* installing *source* package 'ape' ...
** package 'ape' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp0ildSK/R.INSTALL90781944c3c/ape/src'
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BIONJ.c -o BIONJ.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NNI.c -o NNI.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPR.c -o SPR.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c additive.c -o additive.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ape.c -o ape.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bNNI.c -o bNNI.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bionjs.c -o bionjs.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bipartition.c -o bipartition.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bitsplits.c -o bitsplits.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c delta_plot.c -o delta_plot.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dist_nodes.c -o dist_nodes.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ewLasso.c -o ewLasso.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c heap.c -o heap.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mat_expo.c -o mat_expo.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c me_balanced.c -o me_balanced.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c me_ols.c -o me_ols.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mvrs.c -o mvrs.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c njs.c -o njs.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pic.c -o pic.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plot_phylo.c -o plot_phylo.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c prop_part.cpp -o prop_part.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rTrait.c -o rTrait.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_dna.c -o read_dna.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reorder_Rcpp.cpp -o reorder_Rcpp.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reorder_phylo.c -o reorder_phylo.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c treePop.c -o treePop.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tree_build.c -o tree_build.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tree_phylo.c -o tree_phylo.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c triangMtd.c -o triangMtd.o
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ultrametric.c -o ultrametric.o
g++ -std=gnu++17 -shared -s -static-libgcc -o ape.dll tmp.def 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 -LD:/RCompile/recent/R-4.4.2/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp0ildSK/R.INSTALL90781944c3c/ape/src'
make[1]: Entering directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp0ildSK/R.INSTALL90781944c3c/ape/src'
make[1]: Leaving directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp0ildSK/R.INSTALL90781944c3c/ape/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-ape/00new/ape/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'ape' as ape_5.8-1.zip
* DONE (ape)