starting phase `separate-from-pid1'
build process now running as PID 18
phase `separate-from-pid1' succeeded after 0.0 seconds
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starting phase `set-paths'
environment variable `PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/bin:/gnu/store/3b0gvggch0dpclmcpsa5fxvinbn66w38-binutils-cross-x86_64-pc-gnu-2.41/bin:/gnu/store/j5zgzgsmbjgywr67r86h1n6s4qiabv5q-tar-1.34/bin:/gnu/store/0r2fx1lr1h2i3cl1x5fw4s4ly95qspya-gzip-1.13/bin:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/bin:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/bin:/gnu/store/swmflx2bmqpf0drm167pxfpgyr7ckcam-diffutils-3.10/bin:/gnu/store/4jhlsg65s1zx90gnnfmaax52i8prnl45-patch-2.7.6/bin:/gnu/store/b5c62i99dsfa5j0j3f8g2j1xdi6fih22-findutils-4.9.0/bin:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/bin:/gnu/store/3f0fjq25n2kwcmi0zyrf216wa6g8xpjw-zstd-1.5.2/bin:/gnu/store/3i4fr8riqw9azh1p4mqggl5vdz23kyr8-sed-4.8/bin:/gnu/store/7k8b93779dqpwcg2qjdvnf4nl43jv7hf-grep-3.11/bin:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/bin:/gnu/store/7h0mnlwalw23j9jmvz5n1i5mqkgb4d06-coreutils-9.1/bin:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/bin:/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin:/gnu/store/3k6lyifyg024lk3gncsgf2gzjzvc70gv-ld-wrapper-0/bin:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/bin:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/bin:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/bin:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/sbin'
environment variable `CROSS_LIBRARY_PATH' set to `/gnu/store/rlcvjs8ijkjz8vqfji9gzgwxks5cpli7-glibc-cross-x86_64-pc-gnu-2.39/lib:/gnu/store/hx26xdxfk4f6pqmagf292829s9rj811m-glibc-cross-x86_64-pc-gnu-2.39-static/lib:/gnu/store/nnkx39zmih4zafvdrlh5hrg7qqxkrh5x-hurd-core-headers-cross-x86_64-pc-gnu-0.9.git20240714/lib'
environment variable `CROSS_C_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/rlcvjs8ijkjz8vqfji9gzgwxks5cpli7-glibc-cross-x86_64-pc-gnu-2.39/include:/gnu/store/nnkx39zmih4zafvdrlh5hrg7qqxkrh5x-hurd-core-headers-cross-x86_64-pc-gnu-0.9.git20240714/include'
environment variable `CROSS_CPLUS_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include/c++:/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/rlcvjs8ijkjz8vqfji9gzgwxks5cpli7-glibc-cross-x86_64-pc-gnu-2.39/include:/gnu/store/nnkx39zmih4zafvdrlh5hrg7qqxkrh5x-hurd-core-headers-cross-x86_64-pc-gnu-0.9.git20240714/include'
environment variable `CROSS_OBJC_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/rlcvjs8ijkjz8vqfji9gzgwxks5cpli7-glibc-cross-x86_64-pc-gnu-2.39/include:/gnu/store/nnkx39zmih4zafvdrlh5hrg7qqxkrh5x-hurd-core-headers-cross-x86_64-pc-gnu-0.9.git20240714/include'
environment variable `CROSS_OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/rlcvjs8ijkjz8vqfji9gzgwxks5cpli7-glibc-cross-x86_64-pc-gnu-2.39/include:/gnu/store/nnkx39zmih4zafvdrlh5hrg7qqxkrh5x-hurd-core-headers-cross-x86_64-pc-gnu-0.9.git20240714/include'
environment variable `AWKPATH' unset
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environment variable `C_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/3b0gvggch0dpclmcpsa5fxvinbn66w38-binutils-cross-x86_64-pc-gnu-2.41/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include/c++:/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/3b0gvggch0dpclmcpsa5fxvinbn66w38-binutils-cross-x86_64-pc-gnu-2.41/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include/c++:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/3b0gvggch0dpclmcpsa5fxvinbn66w38-binutils-cross-x86_64-pc-gnu-2.41/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include/c++:/gnu/store/c3sga7kz59f9l50izk16jp01vd9aff5a-gcc-cross-x86_64-pc-gnu-14.2.0/include:/gnu/store/3b0gvggch0dpclmcpsa5fxvinbn66w38-binutils-cross-x86_64-pc-gnu-2.41/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include/c++:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/3b0gvggch0dpclmcpsa5fxvinbn66w38-binutils-cross-x86_64-pc-gnu-2.41/lib:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/lib:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/lib:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/lib:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/lib:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/lib:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/lib:/gnu/store/vqdiyyqbrv4akp68pfya4j6m3pdbnhca-glibc-2.39-static/lib'
environment variable `GUIX_LOCPATH' set to `/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/lib/locale'
environment variable `TZDIR' unset
phase `set-paths' succeeded after 0.0 seconds
starting phase `install-locale'
using 'C.UTF-8' locale for category "LC_ALL"
phase `install-locale' succeeded after 0.0 seconds
starting phase `unpack'
paml4.9e/
paml4.9e/3s.trees
paml4.9e/4s.trees
paml4.9e/5s.trees
paml4.9e/6s.trees
paml4.9e/GeneticCode.txt
paml4.9e/MCaa.dat
paml4.9e/MCbase.dat
paml4.9e/MCbaseRandomTree.dat
paml4.9e/MCcodon.dat
paml4.9e/README.txt
paml4.9e/Technical/
paml4.9e/Technical/Pt/
paml4.9e/Technical/Pt/eigenQREV.pdf
paml4.9e/Technical/Pt/testPMat.c
paml4.9e/Technical/Simulation/
paml4.9e/Technical/Simulation/Codon/
paml4.9e/Technical/Simulation/Codon/MCcodonNSbranches.dat
paml4.9e/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
paml4.9e/Technical/Simulation/Codon/MCcodonNSclade.dat
paml4.9e/Technical/Simulation/Codon/MCcodonNSsites.dat
paml4.9e/Technical/Simulation/Codon/PositiveSites.c
paml4.9e/Technical/Simulation/Codon/README.txt
paml4.9e/Technical/Simulation/Codon/codeml.ctl
paml4.9e/Technical/Simulation/multiruns.c
paml4.9e/Technical/Simulation/multiruns.txt
paml4.9e/aaml.ctl
paml4.9e/baseml.ctl
paml4.9e/bin/
paml4.9e/brown.nuc
paml4.9e/brown.rooted.trees
paml4.9e/brown.trees
paml4.9e/codeml.ctl
paml4.9e/codonml.ctl
paml4.9e/dat/
paml4.9e/dat/MtZoa.dat
paml4.9e/dat/cpREV10.dat
paml4.9e/dat/cpREV64.dat
paml4.9e/dat/dayhoff-dcmut.dat
paml4.9e/dat/dayhoff.dat
paml4.9e/dat/g1974a.dat
paml4.9e/dat/g1974c.dat
paml4.9e/dat/g1974p.dat
paml4.9e/dat/g1974v.dat
paml4.9e/dat/grantham.dat
paml4.9e/dat/jones-dcmut.dat
paml4.9e/dat/jones.dat
paml4.9e/dat/lg.dat
paml4.9e/dat/miyata.dat
paml4.9e/dat/mtArt.dat
paml4.9e/dat/mtREV24.dat
paml4.9e/dat/mtmam.dat
paml4.9e/dat/wag.dat
paml4.9e/doc/
paml4.9e/doc/MCMCtree.Tutorials.pdf
paml4.9e/doc/MCMCtreeDOC.pdf
paml4.9e/doc/pamlDOC.pdf
paml4.9e/doc/pamlFAQs.pdf
paml4.9e/doc/pamlHistory.txt
paml4.9e/examples/
paml4.9e/examples/9s.trees
paml4.9e/examples/CladeModelCD/
paml4.9e/examples/CladeModelCD/ECP_EDN_15.nuc
paml4.9e/examples/CladeModelCD/PAMLCladeModelCDnotes.pdf
paml4.9e/examples/CladeModelCD/codeml.CladeC.ctl
paml4.9e/examples/CladeModelCD/codeml.CladeD.ctl
paml4.9e/examples/CladeModelCD/tree.txt
paml4.9e/examples/DatingSoftBound/
paml4.9e/examples/DatingSoftBound/BF.Clock23.xlsx
paml4.9e/examples/DatingSoftBound/BFdriverDOC.pdf
paml4.9e/examples/DatingSoftBound/FixedDsClock23.txt
paml4.9e/examples/DatingSoftBound/README.BayesFactor.txt
paml4.9e/examples/DatingSoftBound/README.txt
paml4.9e/examples/DatingSoftBound/SeedUsed
paml4.9e/examples/DatingSoftBound/bf1/
paml4.9e/examples/DatingSoftBound/bf1/mcmctree.ctl
paml4.9e/examples/DatingSoftBound/bf2/
paml4.9e/examples/DatingSoftBound/bf2/mcmctree.ctl
paml4.9e/examples/DatingSoftBound/mcmctree.Infinitesites.ctl
paml4.9e/examples/DatingSoftBound/mcmctree.ctl
paml4.9e/examples/DatingSoftBound/mtCDNApri.trees
paml4.9e/examples/DatingSoftBound/mtCDNApri123.txt
paml4.9e/examples/DatingSoftBound/out.txt
paml4.9e/examples/HIVNSsites/
paml4.9e/examples/HIVNSsites/HIVenvSweden.trees
paml4.9e/examples/HIVNSsites/HIVenvSweden.txt
paml4.9e/examples/HIVNSsites/HIVenvSweden4s.trees
paml4.9e/examples/HIVNSsites/HIVenvSweden4s.txt
paml4.9e/examples/HIVNSsites/README.txt
paml4.9e/examples/HIVNSsites/codeml.ctl
paml4.9e/examples/MHC.Swanson2002MBE/
paml4.9e/examples/MHC.Swanson2002MBE/README.txt
paml4.9e/examples/MHC.Swanson2002MBE/bigmhc.phy
paml4.9e/examples/MHC.Swanson2002MBE/bigmhc.trees
paml4.9e/examples/MHC.Swanson2002MBE/codeml.ctl
paml4.9e/examples/MouseLemurs/
paml4.9e/examples/MouseLemurs/MouseLemurs.aa
paml4.9e/examples/MouseLemurs/MouseLemurs.nuc
paml4.9e/examples/MouseLemurs/MouseLemurs.trees
paml4.9e/examples/MouseLemurs/MouseLemurs123.nuc
paml4.9e/examples/MouseLemurs/README.txt
paml4.9e/examples/MouseLemurs/README2.txt
paml4.9e/examples/MouseLemurs/aaml.ctl
paml4.9e/examples/MouseLemurs/aaml2.ctl
paml4.9e/examples/MouseLemurs/baseml.ctl
paml4.9e/examples/MouseLemurs/baseml2.ctl
paml4.9e/examples/MouseLemurs/codeml.ctl
paml4.9e/examples/MouseLemurs/codonml.ctl
paml4.9e/examples/MouseLemurs/codonml2.ctl
paml4.9e/examples/MouseLemurs/mtmam.dat
paml4.9e/examples/README.txt
paml4.9e/examples/TipDate.FluH1/
paml4.9e/examples/TipDate.FluH1/H1.Beast.Nulldata.xml
paml4.9e/examples/TipDate.FluH1/H1.Beast.xml
paml4.9e/examples/TipDate.FluH1/H1.NodeNumbers.tre
paml4.9e/examples/TipDate.FluH1/H1.nexus
paml4.9e/examples/TipDate.FluH1/H1.tre
paml4.9e/examples/TipDate.FluH1/H1.txt
paml4.9e/examples/TipDate.FluH1/baseml.ctl
paml4.9e/examples/TipDate.FluH1/commands.txt
paml4.9e/examples/TipDate.FluH1/in.BV.HKYG5
paml4.9e/examples/TipDate.FluH1/mcmctreeClock1.ctl
paml4.9e/examples/TipDate.FluH1/mcmctreeClock2.ctl
paml4.9e/examples/TipDate.FluH1/mcmctreeClock3.ctl
paml4.9e/examples/TipDate.HIV2/
paml4.9e/examples/TipDate.HIV2/HIV2ge.tre
paml4.9e/examples/TipDate.HIV2/HIV2ge.txt
paml4.9e/examples/TipDate.HIV2/README.txt
paml4.9e/examples/TipDate.HIV2/baseml.ctl
paml4.9e/examples/TipDate.HIV2/in.BV.HKYG5
paml4.9e/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
paml4.9e/examples/TipDate.HIV2/mcmctree.ctl
paml4.9e/examples/YN00abglobin.result
paml4.9e/examples/abglobin.aa
paml4.9e/examples/abglobin.nuc
paml4.9e/examples/abglobin.trees
paml4.9e/examples/dNdSGene1.nuc
paml4.9e/examples/horai.nuc
paml4.9e/examples/horai.trees
paml4.9e/examples/lysin/
paml4.9e/examples/lysin/README.txt
paml4.9e/examples/lysin/RasMol.txt
paml4.9e/examples/lysin/SiteNumbering.txt
paml4.9e/examples/lysin/codeml.ctl
paml4.9e/examples/lysin/codemlYangSwanson2002.ctl
paml4.9e/examples/lysin/lysin.nuc
paml4.9e/examples/lysin/lysin.trees
paml4.9e/examples/lysin/lysinYangSwanson2002.nuc
paml4.9e/examples/lysozyme/
paml4.9e/examples/lysozyme/README.txt
paml4.9e/examples/lysozyme/codeml.ctl
paml4.9e/examples/lysozyme/lysozymeLarge.ctl
paml4.9e/examples/lysozyme/lysozymeLarge.nuc
paml4.9e/examples/lysozyme/lysozymeLarge.trees
paml4.9e/examples/lysozyme/lysozymeSmall.ctl
paml4.9e/examples/lysozyme/lysozymeSmall.nuc
paml4.9e/examples/lysozyme/lysozymeSmall.trees
paml4.9e/examples/lysozyme/lysozymeSmall.txt
paml4.9e/examples/mtCDNA/
paml4.9e/examples/mtCDNA/README.txt
paml4.9e/examples/mtCDNA/codeml.ctl
paml4.9e/examples/mtCDNA/miyata.dat
paml4.9e/examples/mtCDNA/mtCDNAmam.nuc
paml4.9e/examples/mtCDNA/mtCDNAmam.trees
paml4.9e/examples/mtCDNA/mtCDNApri.aa
paml4.9e/examples/mtCDNA/mtCDNApri.nuc
paml4.9e/examples/mtCDNA/mtCDNApri.trees
paml4.9e/examples/mtCDNAape/
paml4.9e/examples/mtCDNAape/2s.trees
paml4.9e/examples/mtCDNAape/OmegaAA.dat
paml4.9e/examples/mtCDNAape/README.txt
paml4.9e/examples/mtCDNAape/codeml.HC.ctl
paml4.9e/examples/mtCDNAape/codeml.ctl
paml4.9e/examples/mtCDNAape/mtCDNA.HC.txt
paml4.9e/examples/mtCDNAape/mtCDNAape.trees
paml4.9e/examples/mtCDNAape/mtCDNAape.txt
paml4.9e/examples/mtprim9.nuc
paml4.9e/mcmctree.ctl
paml4.9e/pamp.ctl
paml4.9e/paupblock
paml4.9e/paupend
paml4.9e/paupstart
paml4.9e/src/
paml4.9e/src/BFdriver.c
paml4.9e/src/Makefile
paml4.9e/src/Makefile.MSVC
paml4.9e/src/README.txt
paml4.9e/src/TreeTimeJeff.c
paml4.9e/src/baseml.c
paml4.9e/src/basemlg.c
paml4.9e/src/chi2.c
paml4.9e/src/codeml.c
paml4.9e/src/ds.c
paml4.9e/src/evolver.c
paml4.9e/src/mcmctree.c
paml4.9e/src/paml.h
paml4.9e/src/pamp.c
paml4.9e/src/tools.c
paml4.9e/src/treespace.c
paml4.9e/src/treesub.c
paml4.9e/src/yn00.c
paml4.9e/stewart.aa
paml4.9e/stewart.trees
paml4.9e/yn00.ctl
phase `unpack' succeeded after 0.1 seconds
starting phase `bootstrap'
no 'configure.ac' or anything like that, doing nothing
phase `bootstrap' succeeded after 0.0 seconds
starting phase `patch-usr-bin-file'
phase `patch-usr-bin-file' succeeded after 0.0 seconds
starting phase `patch-source-shebangs'
phase `patch-source-shebangs' succeeded after 0.0 seconds
starting phase `configure'
phase `configure' succeeded after 0.0 seconds
starting phase `patch-generated-file-shebangs'
phase `patch-generated-file-shebangs' succeeded after 0.0 seconds
starting phase `build'
gcc -fcommon -O3 -o baseml baseml.c tools.c -lm 
gcc -fcommon -O3 -o codeml codeml.c tools.c -lm 
gcc -fcommon -O3 -o basemlg basemlg.c tools.c -lm 
gcc -fcommon -O3 -o mcmctree mcmctree.c tools.c -lm 
gcc -fcommon -O3 -o pamp pamp.c tools.c -lm 
gcc -fcommon -O3 -o evolver evolver.c tools.c -lm 
gcc -fcommon -O3 -o yn00 yn00.c tools.c -lm 
gcc -fcommon -O3 -o chi2 chi2.c -lm 
In file included from basemlg.c:80:
treesub.c: In function ‘ReadSeq’:
treesub.c:840:30: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  840 |             printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL);
      |                           ~~~^~~~~~~
      |                              |
      |                              unsigned char **
In file included from basemlg.c:11:
paml.h:144:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  144 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from basemlg.c:80:
treesub.c:848:26: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  848 |         printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL);
      |                       ~~~^~~~~~~
      |                          |
      |                          unsigned char **
In file included from basemlg.c:11:
paml.h:144:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  144 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from basemlg.c:80:
treesub.c: In function ‘printPatterns’:
treesub.c:1062:26: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
 1062 |         printsma(fout,com.spname,com.z,com.ns, com.npatt,com.npatt, gap, com.seqtype, 1, 0, NULL);
      |                       ~~~^~~~~~~
      |                          |
      |                          unsigned char **
In file included from basemlg.c:11:
paml.h:144:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  144 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from basemlg.c:80:
treesub.c: In function ‘AllPatterns’:
treesub.c:1292:26: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
 1292 |         printsma(fout,com.spname,com.z,com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL);
      |                       ~~~^~~~~~~
      |                          |
      |                          unsigned char **
In file included from basemlg.c:11:
paml.h:144:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  144 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from mcmctree.c:191:
mcmctree.c: In function ‘ReadSeq’:
treesub.c:583:42: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations]
  583 |             for(i=0;i<3;i++) com.lgene[i]=com.ls/3;
      |                              ~~~~~~~~~~~~^~~~~~~~~
treesub.c:583:22: note: within this loop
  583 |             for(i=0;i<3;i++) com.lgene[i]=com.ls/3;
      |                     ~^~
gcc -fcommon -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -lm 
In file included from mcmctree.c:191:
mcmctree.c: In function ‘ReadSeq’:
treesub.c:583:42: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations]
  583 |             for(i=0;i<3;i++) com.lgene[i]=com.ls/3;
      |                              ~~~~~~~~~~~~^~~~~~~~~
treesub.c:583:22: note: within this loop
  583 |             for(i=0;i<3;i++) com.lgene[i]=com.ls/3;
      |                     ~^~
phase `build' succeeded after 35.0 seconds
starting phase `check'
test suite not run
phase `check' succeeded after 0.0 seconds
starting phase `install'
`../doc/pamlHistory.txt' -> `/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/share/doc/paml/pamlHistory.txt'
`../doc/MCMCtree.Tutorials.pdf' -> `/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/share/doc/paml/MCMCtree.Tutorials.pdf'
`../doc/pamlFAQs.pdf' -> `/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/share/doc/paml/pamlFAQs.pdf'
`../doc/MCMCtreeDOC.pdf' -> `/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/share/doc/paml/MCMCtreeDOC.pdf'
`../doc/pamlDOC.pdf' -> `/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/share/doc/paml/pamlDOC.pdf'
phase `install' succeeded after 0.0 seconds
starting phase `patch-shebangs'
phase `patch-shebangs' succeeded after 0.0 seconds
starting phase `strip'
stripping binaries in "/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/bin" with "x86_64-pc-gnu-strip" and flags ("--strip-unneeded" "--enable-deterministic-archives")
phase `strip' succeeded after 0.1 seconds
starting phase `validate-runpath'
validating RUNPATH of 7 binaries in "/gnu/store/43vw5i2wpv4ypd9852x4kl8c62ldfdkb-paml-4.9e/bin"...
phase `validate-runpath' succeeded after 0.0 seconds
starting phase `validate-documentation-location'
phase `validate-documentation-location' succeeded after 0.0 seconds
starting phase `delete-info-dir-file'
phase `delete-info-dir-file' succeeded after 0.0 seconds
starting phase `patch-dot-desktop-files'
phase `patch-dot-desktop-files' succeeded after 0.0 seconds
starting phase `make-dynamic-linker-cache'
ld.so cache not built
phase `make-dynamic-linker-cache' succeeded after 0.0 seconds
starting phase `install-license-files'
installing 0 license files from '.'
phase `install-license-files' succeeded after 0.0 seconds
starting phase `reset-gzip-timestamps'
phase `reset-gzip-timestamps' succeeded after 0.0 seconds
starting phase `compress-documentation'
phase `compress-documentation' succeeded after 0.0 seconds