starting phase `separate-from-pid1'
build process now running as PID 18
phase `separate-from-pid1' succeeded after 0.0 seconds
starting phase `set-SOURCE-DATE-EPOCH'
phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds
starting phase `set-paths'
environment variable `PATH' set to `/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-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:/gnu/store/b3fb4cpvyp7ph43pcidhaylz6nqziqsb-hdf5-1.10.9/bin:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/bin:/gnu/store/9amfkw1z77nqc3idjqxggs9sbmv1j4jp-pandoc-2.19.2/bin'
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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:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/b3fb4cpvyp7ph43pcidhaylz6nqziqsb-hdf5-1.10.9/include:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/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:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/b3fb4cpvyp7ph43pcidhaylz6nqziqsb-hdf5-1.10.9/include:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/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:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/b3fb4cpvyp7ph43pcidhaylz6nqziqsb-hdf5-1.10.9/include:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/include'
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environment variable `GUIX_LOCPATH' set to `/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/lib/locale'
environment variable `TZDIR' unset
environment variable `SSL_CERT_DIR' unset
environment variable `SSL_CERT_FILE' unset
environment variable `CURL_CA_BUNDLE' 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'
mia/CONTRIBUTING.md
mia/DESCRIPTION
mia/LICENSE
mia/MD5
mia/NAMESPACE
mia/NEWS
mia/R/
mia/R/AllGenerics.R
mia/R/RcppExports.R
mia/R/addAlpha.R
mia/R/addDissimilarity.R
mia/R/addDivergence.R
mia/R/addLDA.R
mia/R/addNMF.R
mia/R/agglomerate.R
mia/R/calculateDMM.R
mia/R/calculateJSD.R
mia/R/calculateOverlap.R
mia/R/calculateUnifrac.R
mia/R/cluster.R
mia/R/convertFromBIOM.R
mia/R/convertFromDADA2.R
mia/R/convertFromPhyloseq.R
mia/R/convertToPhyloseq.R
mia/R/decontam.R
mia/R/deprecate.R
mia/R/estimateDiversity.R
mia/R/estimateDominance.R
mia/R/estimateEvenness.R
mia/R/estimateRichness.R
mia/R/getAbundant.R
mia/R/getCrossAssociation.R
mia/R/getDominant.R
mia/R/getMDS.R
mia/R/getPERMANOVA.R
mia/R/getPrevalence.R
mia/R/importHumann.R
mia/R/importMetaphlan.R
mia/R/importMothur.R
mia/R/importQIIME2.R
mia/R/importTaxpasta.R
mia/R/mediate.R
mia/R/meltAssay.R
mia/R/merge.R
mia/R/mergeSEs.R
mia/R/mia.R
mia/R/rarefyAssay.R
mia/R/runCCA.R
mia/R/runDPCoA.R
mia/R/runNMDS.R
mia/R/splitByRanks.R
mia/R/splitOn.R
mia/R/subset.R
mia/R/summaries.R
mia/R/taxonomy.R
mia/R/transformCounts.R
mia/R/utilization_functions.R
mia/R/utils.R
mia/README.md
mia/build/
mia/build/vignette.rds
mia/data/
mia/data/GlobalPatterns.rda
mia/data/HintikkaXOData.rda
mia/data/Tengeler2020.rda
mia/data/Tito2024QMP.rda
mia/data/datalist
mia/data/dmn_se.rda
mia/data/enterotype.rda
mia/data/esophagus.rda
mia/data/peerj13075.rda
mia/inst/
mia/inst/doc/
mia/inst/doc/mia.R
mia/inst/doc/mia.Rmd
mia/inst/doc/mia.html
mia/inst/extdata/
mia/inst/extdata/Aggregated_humanization2.biom
mia/inst/extdata/Data_humanization_phylo_aggregation.tre
mia/inst/extdata/Mapping_file_ADHD_aggregated.csv
mia/inst/extdata/complete.biom
mia/inst/extdata/humann_output.tsv
mia/inst/extdata/less_ranks.biom
mia/inst/extdata/merged_abundance_table.txt
mia/inst/extdata/more_ranks.biom
mia/inst/extdata/mothur_example.cons.taxonomy
mia/inst/extdata/mothur_example.design
mia/inst/extdata/mothur_example.shared
mia/inst/extdata/mothur_example.taxonomy
mia/inst/extdata/refseq.qza
mia/inst/extdata/sample-metadata.tsv
mia/inst/extdata/simple.biom
mia/inst/extdata/table-rownamesInSeq.qza
mia/inst/extdata/table.qza
mia/inst/extdata/taxonomy.qza
mia/inst/extdata/taxpasta_no_type.biom
mia/inst/extdata/tree.qza
mia/inst/scripts/
mia/inst/scripts/Tito2024QMP.R
mia/inst/scripts/biom_test_data.py
mia/inst/scripts/import.R
mia/man/
mia/man/GlobalPatterns.Rd
mia/man/HintikkaXOData.Rd
mia/man/Tengeler2020.Rd
mia/man/Tito2024QMP.Rd
mia/man/addAlpha.Rd
mia/man/addCluster.Rd
mia/man/addDivergence.Rd
mia/man/addLDA.Rd
mia/man/addMDS.Rd
mia/man/addNMF.Rd
mia/man/agglomerate-methods.Rd
mia/man/agglomerateByPrevalence.Rd
mia/man/calculateDMN.Rd
mia/man/convertFromDADA2.Rd
mia/man/convertFromPhyloseq.Rd
mia/man/deprecate.Rd
mia/man/dmn_se.Rd
mia/man/enterotype.Rd
mia/man/esophagus.Rd
mia/man/figures/
mia/man/figures/mia_logo.png
mia/man/getAbundant.Rd
mia/man/getCrossAssociation.Rd
mia/man/getDissimilarity.Rd
mia/man/getDominant.Rd
mia/man/getMediation.Rd
mia/man/getPERMANOVA.Rd
mia/man/getPrevalence.Rd
mia/man/hierarchy-tree.Rd
mia/man/importBIOM.Rd
mia/man/importHUMAnN.Rd
mia/man/importMetaPhlAn.Rd
mia/man/importMothur.Rd
mia/man/importQIIME2.Rd
mia/man/importTaxpasta.Rd
mia/man/isContaminant.Rd
mia/man/meltSE.Rd
mia/man/mergeSEs.Rd
mia/man/mia-datasets.Rd
mia/man/mia-package.Rd
mia/man/peerj13075.Rd
mia/man/rarefyAssay.Rd
mia/man/runCCA.Rd
mia/man/runDPCoA.Rd
mia/man/runNMDS.Rd
mia/man/splitOn.Rd
mia/man/summary.Rd
mia/man/taxonomy-methods.Rd
mia/man/transformAssay.Rd
mia/man/utilization_functions.Rd
mia/src/
mia/src/RcppExports.cpp
mia/src/assay.cpp
mia/src/assay.h
mia/src/faith_R.cpp
mia/src/propmap.cpp
mia/src/propmap.h
mia/src/transformCounts.cpp
mia/src/tree.cpp
mia/src/tree.h
mia/tests/
mia/tests/testthat/
mia/tests/testthat.R
mia/tests/testthat/test-0divergence.R
mia/tests/testthat/test-0diversity.R
mia/tests/testthat/test-0utilites.R
mia/tests/testthat/test-2merge.R
mia/tests/testthat/test-2mergeSEs.R
mia/tests/testthat/test-2taxonomy.R
mia/tests/testthat/test-3agglomerate.R
mia/tests/testthat/test-4IO.R
mia/tests/testthat/test-4splitByRanks.R
mia/tests/testthat/test-4splitOn.R
mia/tests/testthat/test-5Unifrac.R
mia/tests/testthat/test-5addLDA.R
mia/tests/testthat/test-5addNMF.R
mia/tests/testthat/test-5calculateOverlap.R
mia/tests/testthat/test-5dominance.R
mia/tests/testthat/test-5dominantTaxa.R
mia/tests/testthat/test-5evenness.R
mia/tests/testthat/test-5getCrossAssociation.R
mia/tests/testthat/test-5getDissimilarity.R
mia/tests/testthat/test-5prevalence.R
mia/tests/testthat/test-5richness.R
mia/tests/testthat/test-5runDPCoA.R
mia/tests/testthat/test-5runNMDS.R
mia/tests/testthat/test-5transformCounts.R
mia/tests/testthat/test-6cca.R
mia/tests/testthat/test-7decontam.R
mia/tests/testthat/test-8subsample.R
mia/tests/testthat/test-8summaries.R
mia/tests/testthat/test-9cluster.R
mia/tests/testthat/test-addAlpha.R
mia/tests/testthat/test-addMDS.R
mia/tests/testthat/test-getAbundant.R
mia/tests/testthat/test-getPERMANOVA.R
mia/tests/testthat/test-importTaxpasta.R
mia/tests/testthat/test-mediate.R
mia/tests/testthat/test-utilization_functions.R
mia/vignettes/
mia/vignettes/mia.Rmd
mia/vignettes/references.bib
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* installing *source* package ‘mia’ ...
** this is package ‘mia’ version ‘1.18.0’
** package ‘mia’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.3.0’
g++ -std=gnu++17 -I"/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/42z8r975js84k3062hq9jr4ydp11zr60-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++17 -I"/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/42z8r975js84k3062hq9jr4ydp11zr60-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c assay.cpp -o assay.o
g++ -std=gnu++17 -I"/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/42z8r975js84k3062hq9jr4ydp11zr60-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c faith_R.cpp -o faith_R.o
g++ -std=gnu++17 -I"/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/42z8r975js84k3062hq9jr4ydp11zr60-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c propmap.cpp -o propmap.o
g++ -std=gnu++17 -I"/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/42z8r975js84k3062hq9jr4ydp11zr60-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c transformCounts.cpp -o transformCounts.o
g++ -std=gnu++17 -I"/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/include" -DNDEBUG  -I'/gnu/store/42z8r975js84k3062hq9jr4ydp11zr60-r-rcpp-1.1.0/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c tree.cpp -o tree.o
g++ -std=gnu++17 -shared -L/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/lib -L/usr/local/lib -o mia.so RcppExports.o assay.o faith_R.o propmap.o transformCounts.o tree.o -L/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib/R/lib -lR
installing to /gnu/store/m5a7bcy5hvxiv1x9n8xv3kf3kp4ia32i-r-mia-1.18.0/site-library/00LOCK-mia/00new/mia/libs
** R
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** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
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* DONE (mia)
phase `install' succeeded after 110.3 seconds
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Running specific tests for package ‘mia’
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