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environment variable `PATH' set to `/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/bin:/gnu/store/x5nk7jclncdrrsjhpmjjfl2z9p36bxyw-tar-1.35/bin:/gnu/store/vcmbby8alqahhhd5qnidpf5pbvr102jl-gzip-1.14/bin:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/bin:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/bin:/gnu/store/d7q1jypzi0hjx0gf2034yzljvapy7fvy-diffutils-3.12/bin:/gnu/store/3yky2jh15qsknnxnzplhj4by14sqmfig-patch-2.7.6/bin:/gnu/store/nfs39m8hsbx905q5kgjiw1irfrllkk00-findutils-4.10.0/bin:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/bin:/gnu/store/d4bzgx28m0640plahv0x3h5hxlh1npnj-zstd-1.5.6/bin:/gnu/store/5a3p82yj9nrj6rhk11f7b2sb84wirc2k-sed-4.9/bin:/gnu/store/1lkl6hik16bbhpjjsl825fivp2dsr9vi-grep-3.11/bin:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/bin:/gnu/store/pai3hvsiihllqi03b2198qi5qq9a28ga-coreutils-9.1/bin:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/bin:/gnu/store/k66i68s5l93n1lgxp29vn2292nsywp1v-bash-minimal-5.2.37/bin:/gnu/store/pazcfyngzb35khc8ad33dmsb22ibnl80-ld-wrapper-0/bin:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/bin:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/bin:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/bin:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/sbin'
environment variable `R_LIBS_SITE' set to `/gnu/store/6m8506f1hsqzdib8x8zl35qq9z7j4kqh-r-coda-0.19-4.1/site-library/:/gnu/store/01jmpq3rxwkdpd7zzd7pfbywryn8ggrw-r-knitr-1.50/site-library/:/gnu/store/b3b9v5wvm15nlxxbz8s122nf4viz45j3-r-purrr-1.2.0/site-library/:/gnu/store/ilq5rvk514m0qwrqdymrbvw5xw033ir0-r-testthat-3.3.0/site-library/:/gnu/store/9ybiwnwzidhj4ywr75mninwvpsj4s6vr-r-ape-5.8-1/site-library/:/gnu/store/fmwnbybr2nzsrxyzsgr63gpvr78ii1gd-r-rcpp-1.1.0/site-library/:/gnu/store/h1v0a657shh8x5f5mjwrs8gkwvccl3yg-r-lattice-0.22-7/site-library/:/gnu/store/lya35pzwmilz34j0xjy93nzkfabrd0k3-r-yaml-2.3.10/site-library/:/gnu/store/211ymkqka9r3nwpvpndh5553lyqkzs5l-r-xfun-0.54/site-library/:/gnu/store/648m3jwa1n8pyziji1bzd25fzhb0v1mh-r-highr-0.11/site-library/:/gnu/store/3m2iaw61xgr6nms17y72il0lj21j32jb-r-evaluate-1.0.5/site-library/:/gnu/store/0bksakw9zj510isa7rp33hd72fh0g8nk-r-vctrs-0.6.5/site-library/:/gnu/store/q83z93pn0nzi4agvdk6jdaihw1vdi773-r-rlang-1.1.6/site-library/:/gnu/store/6hl9rdycd0xyzj0z6vldilcmj7blgwj6-r-magrittr-2.0.4/site-library/:/gnu/store/2jm7igf1lhycvxmng0cf6ay06vh0f2ap-r-lifecycle-1.0.4/site-library/:/gnu/store/3vl9ljw22y3w64wf4vgm3z0a6kgr3x0v-r-cli-3.6.5/site-library/:/gnu/store/k7wdvs0n6q4mgjflv3pal0hqyr39sa1d-r-withr-3.0.2/site-library/:/gnu/store/j5hl9n32bj7dq6jdkbdryf76c7ybdmz4-r-waldo-0.6.2/site-library/:/gnu/store/vlkp9qwd7k1jnzz34848h655m8ckx5f3-r-r6-2.6.1/site-library/:/gnu/store/9myi5lmv57kg5zmy9waldzgv3f027kcd-r-ps-1.9.1/site-library/:/gnu/store/4pidqzcmhvkhnigyly1s56a28p29ysxn-r-processx-3.8.6/site-library/:/gnu/store/izdqlxp8dn027aqqwjsl0f2v7y825kn5-r-praise-1.0.0/site-library/:/gnu/store/4gxi14dl2cd8ryzj6plpp7d3lnm8j2mf-r-pkgload-1.4.1/site-library/:/gnu/store/v775nkpib6sbz3q59yshrby71c5ykcp8-r-jsonlite-2.0.0/site-library/:/gnu/store/3bhnqpzr7904rryvgs52zkslw30mpwx6-r-desc-1.4.3/site-library/:/gnu/store/j5bpy1jxpshxrscj1iz6134lnqd1z4li-r-callr-3.7.6/site-library/:/gnu/store/2zbz1m7w1fkmgla3ihh201nyanyxd8bs-r-brio-1.1.5/site-library/:/gnu/store/rdl4rpls8r4x1nk96cx4l5g532fj28vx-r-nlme-3.1-168/site-library/:/gnu/store/hx8rbd3zpdfyidzk4v42glcv3kn37ddp-r-digest-0.6.39/site-library/:/gnu/store/7k1d6dvd3634glwvargf1aa80brnyipr-r-glue-1.8.0/site-library/:/gnu/store/1r396sk76yw5cshcsbi3zpsknbnzll94-r-diffobj-0.3.6/site-library/:/gnu/store/4bnn8sdfg8xfdv3a6pw5xqg1nnqpr3ig-r-rprojroot-2.1.1/site-library/:/gnu/store/ikcghj4c12r0lzjdp9v9g50bif8h98d6-r-pkgbuild-1.4.8/site-library/:/gnu/store/w6bj9giz3lidzraqypj7gypfdv6y2w2q-r-fs-1.6.6/site-library/:/gnu/store/k47c8nw7vi5m46v1kg7sjrvljji05svm-r-crayon-1.5.3/site-library/'
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environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include/c++:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include'
environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include'
environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include/c++:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/lib:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/lib:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/lib:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/lib:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/lib:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/lib:/gnu/store/q1s19kv8bdq9ssfdgznzgkmfmj90vdfd-glibc-2.41-static/lib'
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TransPhylo/
TransPhylo/NAMESPACE
TransPhylo/README.md
TransPhylo/man/
TransPhylo/man/makeCTreeFromPTree.Rd
TransPhylo/man/probTTree.Rd
TransPhylo/man/plot.ptree.Rd
TransPhylo/man/consTTree.Rd
TransPhylo/man/getOffspringDist.Rd
TransPhylo/man/extractCTree.Rd
TransPhylo/man/infer_multittree_share_param.Rd
TransPhylo/man/summary.resTransPhylo.Rd
TransPhylo/man/makeTTree.Rd
TransPhylo/man/plot.ttree.Rd
TransPhylo/man/inferTTree.Rd
TransPhylo/man/TransPhylo-package.Rd
TransPhylo/man/medTTree.Rd
TransPhylo/man/getInfectionTimeDist.Rd
TransPhylo/man/probTTreeR.Rd
TransPhylo/man/probPTreeGivenTTreeR.Rd
TransPhylo/man/convertToCoda.Rd
TransPhylo/man/plotTTree2.Rd
TransPhylo/man/getGenerationTimeDist.Rd
TransPhylo/man/as.mcmc.resTransPhylo.Rd
TransPhylo/man/selectTTree.Rd
TransPhylo/man/print.ttree.Rd
TransPhylo/man/print.resTransPhylo.Rd
TransPhylo/man/plotCTree.Rd
TransPhylo/man/computeMatTDist.Rd
TransPhylo/man/ptreeFromPhylo.Rd
TransPhylo/man/print.ctree.Rd
TransPhylo/man/simulateOutbreak.Rd
TransPhylo/man/plot.ctree.Rd
TransPhylo/man/dateLastSample.Rd
TransPhylo/man/computeMatWIW.Rd
TransPhylo/man/extractTTree.Rd
TransPhylo/man/extractPTree.Rd
TransPhylo/man/plot.resTransPhylo.Rd
TransPhylo/man/plotTraces.Rd
TransPhylo/man/phyloFromPTree.Rd
TransPhylo/man/getSamplingTimeDist.Rd
TransPhylo/man/plotTTree.Rd
TransPhylo/man/getIncidentCases.Rd
TransPhylo/man/probPTreeGivenTTree.Rd
TransPhylo/man/print.ptree.Rd
TransPhylo/DESCRIPTION
TransPhylo/build/
TransPhylo/build/vignette.rds
TransPhylo/tests/
TransPhylo/tests/testthat/
TransPhylo/tests/testthat/test_session.R
TransPhylo/tests/testthat/Rplots.pdf
TransPhylo/tests/testthat/test_trans.R
TransPhylo/tests/testthat/test_coal.R
TransPhylo/tests/testthat.R
TransPhylo/src/
TransPhylo/src/probTTree.cpp
TransPhylo/src/probPTreeGivenTTree.cpp
TransPhylo/src/RcppExports.cpp
TransPhylo/vignettes/
TransPhylo/vignettes/simulate.rmd
TransPhylo/vignettes/multitree.Rmd
TransPhylo/vignettes/infer.Rmd
TransPhylo/vignettes/TransPhylo.Rmd
TransPhylo/R/
TransPhylo/R/proposal.R
TransPhylo/R/methods.R
TransPhylo/R/plotCTree.R
TransPhylo/R/probPTreeGivenTTree.R
TransPhylo/R/ptreeFromPhylo.R
TransPhylo/R/infer_multittree_share_param.R
TransPhylo/R/medTTree.R
TransPhylo/R/TransPhylo-package.R
TransPhylo/R/selectTTree.R
TransPhylo/R/computeHost.R
TransPhylo/R/extractPTree.R
TransPhylo/R/inferTTree.R
TransPhylo/R/plotTTree2.R
TransPhylo/R/interpret.R
TransPhylo/R/RcppExports.R
TransPhylo/R/makeCTreeFromPTree.R
TransPhylo/R/phyloFromPTree.R
TransPhylo/R/makeTTree.R
TransPhylo/R/probTTree.R
TransPhylo/R/withinhost.R
TransPhylo/R/computeMats.R
TransPhylo/R/extras/
TransPhylo/R/extras/transphylo_extras.R
TransPhylo/R/extras/getIncidentCases.R
TransPhylo/R/extractTTree.R
TransPhylo/R/simulateOutbreak.R
TransPhylo/R/convergence.R
TransPhylo/R/plotTTree.R
TransPhylo/R/consTTree.R
TransPhylo/R/glueTrees.R
TransPhylo/MD5
TransPhylo/inst/
TransPhylo/inst/doc/
TransPhylo/inst/doc/TransPhylo.R
TransPhylo/inst/doc/simulate.html
TransPhylo/inst/doc/simulate.rmd
TransPhylo/inst/doc/infer.R
TransPhylo/inst/doc/simulate.R
TransPhylo/inst/doc/infer.html
TransPhylo/inst/doc/multitree.Rmd
TransPhylo/inst/doc/infer.Rmd
TransPhylo/inst/doc/multitree.html
TransPhylo/inst/doc/TransPhylo.Rmd
TransPhylo/inst/doc/TransPhylo.html
TransPhylo/inst/doc/multitree.R
TransPhylo/inst/CITATION
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* installing *source* package ‘TransPhylo’ ...
** this is package ‘TransPhylo’ version ‘1.4.5’
** package ‘TransPhylo’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.3.0’
using C++11
g++ -std=gnu++11 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/fmwnbybr2nzsrxyzsgr63gpvr78ii1gd-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/fmwnbybr2nzsrxyzsgr63gpvr78ii1gd-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c probPTreeGivenTTree.cpp -o probPTreeGivenTTree.o
g++ -std=gnu++11 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/fmwnbybr2nzsrxyzsgr63gpvr78ii1gd-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c probTTree.cpp -o probTTree.o
g++ -std=gnu++11 -shared -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -L/usr/local/lib -o TransPhylo.so RcppExports.o probPTreeGivenTTree.o probTTree.o -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lR
installing to /gnu/store/qzfwa4bm8abf1wn31bm1xbr8dlzdcqsn-r-transphylo-1.4.5/site-library/00LOCK-TransPhylo/00new/TransPhylo/libs
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (TransPhylo)
phase `install' succeeded after 19.3 seconds
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Running specific tests for package ‘TransPhylo’
  Running ‘testthat.R’
Running vignettes for package ‘TransPhylo’
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