Mock Version: 1.4.14
Mock Version: 1.4.14
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f31-build-97137-32906/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x1558116588>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1565481600
Wrote: /builddir/build/SRPMS/R-ape-5.3-3.fc31.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f31-build-97137-32906/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x1558116588>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1565481600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Jdx64O
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf ape
+ /usr/bin/mkdir -p ape
+ cd ape
+ /usr/bin/gzip -dc /builddir/build/SOURCES/ape_5.3.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.pb4doN
+ umask 022
+ cd /builddir/build/BUILD
+ cd ape
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.DKACoM
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64
+ cd ape
+ mkdir -p /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64/usr/lib64/R/library
+ /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64/usr/lib64/R/library ape
BUILDSTDERR: * installing *source* package 'ape' ...
BUILDSTDERR: ** package 'ape' successfully unpacked and MD5 sums checked
BUILDSTDERR: ** using staged installation
BUILDSTDERR: ** libs
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c BIONJ.c -o BIONJ.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c NNI.c -o NNI.o
g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c RcppExports.cpp -o RcppExports.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c SPR.c -o SPR.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c TBR.c -o TBR.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c additive.c -o additive.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c ape.c -o ape.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c bNNI.c -o bNNI.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c bionjs.c -o bionjs.o
BUILDSTDERR: gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpmdist_dna.c: In function 'dist_dna':
BUILDSTDERR: dist_dna.c:1173:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1173 |              else distDNA_raw(x, n, s, d, 1); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1173:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1173 |              else distDNA_raw(x, n, s, d, 1); break;
BUILDSTDERR:       |                                               ^~~~~
BUILDSTDERR: dist_dna.c:1175:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1175 |              else distDNA_JC69(x, n, s, d, variance, var, gamma, alpha); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1175:74: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1175 |              else distDNA_JC69(x, n, s, d, variance, var, gamma, alpha); break;
BUILDSTDERR:       |                                                                          ^~~~~
BUILDSTDERR: dist_dna.c:1177:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1177 |              else distDNA_K80(x, n, s, d, variance, var, gamma, alpha); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1177:73: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1177 |              else distDNA_K80(x, n, s, d, variance, var, gamma, alpha); break;
BUILDSTDERR:       |                                                                         ^~~~~
BUILDSTDERR: dist_dna.c:1179:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1179 |              else distDNA_F81(x, n, s, d, BF, variance, var, gamma, alpha); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1179:77: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1179 |              else distDNA_F81(x, n, s, d, BF, variance, var, gamma, alpha); break;
BUILDSTDERR:       |                                                                             ^~~~~
BUILDSTDERR: dist_dna.c:1181:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1181 |              else distDNA_K81(x, n, s, d, variance, var); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1181:59: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1181 |              else distDNA_K81(x, n, s, d, variance, var); break;
BUILDSTDERR:       |                                                           ^~~~~
BUILDSTDERR: dist_dna.c:1183:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1183 |              else distDNA_F84(x, n, s, d, BF, variance, var); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1183:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1183 |              else distDNA_F84(x, n, s, d, BF, variance, var); break;
BUILDSTDERR:       |                                                               ^~~~~
BUILDSTDERR: dist_dna.c:1185:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1185 |              else distDNA_T92(x, n, s, d, BF, variance, var); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1185:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1185 |              else distDNA_T92(x, n, s, d, BF, variance, var); break;
BUILDSTDERR:       |                                                               ^~~~~
BUILDSTDERR: dist_dna.c:1187:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1187 |              else distDNA_TN93(x, n, s, d, BF, variance, var, gamma, alpha); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1187:78: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1187 |              else distDNA_TN93(x, n, s, d, BF, variance, var, gamma, alpha); break;
BUILDSTDERR:       |                                                                              ^~~~~
BUILDSTDERR: dist_dna.c:1189:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1189 |              else distDNA_GG95(x, n, s, d, variance, var); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1189:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1189 |              else distDNA_GG95(x, n, s, d, variance, var); break;
BUILDSTDERR:       |                                                            ^~~~~
BUILDSTDERR: dist_dna.c:1191:15: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1191 |               else distDNA_LogDet(x, n, s, d, variance, var); break;
BUILDSTDERR:       |               ^~~~
BUILDSTDERR: dist_dna.c:1191:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1191 |               else distDNA_LogDet(x, n, s, d, variance, var); break;
BUILDSTDERR:       |                                                               ^~~~~
BUILDSTDERR: dist_dna.c:1194:15: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1194 |               else distDNA_ParaLin(x, n, s, d, variance, var); break;
BUILDSTDERR:       |               ^~~~
BUILDSTDERR: dist_dna.c:1194:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1194 |               else distDNA_ParaLin(x, n, s, d, variance, var); break;
BUILDSTDERR:       |                                                                ^~~~~
BUILDSTDERR: dist_dna.c:1196:14: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1196 |              else distDNA_raw(x, n, s, d, 0); break;
BUILDSTDERR:       |              ^~~~
BUILDSTDERR: dist_dna.c:1196:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1196 |              else distDNA_raw(x, n, s, d, 0); break;
BUILDSTDERR:       |                                               ^~~~~
BUILDSTDERR: dist_dna.c:1198:6: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1198 |      else distDNA_TsTv(x, n, s, d, 1, 0); break;
BUILDSTDERR:       |      ^~~~
BUILDSTDERR: dist_dna.c:1198:43: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1198 |      else distDNA_TsTv(x, n, s, d, 1, 0); break;
BUILDSTDERR:       |                                           ^~~~~
BUILDSTDERR: dist_dna.c:1200:6: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:  1200 |      else distDNA_TsTv(x, n, s, d, 0, 0); break;
BUILDSTDERR:       |      ^~~~
BUILDSTDERR: dist_dna.c:1200:43: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:  1200 |      else distDNA_TsTv(x, n, s, d, 0, 0); break;
BUILDSTDERR:       |                                           ^~~~~
BUILDSTDERR: dist_dna.c: In function 'distDNA_LogDet':
BUILDSTDERR: dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   806 |     case 40 : m += 8; break;\
BUILDSTDERR:       |                 ^~
BUILDSTDERR: dist_dna.c:834:20: note: 'm' was declared here
BUILDSTDERR:   834 |     int i1, i2, k, m, s1, s2, target, L, Ntab[16], ndim = 4, info, ipiv[16];
BUILDSTDERR:       |                    ^
BUILDSTDERR: dist_dna.c: In function 'distDNA_LogDet_pairdel':
BUILDSTDERR: dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   806 |     case 40 : m += 8; break;\
BUILDSTDERR:       |                 ^~
BUILDSTDERR: dist_dna.c:855:20: note: 'm' was declared here
BUILDSTDERR:   855 |     int i1, i2, k, m, s1, s2, target, L, Ntab[16], ndim = 4, info, ipiv[16];
BUILDSTDERR:       |                    ^
BUILDSTDERR: dist_dna.c: In function 'distDNA_BH87':
BUILDSTDERR: dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   806 |     case 40 : m += 8; break;\
BUILDSTDERR:       |                 ^~
BUILDSTDERR: dist_dna.c:882:32: note: 'm' was declared here
BUILDSTDERR:   882 |     int i1, i2, k, kb, s1, s2, m, Ntab[16], ROWsums[4];
BUILDSTDERR:       |                                ^
BUILDSTDERR: dist_dna.c: In function 'distDNA_ParaLin':
BUILDSTDERR: dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   806 |     case 40 : m += 8; break;\
BUILDSTDERR:       |                 ^~
BUILDSTDERR: dist_dna.c:959:28: note: 'm' was declared here
BUILDSTDERR:   959 |     int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16];
BUILDSTDERR:       |                            ^
BUILDSTDERR: dist_dna.c: In function 'distDNA_ParaLin_pairdel':
BUILDSTDERR: dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   806 |     case 40 : m += 8; break;\
BUILDSTDERR:       |                 ^~
BUILDSTDERR: dist_dna.c:998:28: note: 'm' was declared here
BUILDSTDERR:   998 |     int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16];
BUILDSTDERR:       |                            ^
BUILDSTDERR: me.c: In function 'detrifurcate':
BUILDSTDERR: me.c:295:11: warning: 'w' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   295 |   T->root = w;
BUILDSTDERR:       |   ~~~~~~~~^~~
/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c bipartition.c -o bipartition.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c bitsplits.c -o bitsplits.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c delta_plot.c -o delta_plot.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c dist_dna.c -o dist_dna.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c dist_nodes.c -o dist_nodes.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c ewLasso.c -o ewLasso.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c heap.c -o heap.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c mat_expo.c -o mat_expo.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c me.c -o me.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c me_balanced.c -o me_balanced.o
BUILDSTDERR: gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/mvr.c: In function 'C_mvr':
BUILDSTDERR: mvr.c:164:19: warning: 'OTU2' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   164 |     if (j == OTU1 || j == OTU2) continue;
BUILDSTDERR:       |         ~~~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: mvr.c:164:8: warning: 'OTU1' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   164 |     if (j == OTU1 || j == OTU2) continue;
BUILDSTDERR:       |        ^
BUILDSTDERR: nj.c: In function 'C_nj':
BUILDSTDERR: nj.c:130:19: warning: 'OTU2' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   130 |     if (j == OTU1 || j == OTU2) continue;
BUILDSTDERR:       |         ~~~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: nj.c:130:8: warning: 'OTU1' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   130 |     if (j == OTU1 || j == OTU2) continue;
BUILDSTDERR:       |        ^
BUILDSTDERR: nj.c:103:8: warning: 'smallest' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   103 |   A = D[smallest];
BUILDSTDERR:       |        ^
BUILDSTDERR: prop_part.cpp: In function 'Rcpp::List prop_part2(SEXP, int)':
BUILDSTDERR: prop_part.cpp:49:29: warning: unused variable 'KeepPartition' [-Wunused-variable]
BUILDSTDERR:    49 |     int nbtree = tr.size(), KeepPartition=1;
BUILDSTDERR:       |                             ^~~~~~~~~~~~~
local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c me_ols.c -o me_ols.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c mvr.c -o mvr.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c mvrs.c -o mvrs.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c nj.c -o nj.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c njs.c -o njs.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c pic.c -o pic.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c plot_phylo.c -o plot_phylo.o
g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c prop_part.cpp -o prop_part.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c rTrait.c -o rTrait.o
BUILDSTDERR: gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasread_dna.c: In function 'charVectorToDNAbinVector':
BUILDSTDERR: read_dna.c:341:54: warning: array subscript has type 'char' [-Wchar-subscripts]
BUILDSTDERR:   341 |     for (long i = 0; i < n; i++) rs[i] = tab_trans[xr[i]];
BUILDSTDERR:       |                                                    ~~^~~
ynchronous-unwind-tables -fstack-clash-protection  -c read_dna.c -o read_dna.o
g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c reorder_Rcpp.cpp -o reorder_Rcpp.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c reorder_phylo.c -o reorder_phylo.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c treePop.c -o treePop.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c tree_build.c -o tree_build.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c tree_phylo.c -o tree_phylo.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c triangMtd.c -o triangMtd.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c triangMtds.c -o triangMtds.o
gcc -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c ultrametric.c -o ultrametric.o
BUILDSTDERR: g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o TBR.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 -L/usr/lib64/R/lib -linstalling to /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64/usr/lib64/R/library/00LOCK-ape/00new/ape/libs
BUILDSTDERR: ** R
BUILDSTDERR: ** data
BUILDSTDERR: ** inst
BUILDSTDERR: ** byte-compile and prepare package for lazy loading
BUILDSTDERR: ** help
BUILDSTDERR: *** installing help indices
BUILDSTDERR:     finding HTML links ... done
Rlapack -L/usr/lib64/R/lib -lRblas -L -L -lgfortran -lm -L/usr/lib64/R/lib -lR
  converting help for package 'ape'
    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  
Rd warning: /builddir/build/BUILD/ape/ape/man/all.equal.DNAbin.Rd:25: file link 'isTRUE' in package 'base' does not exist and so has been treated as a topic
    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  
Rd warning: /builddir/build/BUILD/ape/ape/man/compar.gee.Rd:105: file link 'drop1' in package 'stats' does not exist and so has been treated as a topic
    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  
    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  
    hivtree                                 html  
    howmanytrees                            html  
    identify.phylo                          html  
    image.DNAbin                            html  
Rd warning: /builddir/build/BUILD/ape/ape/man/image.DNAbin.Rd:40: file link 'image.default' in package 'graphics' does not exist and so has been treated as a topic
    is.binary.tree                          html  
    is.compatible                           html  
    is.monophyletic                         html  
    is.ultrametric                          html  
Rd warning: /builddir/build/BUILD/ape/ape/man/is.ultrametric.Rd:34: file link '.Machine' in package 'base' does not exist and so has been treated as a topic
    kronoviz                                html  
    label2table                             html  
    ladderize                               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  
Rd warning: /builddir/build/BUILD/ape/ape/man/phydataplot.Rd:48: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
    phymltest                               html  
    pic                                     html  
    pic.ortho                               html  
    plot.correlogram                        html  
    plot.phylo                              html  
    plot.phyloExtra                         html  
    plot.varcomp                            html  
    plotTreeTime                            html  
Rd warning: /builddir/build/BUILD/ape/ape/man/plotTreeTime.Rd:26: file link 'Date' in package 'base' does not exist and so has been treated as a topic
    print.phylo                             html  
    rDNAbin                                 html  
    rTraitCont                              html  
    rTraitDisc                              html  
    rTraitMult                              html  
    read.GenBank                            html  
    read.caic                               html  
BUILDSTDERR:     read.dna                                html ** building package indices
BUILDSTDERR: ** installing vignettes
BUILDSTDERR: ** testing if installed package can be loaded from temporary location
BUILDSTDERR: ** checking absolute paths in shared objects and dynamic libraries
BUILDSTDERR: ** testing if installed package can be loaded from final location
BUILDSTDERR: ** testing if installed package keeps a record of temporary installation path
BUILDSTDERR: * DONE (ape)
+ test -d ape/src
+ cd ape/src
+ rm -f BIONJ.o NNI.o RcppExports.o SPR.o TBR.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 ape.so
+ rm -f /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64/usr/lib64/R/library/R.css
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 5.3-3.fc31 --unique-debug-suffix -5.3-3.fc31.riscv64 --unique-debug-src-base R-ape-5.3-3.fc31.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/ape
BUILDSTDERR: 631 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
 
    read.gff                                html  
    read.nexus                              html  
    read.nexus.data                         html  
    read.tree                               html  
    reconstruct                             html  
    reorder.phylo                           html  
Rd warning: /builddir/build/BUILD/ape/ape/man/reorder.phylo.Rd:62: file link 'reorder' in package 'stats' does not exist and so has been treated as a topic
    richness.yule.test                      html  
    rlineage                                html  
    root                                    html  
    rotate                                  html  
    rtree                                   html  
    rtt                                     html  
    seg.sites                               html  
    skyline                                 html  
    skylineplot                             html  
    slowinskiguyer.test                     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.tree                              html  
    yule                                    html  
    yule.cov                                html  
    yule.time                               html  
    zoom                                    html  
Rd warning: /builddir/build/BUILD/ape/ape/man/zoom.Rd:37: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/ape/ape/man/zoom.Rd:43: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/ape/ape/man/zoom.Rd:44: file link 'grey' in package 'grDevices' does not exist and so has been treated as a topic
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64/usr/lib64/R/library/ape/libs/ape.so
extracting debug info from /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64/usr/lib64/R/library/ape/libs/ape.so
original debug info size: 2320kB, size after compression: 2108kB
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.oMHdhP
+ umask 022
+ cd /builddir/build/BUILD
+ cd ape
+ /usr/bin/R CMD check ape
BUILDSTDERR: Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
BUILDSTDERR:   cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/bioc/src/contrib:
BUILDSTDERR:   cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES'
BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib:
BUILDSTDERR:   cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES'
BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib:
BUILDSTDERR:   cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PACKAGES'
BUILDSTDERR: See
BUILDSTDERR:   '/builddir/build/BUILD/ape/ape.Rcheck/00check.log'
BUILDSTDERR: for details.
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
* using log directory '/builddir/build/BUILD/ape/ape.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: riscv64-redhat-linux-gnu (64-bit)
* using session charset: ASCII
* checking for file 'ape/DESCRIPTION' ... OK
* this is package 'ape' version '5.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ape' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown packages 'phangorn', 'ade4', 'pegas', 'geiger', 'apTreeshape' in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File 'ape/libs/ape.so':
  Found 'abort', possibly from 'abort' (C)
    Objects: 'RcppExports.o', 'prop_part.o', 'reorder_Rcpp.o'
  Found 'printf', possibly from 'printf' (C)
    Objects: 'RcppExports.o', 'prop_part.o', 'reorder_Rcpp.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
  'MoranI.Rnw'... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs
Processing files: R-ape-5.3-3.fc31.riscv64
Provides: R(ape) = 5.3 R-ape = 5.3-3.fc31 R-ape(riscv-64) = 5.3-3.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(Rcpp) >= 0.12.0 R(graphics) R(lattice) R(methods) R(nlme) R(parallel) R(stats) R(tools) R(utils) R-core >= 3.2.0 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libRlapack.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Suggests: R(expm) R(gee) R(igraph)
Processing files: R-ape-debugsource-5.3-3.fc31.riscv64
Provides: R-ape-debugsource = 5.3-3.fc31 R-ape-debugsource(riscv-64) = 5.3-3.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-ape-debuginfo-5.3-3.fc31.riscv64
Provides: R-ape-debuginfo = 5.3-3.fc31 R-ape-debuginfo(riscv-64) = 5.3-3.fc31 debuginfo(build-id) = e6c4efa0cc6b3bdc8bb69d0d1e91e4ced65ea1a9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-ape-debugsource(riscv-64) = 5.3-3.fc31
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64
Wrote: /builddir/build/RPMS/R-ape-debugsource-5.3-3.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/R-ape-5.3-3.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/R-ape-debuginfo-5.3-3.fc31.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.cx5MIN
+ umask 022
+ cd /builddir/build/BUILD
+ cd ape
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-ape-5.3-3.fc31.riscv64
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Child return code was: 0