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environment variable `R_LIBS_SITE' set to `/gnu/store/ilq5rvk514m0qwrqdymrbvw5xw033ir0-r-testthat-3.3.0/site-library/:/gnu/store/jxi8hkg4g3zn2j493kx2k3wb75ij1fsp-r-expm-1.0-0/site-library/:/gnu/store/w00jbinxgx5v7z5613wny9fgq018is2n-r-generics-0.1.4/site-library/:/gnu/store/gycz68wvcsfaj131gna38yvvkrrlmkdy-r-mvtnorm-1.3-3/site-library/:/gnu/store/ihas8v4708f1xishrns9awnxkpx0ns1m-r-survival-3.8-3/site-library/:/gnu/store/bb12icjh971mvvy2apri9zj19xshw9pg-r-tibble-3.3.0/site-library/:/gnu/store/k7wdvs0n6q4mgjflv3pal0hqyr39sa1d-r-withr-3.0.2/site-library/:/gnu/store/j5hl9n32bj7dq6jdkbdryf76c7ybdmz4-r-waldo-0.6.2/site-library/:/gnu/store/q83z93pn0nzi4agvdk6jdaihw1vdi773-r-rlang-1.1.6/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/6hl9rdycd0xyzj0z6vldilcmj7blgwj6-r-magrittr-2.0.4/site-library/:/gnu/store/2jm7igf1lhycvxmng0cf6ay06vh0f2ap-r-lifecycle-1.0.4/site-library/:/gnu/store/v775nkpib6sbz3q59yshrby71c5ykcp8-r-jsonlite-2.0.0/site-library/:/gnu/store/3m2iaw61xgr6nms17y72il0lj21j32jb-r-evaluate-1.0.5/site-library/:/gnu/store/3bhnqpzr7904rryvgs52zkslw30mpwx6-r-desc-1.4.3/site-library/:/gnu/store/3vl9ljw22y3w64wf4vgm3z0a6kgr3x0v-r-cli-3.6.5/site-library/:/gnu/store/j5bpy1jxpshxrscj1iz6134lnqd1z4li-r-callr-3.7.6/site-library/:/gnu/store/2zbz1m7w1fkmgla3ihh201nyanyxd8bs-r-brio-1.1.5/site-library/:/gnu/store/lflfqa06qdkmgm172piwb4im5ksqr3y5-r-matrix-1.7-4/site-library/:/gnu/store/0bksakw9zj510isa7rp33hd72fh0g8nk-r-vctrs-0.6.5/site-library/:/gnu/store/n7lrqyp0svg4ym01sa5cnh4al7y24z3y-r-pkgconfig-2.0.3/site-library/:/gnu/store/dg28sj91vzpa732g27kdvnwvd25054n6-r-pillar-1.11.1/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/h1v0a657shh8x5f5mjwrs8gkwvccl3yg-r-lattice-0.22-7/site-library/:/gnu/store/rbdqzx67lc0i3mnjaxl65q11c928vygc-r-utf8-1.2.6/site-library/:/gnu/store/k47c8nw7vi5m46v1kg7sjrvljji05svm-r-crayon-1.5.3/site-library/'
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msm/
msm/tests/
msm/tests/testthat/
msm/tests/testthat/test_pearson.R
msm/tests/testthat/test_models_misc.r
msm/tests/testthat/test_analyticp.r
msm/tests/testthat/test_weights.R
msm/tests/testthat/test_models_hmm.r
msm/tests/testthat/test_models.r
msm/tests/testthat/test_deriv.r
msm/tests/testthat/test_datasumm.r
msm/tests/testthat/test_viterbi.R
msm/tests/testthat/test_phase.R
msm/tests/testthat/test_hmodel2list.R
msm/tests/testthat/helper.r
msm/tests/testthat/test_simul.R
msm/tests/testthat/test_utils.r
msm/tests/testthat/test_msm2Surv.R
msm/tests/testthat/test_draic.r
msm/tests/testthat/test_models_hmmmulti.r
msm/tests/testthat/test_ppass.R
msm/tests/testthat/test_tidy.R
msm/tests/testthat/test_boot.R
msm/tests/test_base.R
msm/MD5
msm/R/
msm/R/deltamethod.R
msm/R/plot.R
msm/R/hmodel2list.R
msm/R/hmm-dists.R
msm/R/print.R
msm/R/qgeneric.R
msm/R/pearson.R
msm/R/totlos.R
msm/R/constants.R
msm/R/boot.R
msm/R/msm-package.R
msm/R/tnorm.R
msm/R/mstate.R
msm/R/olddata.R
msm/R/simul.R
msm/R/internals_doc.R
msm/R/MatrixExp.R
msm/R/scoreresid.R
msm/R/draic.R
msm/R/prevalence.R
msm/R/pexp.R
msm/R/msm.R
msm/R/hmm.R
msm/R/tidy.R
msm/R/utils.R
msm/R/phase.R
msm/R/optim.R
msm/R/summary.R
msm/R/viterbi.R
msm/R/medists.R
msm/R/efpt.R
msm/R/outputs.R
msm/R/ppass.R
msm/R/datasets_doc.R
msm/vignettes/
msm/vignettes/Sweave-local.sty
msm/vignettes/msm-manual.Rnw
msm/vignettes/figures/
msm/vignettes/figures/fev_viterbi.pdf
msm/vignettes/figures/p5q1_6_7_11_12.pdf
msm/vignettes/figures/sampling.ps
msm/vignettes/figures/sampling.pdf
msm/vignettes/figures/hidden.pdf
msm/vignettes/figures/p2q12.pdf
msm/vignettes/figures/p4q13569.eps
msm/vignettes/figures/p3q1246.pdf
msm/vignettes/figures/p3q14.pdf
msm/vignettes/figures/general.eps
msm/vignettes/figures/dags/
msm/vignettes/figures/dags/p5q1_6_7_11_12.pdf
msm/vignettes/figures/dags/p2q1.odg
msm/vignettes/figures/dags/p5q1_6_7_11_12.odg
msm/vignettes/figures/dags/p3q1246.odg
msm/vignettes/figures/dags/p2q12.ps
msm/vignettes/figures/dags/p3q12.ps
msm/vignettes/figures/dags/p3q14.odg
msm/vignettes/figures/dags/p2q12.pdf
msm/vignettes/figures/dags/p3q1246.ps
msm/vignettes/figures/dags/p3q1246.pdf
msm/vignettes/figures/dags/p3q14.pdf
msm/vignettes/figures/dags/p3q16.odg
msm/vignettes/figures/dags/p5q1_6_7_11_12.ps
msm/vignettes/figures/dags/p4q159.ps
msm/vignettes/figures/dags/p4q159.odg
msm/vignettes/figures/dags/p4q159.pdf
msm/vignettes/figures/dags/p5q1_4_6_8_11_12_16.ps
msm/vignettes/figures/dags/p4q13569.pdf
msm/vignettes/figures/dags/p5q1_6_11_16.ps
msm/vignettes/figures/dags/p2q12.odg
msm/vignettes/figures/dags/p3q135.pdf
msm/vignettes/figures/dags/p3q16.ps
msm/vignettes/figures/dags/p3q12.odg
msm/vignettes/figures/dags/p5q1_6_11_16.pdf
msm/vignettes/figures/dags/p3q135.odg
msm/vignettes/figures/dags/p2q1.pdf
msm/vignettes/figures/dags/p5q1_4_6_8_11_12_16.pdf
msm/vignettes/figures/dags/p3q124.odg
msm/vignettes/figures/dags/p3q124.ps
msm/vignettes/figures/dags/p3q14.ps
msm/vignettes/figures/dags/p4q13569.odg
msm/vignettes/figures/dags/p3q12.pdf
msm/vignettes/figures/dags/p3q135.ps
msm/vignettes/figures/dags/p4q13569.ps
msm/vignettes/figures/dags/p2q1.ps
msm/vignettes/figures/dags/p3q16.pdf
msm/vignettes/figures/dags/p3q124.pdf
msm/vignettes/figures/dags/p5q1_4_6_8_11_12_16.odg
msm/vignettes/figures/dags/p5q1_6_11_16.odg
msm/vignettes/figures/p3q1246.eps
msm/vignettes/figures/p5q1_6_11_16.eps
msm/vignettes/figures/p4q159.pdf
msm/vignettes/figures/p4q13569.pdf
msm/vignettes/figures/p3q135.pdf
msm/vignettes/figures/p5q1_6_11_16.pdf
msm/vignettes/figures/p5q1_6_7_11_12.eps
msm/vignettes/figures/p3q124.eps
msm/vignettes/figures/p3q135.eps
msm/vignettes/figures/p2q1.pdf
msm/vignettes/figures/illdeath.pdf
msm/vignettes/figures/p3q16.eps
msm/vignettes/figures/p5q1_4_6_8_11_12_16.pdf
msm/vignettes/figures/multistate.eps
msm/vignettes/figures/p4q159.eps
msm/vignettes/figures/multistate.pdf
msm/vignettes/figures/p3q12.pdf
msm/vignettes/figures/illdeath.eps
msm/vignettes/figures/general.pdf
msm/vignettes/figures/p2q1.eps
msm/vignettes/figures/p3q14.eps
msm/vignettes/figures/p3q16.pdf
msm/vignettes/figures/p3q12.eps
msm/vignettes/figures/p3q124.pdf
msm/vignettes/figures/p5q1_4_6_8_11_12_16.eps
msm/vignettes/figures/p2q12.eps
msm/vignettes/figures/hidden.ps
msm/vignettes/msm.bib
msm/data/
msm/data/msmdata.rda
msm/data/bos3.rda
msm/data/bos4.rda
msm/src/
msm/src/pijt.c
msm/src/msm.h
msm/src/hmm.h
msm/src/expm.h
msm/src/Makevars
msm/src/hmmderiv.c
msm/src/hmm.c
msm/src/msm-init.c
msm/src/lik.c
msm/src/analyticp.c
msm/ChangeLog
msm/NAMESPACE
msm/NEWS.md
msm/inst/
msm/inst/CITATION
msm/inst/doc/
msm/inst/doc/msm-manual.R
msm/inst/doc/msm-manual.Rnw
msm/inst/doc/msm-manual.pdf
msm/inst/NEWS
msm/build/
msm/build/vignette.rds
msm/man/
msm/man/prevalence.msm.Rd
msm/man/simmulti.msm.Rd
msm/man/msm2Surv.Rd
msm/man/msm.form.qoutput.Rd
msm/man/updatepars.msm.Rd
msm/man/hmm-dists.Rd
msm/man/plot.prevalence.msm.Rd
msm/man/statetable.msm.Rd
msm/man/printold.msm.Rd
msm/man/plot.survfit.msm.Rd
msm/man/aneur.Rd
msm/man/qratio.msm.Rd
msm/man/pnext.msm.Rd
msm/man/lrtest.msm.Rd
msm/man/pexp.Rd
msm/man/medists.Rd
msm/man/cav.Rd
msm/man/logLik.msm.Rd
msm/man/ematrix.msm.Rd
msm/man/simfitted.msm.Rd
msm/man/tidy.msm.prevalence.Rd
msm/man/qcmodel.object.Rd
msm/man/tidy.msm.estbystate.Rd
msm/man/twophase.Rd
msm/man/hmmMV.Rd
msm/man/hmodel2list.Rd
msm/man/print.msm.Rd
msm/man/totlos.msm.Rd
msm/man/pmatrix.piecewise.msm.Rd
msm/man/hmodel.object.Rd
msm/man/qgeneric.Rd
msm/man/summary.msm.Rd
msm/man/crudeinits.msm.Rd
msm/man/draic.msm.Rd
msm/man/deltamethod.Rd
msm/man/surface.msm.Rd
msm/man/efpt.msm.Rd
msm/man/emodel.object.Rd
msm/man/psor.Rd
msm/man/bos.Rd
msm/man/fev.Rd
msm/man/tidy.msm.Rd
msm/man/pmatrix.msm.Rd
msm/man/cmodel.object.Rd
msm/man/recreate.olddata.Rd
msm/man/boot.msm.Rd
msm/man/ecmodel.object.Rd
msm/man/viterbi.msm.Rd
msm/man/odds.msm.Rd
msm/man/MatrixExp.Rd
msm/man/phasemeans.msm.Rd
msm/man/msm-package.Rd
msm/man/scoreresid.msm.Rd
msm/man/msm.Rd
msm/man/qmatrix.msm.Rd
msm/man/tnorm.Rd
msm/man/coef.msm.Rd
msm/man/sojourn.msm.Rd
msm/man/sim.msm.Rd
msm/man/qmodel.object.Rd
msm/man/model.frame.msm.Rd
msm/man/transient.msm.Rd
msm/man/msm.object.Rd
msm/man/plot.msm.Rd
msm/man/hazard.msm.Rd
msm/man/pearson.msm.Rd
msm/man/paramdata.object.Rd
msm/man/ppass.msm.Rd
msm/man/plotprog.msm.Rd
msm/man/tidy.msm.est.Rd
msm/DESCRIPTION
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* installing *source* package ‘msm’ ...
** this is package ‘msm’ version ‘1.8.2’
** package ‘msm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 14.3.0’
gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c analyticp.c -o analyticp.o
gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c hmm.c -o hmm.o
gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c hmmderiv.c -o hmmderiv.o
gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lik.c -o lik.o
gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c msm-init.c -o msm-init.o
gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c pijt.c -o pijt.o
gcc -std=gnu23 -shared -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -L/usr/local/lib -o msm.so analyticp.o hmm.o hmmderiv.o lik.o msm-init.o pijt.o -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lRlapack -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lRblas -L/gnu/store/qysmiprwgpnly3fjjzbydm29fi85ijrf-gfortran-14.3.0-lib/lib/gcc/x86_64-unknown-linux-gnu/14.3.0 -L/gnu/store/qysmiprwgpnly3fjjzbydm29fi85ijrf-gfortran-14.3.0-lib/lib -lgfortran -lm -lquadmath -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lR
installing to /gnu/store/npy388f0m2xcxr5c51jfx73mhvxq87cp-r-msm-1.8.2/site-library/00LOCK-msm/00new/msm/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (msm)
phase `install' succeeded after 20.6 seconds
starting phase `check'
Running specific tests for package ‘msm’
  Running ‘test_base.R’
Running vignettes for package ‘msm’
  Running ‘msm-manual.Rnw’
phase `check' succeeded after 114.0 seconds
starting phase `patch-shebangs'
phase `patch-shebangs' succeeded after 0.0 seconds
starting phase `strip'
phase `strip' succeeded after 0.0 seconds
starting phase `validate-runpath'
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'
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