Mock Version: 2.3 Mock Version: 2.3 Mock Version: 2.3 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f31-build-21756026-1780675/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1595289600 Wrote: /builddir/build/SRPMS/R-ape-5.4-1.fc31.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f31-build-21756026-1780675/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1595289600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.IipBS1 + 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_5.4.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 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.sh1H03 + umask 022 + cd /builddir/build/BUILD + cd ape + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.XdACM3 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64 ++ dirname /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64 + cd ape + mkdir -p /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64/usr/lib64/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64/usr/lib64/R/library ape * installing *source* package 'ape' ... ** package 'ape' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c BIONJ.c -o BIONJ.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c NNI.c -o NNI.o g++ -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c SPR.c -o SPR.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c additive.c -o additive.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ape.c -o ape.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bNNI.c -o bNNI.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bionjs.c -o bionjs.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bipartition.c -o bipartition.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bitsplits.c -o bitsplits.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c delta_plot.c -o delta_plot.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dist_dna.c -o dist_dna.o dist_dna.c: In function 'SegSites': dist_dna.c:1163:19: warning: unused variable 'b' [-Wunused-variable] 1163 | unsigned char b, *x; | ^ dist_dna.c:1162:13: warning: unused variable 'end' [-Wunused-variable] 1162 | long i, end; | ^~~ dist_dna.c:1162:10: warning: unused variable 'i' [-Wunused-variable] 1162 | long i, end; | ^ dist_dna.c:1161:18: warning: unused variable 'done' [-Wunused-variable] 1161 | int n, s, j, done, *seg; | ^~~~ dist_dna.c:1161:15: warning: unused variable 'j' [-Wunused-variable] 1161 | int n, s, j, done, *seg; | ^ dist_dna.c: In function 'distDNA_LogDet': dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] 806 | case 40 : m += 8; break;\ | ^~ dist_dna.c:834:20: note: 'm' was declared here 834 | 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:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] 806 | case 40 : m += 8; break;\ | ^~ dist_dna.c:855:20: note: 'm' was declared here 855 | 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:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] 806 | case 40 : m += 8; break;\ | ^~ dist_dna.c:882:32: note: 'm' was declared here 882 | int i1, i2, k, kb, s1, s2, m, Ntab[16], ROWsums[4]; | ^ dist_dna.c: In function 'distDNA_ParaLin': dist_dna.c:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] 806 | case 40 : m += 8; break;\ | ^~ dist_dna.c:959:28: note: 'm' was declared here 959 | 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:806:17: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] 806 | case 40 : m += 8; break;\ | ^~ dist_dna.c:998:28: note: 'm' was declared here 998 | int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16]; | ^ gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dist_nodes.c -o dist_nodes.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ewLasso.c -o ewLasso.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c heap.c -o heap.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mat_expo.c -o mat_expo.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c me.c -o me.o me.c: In function 'detrifurcate': me.c:295:11: warning: 'w' may be used uninitialized in this function [-Wmaybe-uninitialized] 295 | T->root = w; | ~~~~~~~~^~~ gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c me_balanced.c -o me_balanced.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c me_ols.c -o me_ols.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mvr.c -o mvr.o mvr.c: In function 'C_mvr': mvr.c:164:24: warning: 'OTU2' may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (j == OTU1 || j == OTU2) continue; | ~~^~~~~~~ mvr.c:164:11: warning: 'OTU1' may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (j == OTU1 || j == OTU2) continue; | ~~^~~~~~~ gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mvrs.c -o mvrs.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c nj.c -o nj.o nj.c: In function 'C_nj': nj.c:130:24: warning: 'OTU2' may be used uninitialized in this function [-Wmaybe-uninitialized] 130 | if (j == OTU1 || j == OTU2) continue; | ~~^~~~~~~ nj.c:130:11: warning: 'OTU1' may be used uninitialized in this function [-Wmaybe-uninitialized] 130 | if (j == OTU1 || j == OTU2) continue; | ~~^~~~~~~ nj.c:103:8: warning: 'smallest' may be used uninitialized in this function [-Wmaybe-uninitialized] 103 | A = D[smallest]; | ^ gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c njs.c -o njs.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pic.c -o pic.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plot_phylo.c -o plot_phylo.o g++ -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c prop_part.cpp -o prop_part.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rTrait.c -o rTrait.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c read_dna.c -o read_dna.o g++ -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c reorder_Rcpp.cpp -o reorder_Rcpp.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c reorder_phylo.c -o reorder_phylo.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c treePop.c -o treePop.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tree_build.c -o tree_build.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tree_phylo.c -o tree_phylo.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c triangMtd.c -o triangMtd.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c triangMtds.c -o triangMtds.o gcc -m64 -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ultrametric.c -o ultrametric.o g++ -m64 -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 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 -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64/usr/lib64/R/library/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 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 getAnnotationsGenBank 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 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 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 read.dna html 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 ** 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) + test -d ape/src + cd ape/src + rm -f 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 ape.so + rm -f /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh -j6 --strict-build-id -m -i --build-id-seed 5.4-1.fc31 --unique-debug-suffix -5.4-1.fc31.x86_64 --unique-debug-src-base R-ape-5.4-1.fc31.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/ape explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64/usr/lib64/R/library/ape/libs/ape.so extracting debug info from /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64/usr/lib64/R/library/ape/libs/ape.so original debug info size: 2912kB, size after compression: 2664kB /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 615 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 Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ZfpXG1 + umask 022 + cd /builddir/build/BUILD + cd ape + /usr/bin/R CMD check ape * using log directory '/builddir/build/BUILD/ape/ape.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'ape/DESCRIPTION' ... OK * this is package 'ape' version '5.4' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.10/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/PACKAGES' 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 ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: R 1.9Mb libs 3.2Mb * 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 ... NOTE 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: 1 WARNING, 2 NOTEs See '/builddir/build/BUILD/ape/ape.Rcheck/00check.log' for details. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-ape-5.4-1.fc31.x86_64 Provides: R(ape) = 5.4 R-ape = 5.4-1.fc31 R-ape(x86-64) = 5.4-1.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 libR.so()(64bit) libRlapack.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(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_3.4.20)(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-5.4-1.fc31.x86_64 Provides: R-ape-debugsource = 5.4-1.fc31 R-ape-debugsource(x86-64) = 5.4-1.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-5.4-1.fc31.x86_64 Provides: R-ape-debuginfo = 5.4-1.fc31 R-ape-debuginfo(x86-64) = 5.4-1.fc31 debuginfo(build-id) = cd533bb590db01988f8e7a27dc728ff6f69533a9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-ape-debugsource(x86-64) = 5.4-1.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64 Wrote: /builddir/build/RPMS/R-ape-debugsource-5.4-1.fc31.x86_64.rpm Wrote: /builddir/build/RPMS/R-ape-debuginfo-5.4-1.fc31.x86_64.rpm Wrote: /builddir/build/RPMS/R-ape-5.4-1.fc31.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.e0A9p3 + umask 022 + cd /builddir/build/BUILD + cd ape + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-ape-5.4-1.fc31.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0