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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/bin:/gnu/store/hqysqhh80g7qy8287b8p2gwz0379vh50-tar-1.34/bin:/gnu/store/8rvnivj15gmirawhikgbjaang5b4w779-gzip-1.10/bin:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/bin:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/bin:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/bin:/gnu/store/49j4cjqc8sckyh4qhf9j9dmc6anc8wk9-diffutils-3.8/bin:/gnu/store/znjj5y98lvi46fll85qg22ngz966gx1d-patch-2.7.6/bin:/gnu/store/yq3xalg1p2p5p5hfpw4v5jx0v86qw45w-findutils-4.8.0/bin:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/bin:/gnu/store/dsldg7i4y6hxdknh7cv93rbxbp17xm93-sed-4.8/bin:/gnu/store/4znchc8whjbs50mvxgc0skmkvyhy9xk1-grep-3.6/bin:/gnu/store/wllq3y3sl5bldm9vsx2fcwhcmks4i9ar-coreutils-8.32/bin:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/bin:/gnu/store/2an4h5ndc22dv62q3l985ciq862q4bj7-bash-minimal-5.1.8/bin:/gnu/store/g58zxpycy64m790vwjlzpadmbn065fia-ld-wrapper-0/bin:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/bin:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/bin:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/bin:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/sbin' environment variable `R_LIBS_SITE' set to `/gnu/store/a5ms2xqsialxlxx84qqqrlbzifm29z0d-r-evaluate-0.14/site-library/:/gnu/store/kqxwskrp6ibs25c97rg9fkdmprjjjm6b-r-highr-0.9/site-library/:/gnu/store/xsp9rs2dryj4p37r9kp81y2fyfx6jczb-r-stringr-1.4.0/site-library/:/gnu/store/qdvq4f6n1q469054glyihsggyamx4z0z-r-xfun-0.29/site-library/:/gnu/store/g318xp0lbn7mvcbjbdjzshiz0s18pq4q-r-yaml-2.2.1/site-library/:/gnu/store/3926n38rv4wy355n8xxi4kf8s4im0dj0-r-stringi-1.7.6/site-library/:/gnu/store/fd4abysk2s9q3p76ab16rl402fccqxis-r-magrittr-2.0.1/site-library/:/gnu/store/n8p7yv81vwcddgba17ayrw3d7fkc5c5k-r-glue-1.6.0/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/include:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/include:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/include:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/include:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/include:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/include:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/include:/gnu/store/k8xlwnnmhgmvzyxxfjq3z3fci73zx7x9-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/include:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/include:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/include:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/include:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/include:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/include:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include/c++:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/include:/gnu/store/k8xlwnnmhgmvzyxxfjq3z3fci73zx7x9-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to `/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/lib:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/lib:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/lib:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/lib:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/lib:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/lib:/gnu/store/88bdm10sayqjnggrxlbdmk3rv1qqdrvl-glibc-2.33-static/lib:/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-glibc-utf8-locales-2.33/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-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/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/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/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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/bin/Rscript' patch-shebang: ./inst/examples/knit-all.R: changing `/usr/bin/env Rscript' to `/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/bin/Rscript' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' * 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 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) phase `install' succeeded after 11.0 seconds starting phase `check' Testing examples for package ‘knitr’ phase `check' succeeded after 1.4 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