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/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/bin:/gnu/store/99c25918hl9pihix8hparmc96q6zrpwy-tar-1.34/bin:/gnu/store/l0yga4lrwwf74rz7fb0dadglg27ajpsx-gzip-1.10/bin:/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/bin:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/bin:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/bin:/gnu/store/h0rx6y95zin61fp5wlyjly4g9j2hma18-diffutils-3.8/bin:/gnu/store/7j8j7m0kgb7kv2fc18qvrdj7gs3jc4mx-patch-2.7.6/bin:/gnu/store/x4yglk9pn2s2ixl1b4lj151bd2yvlgww-findutils-4.8.0/bin:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/bin:/gnu/store/cnwr7widbi6470kfyb13krx46kz5anmy-sed-4.8/bin:/gnu/store/bx47clwnxn51m7jdwfimz4lw2fh8g21v-grep-3.6/bin:/gnu/store/9a0cjh929maqvkxn3inv6jqbxn72fkx0-coreutils-8.32/bin:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/bin:/gnu/store/7s2zlc4r9wqvlh9x2gqmzm4lnmbsdzmn-bash-minimal-5.1.8/bin:/gnu/store/4bzvr16pyax9224v9r72rqxswj9931sb-ld-wrapper-0/bin:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/bin:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/bin:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/bin:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/sbin' environment variable `R_LIBS_SITE' set to `/gnu/store/ds1cffn0c2xgihll60bqr1kgnnd61ixy-r-evaluate-0.15/site-library/:/gnu/store/ig10kl87xzcjhzw3kv2w4ychf42yp19c-r-highr-0.9/site-library/:/gnu/store/iyp7hrr5188mrdhahs3irq3i74zlyndn-r-stringr-1.4.0/site-library/:/gnu/store/yhb7aqvv6q7niskk8abkfm6c49l2jwzd-r-xfun-0.31/site-library/:/gnu/store/gncaf9nlzjp7z6j7rjnhmpi3id7f3d2z-r-yaml-2.3.5/site-library/:/gnu/store/kdy7lp6f2v7jzg1w6mp9rcn1n8azfg7g-r-stringi-1.7.6/site-library/:/gnu/store/wg7w9ix2cjgsx2c5skx8pij7mjifi4w8-r-magrittr-2.0.3/site-library/:/gnu/store/1n4f86cwnddvq0dmcqp9y6ak1mdk9wf1-r-glue-1.6.2/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/include:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/include:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/include:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/include:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/include:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/include:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/include:/gnu/store/wsx4kz1gh6cpdhx393frhqknmswbggq8-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/include:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/include:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/include:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/include:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/include:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/include:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include/c++:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/include:/gnu/store/wsx4kz1gh6cpdhx393frhqknmswbggq8-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to `/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib:/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/lib:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/lib:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/lib:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/lib:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/lib:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/lib:/gnu/store/1s4k8h3h1ka9za4yzg0dfjnlhab5k14p-glibc-2.33-static/lib:/gnu/store/6p5m4cv8psfzy5xn5yhvhmjl261wg34m-glibc-utf8-locales-2.33/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/6p5m4cv8psfzy5xn5yhvhmjl261wg34m-glibc-utf8-locales-2.33/lib/locale' phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' knitr/ knitr/NAMESPACE knitr/demo/ knitr/demo/gwidgets.R knitr/demo/notebook.R knitr/demo/00Index knitr/.Rinstignore knitr/man/ knitr/man/engine_output.Rd knitr/man/stitch.Rd knitr/man/read_rforge.Rd knitr/man/knit_params.Rd knitr/man/include_url.Rd knitr/man/inline_expr.Rd knitr/man/knitr-package.Rd knitr/man/set_header.Rd knitr/man/partition_chunk.Rd knitr/man/dep_auto.Rd knitr/man/opts_hooks.Rd knitr/man/vignette_engines.Rd knitr/man/hook_plot.Rd knitr/man/current_input.Rd knitr/man/write_bib.Rd knitr/man/rst2pdf.Rd knitr/man/knit_global.Rd knitr/man/rnw2pdf.Rd knitr/man/knit2wp.Rd knitr/man/knit_watch.Rd knitr/man/knit_patterns.Rd knitr/man/all_patterns.Rd knitr/man/is_low_change.Rd knitr/man/asis_output.Rd knitr/man/pandoc.Rd knitr/man/opts_template.Rd knitr/man/hook_animation.Rd knitr/man/raw_output.Rd knitr/man/dep_prev.Rd knitr/man/all_labels.Rd knitr/man/knit_code.Rd knitr/man/set_alias.Rd knitr/man/raw_block.Rd knitr/man/image_uri.Rd knitr/man/kable.Rd knitr/man/spin_child.Rd knitr/man/knit_filter.Rd knitr/man/knit_theme.Rd knitr/man/knit_rd.Rd knitr/man/combine_words.Rd knitr/man/hook_document.Rd knitr/man/rand_seed.Rd knitr/man/sew.Rd knitr/man/rocco.Rd knitr/man/imgur_upload.Rd knitr/man/Sweave2knitr.Rd knitr/man/opts_knit.Rd knitr/man/knit_params_yaml.Rd knitr/man/knit_child.Rd knitr/man/knit_print.Rd knitr/man/wrap_rmd.Rd knitr/man/fig_path.Rd knitr/man/opts_chunk.Rd knitr/man/fig_chunk.Rd knitr/man/plot_crop.Rd knitr/man/output_type.Rd knitr/man/knit_engines.Rd knitr/man/knit_expand.Rd knitr/man/load_cache.Rd knitr/man/set_parent.Rd knitr/man/knit2pandoc.Rd knitr/man/chunk_hook.Rd knitr/man/knit_hooks.Rd knitr/man/spin.Rd knitr/man/read_chunk.Rd knitr/man/knit_meta.Rd knitr/man/clean_cache.Rd knitr/man/knit2html.Rd knitr/man/pat_fun.Rd knitr/man/include_graphics.Rd knitr/man/knit2pdf.Rd knitr/man/cache_engines.Rd knitr/man/knit_exit.Rd knitr/man/output_hooks.Rd knitr/man/knit.Rd knitr/DESCRIPTION knitr/build/ knitr/build/vignette.rds knitr/tests/ knitr/tests/run-all.R knitr/tests/testit/ knitr/tests/testit/test-table.R knitr/tests/testit/test-tangle.R knitr/tests/testit/knit-tikzDevice.Rnw knitr/tests/testit/test-envir.R knitr/tests/testit/knit-handlers.Rmd knitr/tests/testit/acid.style knitr/tests/testit/test-block.R knitr/tests/testit/test-params.R knitr/tests/testit/test-patterns.R knitr/tests/testit/test-spin.R knitr/tests/testit/test-citation.R knitr/tests/testit/test-parser.R knitr/tests/testit/test-closure.R knitr/tests/testit/test-plot.R knitr/tests/testit/test-sql.R knitr/tests/testit/test-utils.R knitr/tests/testit/test-themes.R knitr/tests/testit/test-cache.R knitr/tests/testit/test-output.R knitr/tests/testit/test-templates.R knitr/tests/testit/test-hooks-md.R knitr/tests/testit/knit-envir.Rmd knitr/vignettes/ knitr/vignettes/knit_print.Rmd knitr/vignettes/docco-linear.Rmd knitr/vignettes/datatables.Rmd knitr/vignettes/knitr-refcard.Rmd knitr/vignettes/knitr-markdown.Rmd knitr/vignettes/docco-classic.Rmd knitr/vignettes/assets/ knitr/vignettes/assets/template-refcard.tex knitr/vignettes/knitr-html.Rhtml knitr/vignettes/knit_expand.Rmd knitr/vignettes/knitr-intro.Rmd knitr/R/ knitr/R/hooks-asciidoc.R knitr/R/hooks-rst.R knitr/R/utils-sweave.R knitr/R/hooks-latex.R knitr/R/template.R knitr/R/utils.R knitr/R/zzz.R knitr/R/pandoc.R knitr/R/table.R knitr/R/engine.R knitr/R/hooks-html.R knitr/R/utils-conversion.R knitr/R/parser.R knitr/R/concordance.R knitr/R/hooks-chunk.R knitr/R/params.R knitr/R/hooks-extra.R knitr/R/hooks.R knitr/R/spin.R knitr/R/hooks-md.R knitr/R/utils-upload.R knitr/R/defaults.R knitr/R/block.R knitr/R/rocco.R knitr/R/hooks-textile.R knitr/R/plot.R knitr/R/cache.R knitr/R/pattern.R knitr/R/highlight.R knitr/R/utils-vignettes.R knitr/R/utils-rd2html.R knitr/R/header.R knitr/R/package.R knitr/R/citation.R knitr/R/output.R knitr/R/themes.R knitr/MD5 knitr/inst/ knitr/inst/opencpu/ knitr/inst/opencpu/apps/ knitr/inst/opencpu/apps/index.html knitr/inst/examples/ knitr/inst/examples/upload-github.R knitr/inst/examples/knitr-subfloats.Rnw knitr/inst/examples/knitr-minimal.Rnw knitr/inst/examples/knitr-twocolumn.lyx knitr/inst/examples/knitr-minimal.lyx knitr/inst/examples/knitr-manual.Rnw knitr/inst/examples/knitr-themes.lyx knitr/inst/examples/knitr-listings.lyx knitr/inst/examples/knitr-minimal.brew knitr/inst/examples/knitr-minimal.Rmd knitr/inst/examples/knitr-graphics.lyx knitr/inst/examples/knitr-packages.bib knitr/inst/examples/knitr-latex.Rtex knitr/inst/examples/README.md knitr/inst/examples/knitr-beamer.Rnw knitr/inst/examples/knitr-subfloats.lyx knitr/inst/examples/knitr-minimal.Rrst knitr/inst/examples/knitr-spin.Rmd knitr/inst/examples/knit-all.R knitr/inst/examples/knitr-twocolumn.Rnw knitr/inst/examples/knitr-manual.lyx knitr/inst/examples/knitr-graphics.Rnw knitr/inst/examples/knitr-spin.R knitr/inst/examples/knitr-listings.Rnw knitr/inst/examples/knitr-manual.bib knitr/inst/examples/Sweavel.sty knitr/inst/examples/download_count.csv knitr/inst/examples/knitr-input.Rnw knitr/inst/examples/knitr-beamer.lyx knitr/inst/examples/child/ knitr/inst/examples/child/knitr-child.Rmd knitr/inst/examples/child/knitr-child-b.Rnw knitr/inst/examples/child/knitr-main.Rnw knitr/inst/examples/child/knitr-main.Rmd knitr/inst/examples/child/sub/ knitr/inst/examples/child/sub/knitr-child-c.Rnw knitr/inst/examples/child/knitr-child-a.Rnw knitr/inst/examples/child/knitr-parent.Rnw knitr/inst/examples/knitr-themes.Rnw knitr/inst/examples/knitr-input-child.Rnw knitr/inst/examples/knitr-spin.html knitr/inst/misc/ knitr/inst/misc/knitr.css knitr/inst/misc/stitch-test.R knitr/inst/misc/knitr.sty knitr/inst/misc/vignette.html knitr/inst/misc/docco-classic.css knitr/inst/misc/tweak_bib.csv knitr/inst/misc/knitr-template.Rhtml knitr/inst/misc/knitr-template.Rnw knitr/inst/misc/tikz2pdf.tex knitr/inst/misc/knitr-template.Rmd knitr/inst/misc/vignette.css knitr/inst/misc/docco-classic.html knitr/inst/misc/Sweavel.sty knitr/inst/misc/docco-template.html knitr/inst/misc/R.css knitr/inst/misc/gWidgetsWWW2-knitr.R knitr/inst/misc/toggleR.js knitr/inst/misc/datatables.html knitr/inst/doc/ knitr/inst/doc/knitr-html.html knitr/inst/doc/knit_print.Rmd knitr/inst/doc/docco-linear.html knitr/inst/doc/docco-linear.Rmd knitr/inst/doc/knit_expand.html knitr/inst/doc/knitr-refcard.pdf knitr/inst/doc/datatables.Rmd knitr/inst/doc/knitr-refcard.Rmd knitr/inst/doc/knit_print.R knitr/inst/doc/knitr-markdown.Rmd knitr/inst/doc/docco-classic.Rmd knitr/inst/doc/knitr-markdown.R knitr/inst/doc/datatables.R knitr/inst/doc/knit_print.html knitr/inst/doc/knitr-html.Rhtml knitr/inst/doc/knitr-intro.R knitr/inst/doc/knitr-markdown.html knitr/inst/doc/docco-classic.html knitr/inst/doc/knit_expand.Rmd knitr/inst/doc/knitr-intro.Rmd knitr/inst/doc/knitr-html.R knitr/inst/doc/docco-classic.R knitr/inst/doc/docco-linear.R knitr/inst/doc/knitr-intro.html knitr/inst/doc/knit_expand.R knitr/inst/doc/datatables.html knitr/inst/bin/ knitr/inst/bin/knit knitr/inst/CITATION knitr/inst/themes/ knitr/inst/themes/bluegreen.css knitr/inst/themes/anotherdark.css knitr/inst/themes/candy.css knitr/inst/themes/edit-xcode.css knitr/inst/themes/freya.css knitr/inst/themes/lucretia.css knitr/inst/themes/greyscale0.css knitr/inst/themes/camo.css knitr/inst/themes/greyscale2.css knitr/inst/themes/darkspectrum.css knitr/inst/themes/orion.css knitr/inst/themes/darkblue.css knitr/inst/themes/earendel.css knitr/inst/themes/edit-nedit.css knitr/inst/themes/edit-eclipse.css knitr/inst/themes/edit-vim-dark.css knitr/inst/themes/acid.css knitr/inst/themes/leo.css knitr/inst/themes/clarity.css knitr/inst/themes/edit-matlab.css knitr/inst/themes/solarized-light.css knitr/inst/themes/baycomb.css knitr/inst/themes/rand01.css knitr/inst/themes/greyscale1.css knitr/inst/themes/bright.css knitr/inst/themes/biogoo.css knitr/inst/themes/nightshimmer.css knitr/inst/themes/rootwater.css knitr/inst/themes/zmrok.css knitr/inst/themes/denim.css knitr/inst/themes/edit-jedit.css knitr/inst/themes/molokai.css knitr/inst/themes/nuvola.css knitr/inst/themes/maroloccio.css knitr/inst/themes/edit-anjuta.css knitr/inst/themes/zellner.css knitr/inst/themes/default.css knitr/inst/themes/darkness.css knitr/inst/themes/relaxedgreen.css knitr/inst/themes/aiseered.css knitr/inst/themes/neon.css knitr/inst/themes/zenburn.css knitr/inst/themes/xoria256.css knitr/inst/themes/oxygenated.css knitr/inst/themes/navy.css knitr/inst/themes/dante.css knitr/inst/themes/darkbone.css knitr/inst/themes/whitengrey.css knitr/inst/themes/blacknblue.css knitr/inst/themes/darkslategray.css knitr/inst/themes/greenlcd.css knitr/inst/themes/seashell.css knitr/inst/themes/tcsoft.css knitr/inst/themes/moe.css knitr/inst/themes/edit-vim.css knitr/inst/themes/ekvoli.css knitr/inst/themes/peaksea.css knitr/inst/themes/bclear.css knitr/inst/themes/edit-emacs.css knitr/inst/themes/matrix.css knitr/inst/themes/tabula.css knitr/inst/themes/fine_blue.css knitr/inst/themes/navajo-night.css knitr/inst/themes/autumn.css knitr/inst/themes/easter.css knitr/inst/themes/pablo.css knitr/inst/themes/golden.css knitr/inst/themes/vampire.css knitr/inst/themes/fruit.css knitr/inst/themes/manxome.css knitr/inst/themes/bipolar.css knitr/inst/themes/rdark.css knitr/inst/themes/edit-msvs2008.css knitr/inst/themes/andes.css knitr/inst/themes/solarized-dark.css knitr/inst/themes/breeze.css knitr/inst/themes/edit-flashdevelop.css knitr/inst/themes/night.css knitr/inst/themes/olive.css knitr/inst/themes/kellys.css knitr/inst/themes/edit-kwrite.css knitr/inst/themes/edit-gedit.css knitr/inst/themes/moria.css knitr/inst/themes/print.css knitr/inst/themes/dusk.css knitr/inst/shiny/ knitr/inst/shiny/server.R knitr/inst/shiny/www/ knitr/inst/shiny/www/ace-shiny.js knitr/inst/shiny/www/ace-shiny.css knitr/inst/shiny/ui.R knitr/inst/NEWS.Rd phase `unpack' 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' patch-shebang: ./inst/bin/knit: changing `/usr/bin/env Rscript' to `/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/bin/Rscript' patch-shebang: ./inst/examples/knit-all.R: changing `/usr/bin/env Rscript' to `/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/bin/Rscript' phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory * installing *source* package ‘knitr’ ... files ‘inst/bin/knit’, ‘inst/examples/knit-all.R’ have the wrong MD5 checksums ** using staged installation ** R ** demo ** inst ** tests ** byte-compile and prepare package for lazy loading Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** help *** installing help indices ** building package indices Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** installing vignettes ** testing if installed package can be loaded from temporary location Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** testing if installed package can be loaded from final location Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** testing if installed package keeps a record of temporary installation path * DONE (knitr) phase `install' succeeded after 12.8 seconds starting phase `check' Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Testing examples for package ‘knitr’ phase `check' succeeded after 1.5 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