ewLasso.c -o ewLasso.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 heap.c -o heap.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 mat_expo.c -o mat_expo.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 me.c -o me.o
me.c: In function 'detrifurcate':
me.c:295:11: warning: 'w' may be used uninitialized [-Wmaybe-uninitialized]
  295 |   T->root = w;
      |   ~~~~~~~~^~~
me.c:275:13: note: 'w' was declared here
  275 |   node *v, *w;
      |             ^
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 me_balanced.c -o me_balanced.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 me_ols.c -o me_ols.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 mvr.c -o mvr.o
mvr.c: In function 'C_mvr':
mvr.c:97:37: warning: 'OTU1' may be used uninitialized [-Wmaybe-uninitialized]
   97 |                 edge2[k] = otu_label[OTU1];
      |                                     ^
mvr.c:13:39: note: 'OTU1' was declared here
   13 |         int n, i, j, k, ij, smallest, OTU1, OTU2, cur_nod, o_l, *otu_label;
      |                                       ^~~~
mvr.c:98:41: warning: 'OTU2' may be used uninitialized [-Wmaybe-uninitialized]
   98 |                 edge2[k + 1] = otu_label[OTU2];
      |                                         ^
mvr.c:13:45: note: 'OTU2' was declared here
   13 |         int n, i, j, k, ij, smallest, OTU1, OTU2, cur_nod, o_l, *otu_label;
      |                                             ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 mvrs.c -o mvrs.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 nj.c -o nj.o
nj.c: In function 'C_nj':
nj.c:111:14: warning: 'smallest' may be used uninitialized [-Wmaybe-uninitialized]
  111 |         A = D[smallest];
      |              ^
nj.c:56:53: note: 'smallest' was declared here
   56 |     int n, i, j, k, ij, *edge, cur_nod, *otu_label, smallest, OTU1, OTU2, Nedge;
      |                                                     ^~~~~~~~
nj.c:102:36: warning: 'OTU1' may be used uninitialized [-Wmaybe-uninitialized]
  102 |         edge[k + Nedge] = otu_label[OTU1];
      |                                    ^
nj.c:56:63: note: 'OTU1' was declared here
   56 |     int n, i, j, k, ij, *edge, cur_nod, *otu_label, smallest, OTU1, OTU2, Nedge;
      |                                                               ^~~~
nj.c:103:40: warning: 'OTU2' may be used uninitialized [-Wmaybe-uninitialized]
  103 |         edge[k + 1 + Nedge] = otu_label[OTU2];
      |                                        ^
nj.c:56:69: note: 'OTU2' was declared here
   56 |     int n, i, j, k, ij, *edge, cur_nod, *otu_label, smallest, OTU1, OTU2, Nedge;
      |                                                                     ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 njs.c -o njs.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 pic.c -o pic.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 plot_phylo.c -o plot_phylo.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/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 prop_part.cpp -o prop_part.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 rTrait.c -o rTrait.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 read_dna.c -o read_dna.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/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 reorder_Rcpp.cpp -o reorder_Rcpp.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 reorder_phylo.c -o reorder_phylo.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 treePop.c -o treePop.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 tree_build.c -o tree_build.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 tree_phylo.c -o tree_phylo.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 triangMtd.c -o triangMtd.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 triangMtds.c -o triangMtds.o
triangMtds.c: In function 'C_triangMtds':
triangMtds.c:47:11: warning: '*m[1]' may be used uninitialized [-Wmaybe-uninitialized]
   47 |    while(m[ij]==n){ij++;}
      |          ~^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 ultrametric.c -o ultrametric.o
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ape/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ape/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ape/src'
installing to /data/gannet/ripley/R/packages/tests-devel/ape.Rcheck/00LOCK-ape/00new/ape/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 (ape)