Running external command line application(s). This may print messages to stdout and/or stderr. The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist. Command: run_new_richness.R /tmp/tmpzr37jyf4/table.tsv /tmp/q2-AlphaDiversityFormat-nyho7jft During startup - Warning message: Setting LC_CTYPE failed, using "C" R version 4.1.3 (2022-03-10) L1S105 L1S140 L1S208 L1S257 L1S281 L1S57 L1S76 L1S8 L2S155 L2S175 L2S204 1 1566 0 0 0 0 2021 2371 1904 4 3 8 2 844 452 671 613 358 276 219 150 0 0 0 3 524 842 493 269 142 739 598 1158 0 0 0 4 384 0 36 5 144 342 374 0 0 0 2 5 355 0 0 0 0 112 89 0 0 0 0 6 174 478 268 107 199 65 176 82 0 4 12 L2S222 L2S240 L2S309 L2S357 L2S382 L3S242 L3S294 L3S313 L3S341 L3S360 L3S378 1 3 0 0 5 2 283 0 4 6 0 0 2 0 0 0 0 0 13 0 0 0 0 68 3 0 3 7 0 0 181 0 0 2 0 156 4 0 0 6 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 6 4 0 5 4 0 1 0 2 0 0 13 L4S112 L4S137 L4S63 L5S104 L5S155 L5S174 L5S203 L5S222 L5S240 L6S20 L6S68 1 37 0 2 4 0 0 0 0 0 0 0 2 0 3 0 0 0 0 2 0 0 2 0 3 0 0 0 0 3 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 6 28 0 0 0 0 0 0 0 0 0 0 L6S93 1 0 2 0 3 0 4 0 5 0 6 0 ade4 ape askpass assertthat backports base base64enc BH Biobase BiocGenerics BiocParallel biomformat Biostrings bitops boot brew brio cachem callr cli clipr cluster codetools colorspace commonmark compiler covr cpp11 crayon credentials crosstalk curl dada2 data.table datasets DelayedArray desc devtools diffobj digest dplyr DT ellipsis evaluate fansi farver fastmap foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges gert ggplot2 gh git2r gitcreds glue graphics grDevices grid gtable highr hms htmltools htmlwidgets httr hwriter igraph ini IRanges isoband iterators jpeg jquerylib jsonlite knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise methods mgcv mime multtest munsell nlme openssl parallel permute phyloseq pillar pixmap pkgbuild pkgconfig pkgload plyr png praise prettyunits processx progress promises ps purrr R.cache R.methodsS3 R.oo R.rsp R.utils R6 rappdirs rcmdcheck RColorBrewer Rcpp RcppParallel RCurl rematch2 remotes reshape2 rex rhdf5 rhdf5filters Rhdf5lib Rhtslib rlang roxygen2 rprojroot Rsamtools rstudioapi rversions S4Vectors scales sessioninfo ShortRead snow sp splines stats stats4 stringi stringr SummarizedExperiment survival sys tcltk testthat tibble tidyselect tools usethis utf8 utils vctrs vegan viridisLite waldo whisker withr xfun xml2 xopen XVector yaml zip zlibbiocYou have tibble installed! You have magrittr installed! Thank god! devtools is already available Great! phyloseq is already available Attempting to make phyloseq object... [1] "otu_table" attr(,"package") [1] "phyloseq" Downloading GitHub repo adw96/breakaway@HEAD rlang (1.0.2 -> 1.0.4 ) [CRAN] ps (1.7.0 -> 1.7.1 ) [CRAN] processx (3.5.3 -> 3.7.0 ) [CRAN] stringi (1.7.6 -> 1.7.8 ) [CRAN] Rcpp (1.0.8.3 -> 1.0.9 ) [CRAN] pkgload (1.2.4 -> 1.3.0 ) [CRAN] callr (3.7.0 -> 3.7.1 ) [CRAN] farver (2.1.0 -> 2.1.1 ) [CRAN] RcppEigen (NA -> 0.3.3.9.2) [CRAN] nloptr (NA -> 2.0.3 ) [CRAN] minqa (NA -> 1.2.4 ) [CRAN] lme4 (NA -> 1.1-30 ) [CRAN] Skipping 1 packages not available: phyloseq Installing 12 packages: rlang, ps, processx, stringi, Rcpp, pkgload, callr, farver, RcppEigen, nloptr, minqa, lme4 trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.0.4.tar.gz' Content type 'application/x-gzip' length 740971 bytes (723 KB) ================================================== downloaded 723 KB trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.1.tar.gz' Content type 'application/x-gzip' length 128664 bytes (125 KB) ================================================== downloaded 125 KB trying URL 'https://cloud.r-project.org/src/contrib/processx_3.7.0.tar.gz' Content type 'application/x-gzip' length 161751 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.7.8.tar.gz' Content type 'application/x-gzip' length 8032287 bytes (7.7 MB) ================================================== downloaded 7.7 MB trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.9.tar.gz' Content type 'application/x-gzip' length 2957812 bytes (2.8 MB) ================================================== downloaded 2.8 MB trying URL 'https://cloud.r-project.org/src/contrib/pkgload_1.3.0.tar.gz' Content type 'application/x-gzip' length 76008 bytes (74 KB) ================================================== downloaded 74 KB trying URL 'https://cloud.r-project.org/src/contrib/callr_3.7.1.tar.gz' Content type 'application/x-gzip' length 90475 bytes (88 KB) ================================================== downloaded 88 KB trying URL 'https://cloud.r-project.org/src/contrib/farver_2.1.1.tar.gz' Content type 'application/x-gzip' length 1274363 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.3.9.2.tar.gz' Content type 'application/x-gzip' length 1476004 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cloud.r-project.org/src/contrib/minqa_1.2.4.tar.gz' Content type 'application/x-gzip' length 53548 bytes (52 KB) ================================================== downloaded 52 KB trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-30.tar.gz' Content type 'application/x-gzip' length 3307884 bytes (3.2 MB) ================================================== downloaded 3.2 MB During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'rlang' ... ** package 'rlang' successfully unpacked and MD5 sums checked ** using staged installation ** libs x86_64-conda-linux-gnu-cc -I"/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/include" -DNDEBUG -I./rlang/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -I/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -Wl,-rpath-link,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -fvisibility=hidden -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -c capture.c -o capture.o /bin/sh: /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/bin/x86_64-conda-linux-gnu-cc: Text file busy make: *** [/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/etc/Makeconf:170: capture.o] Error 126 ERROR: compilation failed for package 'rlang' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/rlang' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/rlang' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'ps' ... ** package 'ps' successfully unpacked and MD5 sums checked ** using staged installation During startup - Warning message: Setting LC_CTYPE failed, using "C" ** libs x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -Wl,-rpath-link,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -L/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -Wall px.c -o px make: x86_64-conda-linux-gnu-cc: Text file busy make: *** [Makevars:11: px] Error 127 ERROR: compilation failed for package 'ps' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/ps' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/ps' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'stringi' ... ** package 'stringi' successfully unpacked and MD5 sums checked ** using staged installation checking for R_HOME... /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R checking for R... /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/bin/R checking for endianness... little checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /usr/bin/cat checking for local ICUDT_DIR... icu69/data checking for x86_64-conda-linux-gnu-gcc... x86_64-conda-linux-gnu-cc checking whether the C compiler works... no configure: error: in `/tmp/Rtmp8NFQsR/R.INSTALL3159a3889547f/stringi': configure: error: C compiler cannot create executables See `config.log' for more details ERROR: configuration failed for package 'stringi' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/stringi' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/stringi' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'Rcpp' ... ** package 'Rcpp' successfully unpacked and MD5 sums checked ** using staged installation ** libs x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -I/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -Wl,-rpath-link,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -c api.cpp -o api.o /bin/sh: /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/bin/x86_64-conda-linux-gnu-c++: Text file busy make: *** [/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/etc/Makeconf:177: api.o] Error 126 ERROR: compilation failed for package 'Rcpp' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/Rcpp' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/Rcpp' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'farver' ... ** package 'farver' successfully unpacked and MD5 sums checked ** using staged installation ** libs x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -I/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -Wl,-rpath-link,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -c ColorSpace.cpp -o ColorSpace.o /bin/sh: /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/bin/x86_64-conda-linux-gnu-c++: Text file busy make: *** [/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/etc/Makeconf:177: ColorSpace.o] Error 126 ERROR: compilation failed for package 'farver' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/farver' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/farver' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'nloptr' ... ** package 'nloptr' successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... no configure: error: in `/tmp/RtmpAIvBQO/R.INSTALL32be734c42ce3/nloptr': configure: error: C++ compiler cannot create executables See `config.log' for more details ERROR: configuration failed for package 'nloptr' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/nloptr' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'processx' ... ** package 'processx' successfully unpacked and MD5 sums checked ** using staged installation ** libs x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -Wl,-rpath-link,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -L/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -Wall tools/px.c -o tools/px make: x86_64-conda-linux-gnu-cc: Text file busy make: *** [Makevars:14: tools/px] Error 127 ERROR: compilation failed for package 'processx' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/processx' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/processx' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'pkgload' ... ** package 'pkgload' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading During startup - Warning message: Setting LC_CTYPE failed, using "C" Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'rlang' 1.0.2 is being loaded, but >= 1.0.3 is required Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package 'pkgload' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/pkgload' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/pkgload' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'RcppEigen' ... ** package 'RcppEigen' successfully unpacked and MD5 sums checked ** using staged installation ** libs x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/include" -DNDEBUG -I'/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -I/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -Wl,-rpath-link,/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib -I../inst/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -c RcppEigen.cpp -o RcppEigen.o /bin/sh: /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/bin/x86_64-conda-linux-gnu-c++: Text file busy make: *** [/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/etc/Makeconf:177: RcppEigen.o] Error 126 ERROR: compilation failed for package 'RcppEigen' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/RcppEigen' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'minqa' ... ** package 'minqa' successfully unpacked and MD5 sums checked ** using staged installation ** libs x86_64-conda-linux-gnu-gfortran -fno-optimize-sibling-calls -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1648745733215/work=/usr/local/src/conda/r-base-4.1.3 -fdebug-prefix-map=/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2=/usr/local/src/conda-prefix -c altmov.f -o altmov.o make: x86_64-conda-linux-gnu-gfortran: Text file busy make: *** [/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/etc/Makeconf:194: altmov.o] Error 127 ERROR: compilation failed for package 'minqa' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/minqa' During startup - Warning message: Setting LC_CTYPE failed, using "C" * installing *source* package 'callr' ... ** package 'callr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading During startup - Warning message: Setting LC_CTYPE failed, using "C" Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace 'processx' 3.5.3 is being loaded, but >= 3.6.1 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted ERROR: lazy loading failed for package 'callr' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/callr' * restoring previous '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/callr' During startup - Warning message: Setting LC_CTYPE failed, using "C" ERROR: dependencies 'minqa', 'nloptr', 'RcppEigen' are not available for package 'lme4' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/lme4' The downloaded source packages are in '/tmp/RtmpC22ZCM/downloaded_packages' Updating HTML index of packages in '.Library' Making 'packages.html' ... done During startup - Warning message: Setting LC_CTYPE failed, using "C" * checking for file '/tmp/RtmpC22ZCM/remotes2e50f7bf60f6b/adw96-breakaway-3b85a4c/DESCRIPTION' ... OK * preparing 'breakaway': * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building 'breakaway_4.7.6.tar.gz' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'breakaway/vignettes/diversity-hypothesis-testing_cache/gfm/unnamed-chunk-12_1014ead0f4a887398570cf3dd580439b.RData' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'breakaway/vignettes/diversity-hypothesis-testing_cache/gfm/unnamed-chunk-12_1014ead0f4a887398570cf3dd580439b.rdb' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'breakaway/vignettes/diversity-hypothesis-testing_cache/gfm/unnamed-chunk-12_1014ead0f4a887398570cf3dd580439b.rdx' Warning in sprintf(gettext(fmt, domain = domain), ...) : one argument not used by format 'invalid uid value replaced by that for user 'nobody'' Warning: invalid uid value replaced by that for user 'nobody' During startup - Warning message: Setting LC_CTYPE failed, using "C" ERROR: dependency 'lme4' is not available for package 'breakaway' * removing '/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/R/library/breakaway' There were 13 warnings (use warnings() to see them) Error in library(breakaway) : there is no package called 'breakaway' Execution halted Traceback (most recent call last): File "/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__ results = action(**arguments) File "", line 2, in alpha File "/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable outputs = self._callable_executor_(scope, callable_args, File "/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_ output_views = self._callable(**view_args) File "/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_breakaway/_alphas.py", line 54, in alpha run_commands([cmd]) File "/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_breakaway/_alphas.py", line 37, in run_commands subprocess.run(cmd, check=True) File "/home/icb/oleg.vlasovetc/miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['run_new_richness.R', '/tmp/tmpzr37jyf4/table.tsv', '/tmp/q2-AlphaDiversityFormat-nyho7jft']' returned non-zero exit status 1.