* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0NX0vc/R.INSTALL1be6953930a1cf/ape/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BIONJ.c -o BIONJ.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c NNI.c -o NNI.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c SPR.c -o SPR.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c additive.c -o additive.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ape.c -o ape.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bNNI.c -o bNNI.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bionjs.c -o bionjs.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bipartition.c -o bipartition.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bitsplits.c -o bitsplits.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c delta_plot.c -o delta_plot.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dist_nodes.c -o dist_nodes.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ewLasso.c -o ewLasso.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c heap.c -o heap.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mat_expo.c -o mat_expo.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c me_balanced.c -o me_balanced.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c me_ols.c -o me_ols.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mvrs.c -o mvrs.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nj.c -o nj.o
nj.c: In function ‘C_nj’:
nj.c:114:36: warning: ‘OTU1’ may be used uninitialized [-Wmaybe-uninitialized]
114 | edge[k + Nedge] = otu_label[OTU1];
| ^
nj.c:66:49: note: ‘OTU1’ was declared here
66 | int n, i, j, k, *edge, cur_nod, *otu_label, OTU1, OTU2, Nedge;
| ^~~~
nj.c:115:40: warning: ‘OTU2’ may be used uninitialized [-Wmaybe-uninitialized]
115 | edge[k + 1 + Nedge] = otu_label[OTU2];
| ^
nj.c:66:55: note: ‘OTU2’ was declared here
66 | int n, i, j, k, *edge, cur_nod, *otu_label, OTU1, OTU2, Nedge;
| ^~~~
nj.c:123:14: warning: ‘smallest’ may be used uninitialized [-Wmaybe-uninitialized]
123 | A = D[smallest];
| ^
nj.c:67:14: note: ‘smallest’ was declared here
67 | long ij, smallest;
| ^~~~~~~~
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c njs.c -o njs.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pic.c -o pic.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c plot_phylo.c -o plot_phylo.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c prop_part.cpp -o prop_part.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rTrait.c -o rTrait.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_dna.c -o read_dna.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c reorder_Rcpp.cpp -o reorder_Rcpp.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c reorder_phylo.c -o reorder_phylo.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c treePop.c -o treePop.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tree_build.c -o tree_build.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tree_phylo.c -o tree_phylo.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c triangMtd.c -o triangMtd.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ultrametric.c -o ultrametric.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0NX0vc/R.INSTALL1be6953930a1cf/ape/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0NX0vc/R.INSTALL1be6953930a1cf/ape/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0NX0vc/R.INSTALL1be6953930a1cf/ape/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ape/00new/ape/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘ape’
finding HTML links ... done
AAbin html
CADM.global html
DNAbin html
DNAbin2indel html
Initialize.corPhyl html
LTT html
MPR html
MoranI html
SDM html
ace html
add.scale.bar html
additive html
alex html
all.equal.DNAbin html
all.equal.phylo html
alview html
ape-internal html
ape-package html
apetools html
as.alignment html
as.bitsplits html
as.matching html
as.phylo html
as.phylo.formula html
axisPhylo html
balance html
base.freq html
bd.ext html
bd.time html
binaryPGLMM html
bind.tree html
bionj html
bird.families html
bird.orders html
birthdeath html
boot.phylo html
branching.times html
c.phylo html
carnivora html
checkAlignment html
checkLabel html
checkValidPhylo html
cherry html
chiroptera html
chronoMPL html
chronopl html
chronos html
clustal html
coalescent.intervals html
collapse.singles html
collapsed.intervals html
compar.cheverud html
compar.gee html
compar.lynch html
compar.ou html
comparePhylo html
compute.brlen html
compute.brtime html
consensus html
cophenetic.phylo html
cophyloplot html
corBlomberg html
corBrownian html
corClasses html
corGrafen html
corMartins html
corPagel html
corphylo html
correlogram.formula html
cynipids html
dbd html
def html
degree html
del.gaps html
delta.plot html
dist.dna html
dist.gene html
dist.topo html
diversi.gof html
diversi.time html
diversity.contrast.test html
dnds html
drop.tip html
edges html
evonet html
ewLasso html
fastme html
gammaStat html
getAnnotationsGenBank html
hivtree html
howmanytrees html
identify.phylo html
image.DNAbin html
is.binary.tree html
is.compatible html
is.monophyletic html
is.ultrametric html
kronoviz html
label2table html
ladderize html
latag2n html
lmorigin html
ltt.plot html
makeLabel html
makeNodeLabel html
mantel.test html
mat3 html
mat5M3ID html
mat5Mrand html
matexpo html
mcconwaysims.test html
mcmc.popsize html
mixedFontLabel html
mrca html
mst html
multi2di html
multiphylo html
mvr html
nj html
njs html
node.dating html
node.depth html
nodelabels html
nodepath html
parafit html
pcoa html
phydataplot html
phymltest html
pic html
pic.ortho html
plot.correlogram html
plot.phylo html
plot.phyloExtra html
plot.varcomp html
plotTreeTime html
print.phylo html
rDNAbin html
rTraitCont html
rTraitDisc html
rTraitMult html
read.GenBank html
read.caic html
read.dna html
read.gff html
read.nexus html
read.nexus.data html
read.tree html
reconstruct html
reorder.phylo html
richness.yule.test html
rlineage html
root html
rotate html
rtree html
rtt html
seg.sites html
skyline html
skylineplot html
slowinskiguyer.test html
solveAmbiguousBases html
speciesTree html
stree html
subtreeplot html
subtrees html
summary.phylo html
trans html
treePop html
trex html
triangMtd html
unique.multiPhylo html
updateLabel html
varCompPhylip html
varcomp html
vcv.phylo html
vcv2phylo html
weight.taxo html
where html
which.edge html
woodmouse html
write.dna html
write.nexus html
write.nexus.data html
write.phyloXML html
write.tree html
yule html
yule.cov html
yule.time html
zoom 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 (ape)