Error: user-error ("Org export aborted. Unable to resolve link: \"introduction\"
See `org-export-with-broken-links'")
signal(user-error ("Org export aborted. Unable to resolve link: \"introduction\"\nSee `org-export-with-broken-links'"))
user-error("Org export aborted. Unable to resolve link: %S\nSee `org-export-with-broken-links'" "introduction")
org-export-data((link (:standard-properties [115 nil 132 144 146 0 nil nil nil nil nil nil nil nil # nil nil (paragraph (:standard-properties [115 115 115 147 147 0 nil nil nil nil nil nil nil nil # nil nil (item (:standard-properties [113 113 115 147 147 0 (:tag) item nil nil nil nil nil nil # nil ((113 0 "- " nil nil nil 147) (147 0 "- " nil nil nil 209) (209 0 "- " nil nil nil 259)) (plain-list (:standard-properties [113 113 113 259 260 1 nil planning nil nil nil nil nil nil # nil ((113 0 "- " nil nil nil 147) (147 0 "- " nil nil nil 209) (209 0 "- " nil nil nil 259)) (section (:standard-properties [113 113 113 260 260 0 nil section nil nil nil 113 260 nil # nil nil (headline (:standard-properties [35 35 113 260 260 0 (:title) nil nil nil nil 115 258 1 # nil nil (org-data (:standard-properties [1 1 1 2857 2857 0 nil org-data nil nil nil 3 2857 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 35 35 0 nil first-section nil nil nil 1 35 nil # nil nil #30]) (keyword (:standard-properties [1 1 nil nil 35 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Genenetwork2 Dockerized"))) #25 (headline (:standard-properties [260 260 276 926 926 0 (:title) nil nil nil nil 278 924 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [276 276 276 926 926 0 nil section nil nil nil 276 926 nil # nil nil #35]) (paragraph (:standard-properties [276 276 276 599 600 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("The CI(Continuous Integration) system for Genenetwork2 uses " 0 60 (:parent #41)) (link (:standard-properties [336 nil 375 389 391 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/features/actions" :format bracket :raw-link "https://github.com/features/actions" :application nil :search-option nil) #("Github\nActions" 0 14 (:parent #45))) #(". As such, it's important to have a way to run tests using\nfacilities provided by GUIX in a reproducible way. This project\nleverages GUIX to generate a docker container from which the unittests\nare ran from.\n" 0 208 (:parent #41))) (paragraph (:standard-properties [600 600 600 829 830 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Find instructions on how to set docker up inside GUIX " 0 54 (:parent #42)) (link (:standard-properties [654 nil 732 736 738 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker" :application nil :search-option nil) #("here" 0 4 (:parent #46))) #(". This\ndocument will not get into that. It's assumed that you have a working\ndocker setup.\n" 0 91 (:parent #42))) (paragraph (:standard-properties [830 830 830 925 926 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("The rest of this document outlines how the docker container used in\nthe CI builds was created.\n" 0 95 (:parent #43))))) (headline (:standard-properties [926 926 956 2234 2234 0 (:title) nil nil nil nil 958 2232 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 28) t] :title (#("Creating the Docker Images" 0 26 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [956 956 956 2234 2234 0 nil section nil nil nil 956 2234 nil # nil nil #36]) (paragraph (:standard-properties [956 956 956 1070 1071 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("The general idea is that GUIX is used to generate a set of binaries,\nwhich will be added to a base mariaDB image.\n" 0 114 (:parent #42))) (paragraph (:standard-properties [1071 1071 1071 1116 1117 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("First create the gn2 tar archive by running:\n" 0 45 (:parent #43))) (src-block (:standard-properties [1117 1117 nil nil 1343 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 215) t])) (paragraph (:standard-properties [1343 1343 1343 1386 1387 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("The output will look something similar to:\n" 0 43 (:parent #45))) (fixed-width (:standard-properties [1387 1387 nil nil 1454 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "/gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz")) (paragraph (:standard-properties [1454 1454 1454 1639 1640 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Now create a folder from which will host the following dockerfile. You\ncan name this file Dockerfile. Note that mariadb is the base image\nsince it already has mariadb installed for us.\n" 0 185 (:parent #47))) (src-block (:standard-properties [1640 1640 nil nil 1887 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "conf" :switches nil :parameters ":mkdirp yes :tangle ~/docker/Dockerfile" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (57 236) t])) (paragraph (:standard-properties [1887 1887 1887 1934 1935 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Build the image(Note the fullstop at the end):\n" 0 47 (:parent #49))) (fixed-width (:standard-properties [1935 1935 nil nil 1995 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "sudo docker build -t genenetwork2:latest -f Dockerfile .")) (paragraph (:standard-properties [1995 1995 1995 2048 2049 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("To load the image interactively you've just created:\n" 0 53 (:parent #51))) (fixed-width (:standard-properties [2049 2049 nil nil 2094 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "docker run -ti \"genenetwork2:latest\" bash")) (paragraph (:standard-properties [2094 2094 2094 2180 2181 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Assuming you have a docker instance running, you could always run\ncommands in it e.g:\n" 0 86 (:parent #53))) (fixed-width (:standard-properties [2181 2181 nil nil 2234 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "docker run \"genenetwork2:latest\" python --version")))) (headline (:standard-properties [2234 2234 2258 2857 2857 0 (:title) nil nil nil nil 2260 2855 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("Pushing to DockerHub" 0 20 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2258 2258 2258 2857 2857 0 nil section nil nil nil 2258 2857 nil # nil nil #37]) (paragraph (:standard-properties [2258 2258 2258 2364 2365 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("We use DockerHub to store the docker images from which we use on our\nCI environment using Github Actions.\n" 0 106 (:parent #43))) (paragraph (:standard-properties [2365 2365 2365 2486 2487 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To push to dockerhub, first get the image name by running " 0 58 (:parent #44)) (verbatim (:standard-properties [2423 nil nil nil 2438 0 nil nil nil nil nil nil nil nil # nil nil #44] :value [org-element-deferred org-element--substring (1 14) t])) #(". Push to dockerhub using a command similar to:\n" 0 48 (:parent #44))) (fixed-width (:standard-properties [2487 2487 nil nil 2534 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "docker push bonfacekilz/genenetwork2:latest")) (paragraph (:standard-properties [2534 2534 2534 2576 2577 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Right now, we have 2 images on DockerHub:\n" 0 42 (:parent #46))) (plain-list (:standard-properties [2577 2577 2577 2857 2857 0 nil nil nil nil nil nil nil nil # nil ((2577 0 "- " nil nil nil 2741) (2741 0 "- " nil nil nil 2857)) #40] :type unordered) (item (:standard-properties [2577 2577 2579 2741 2741 0 (:tag) item nil nil nil nil nil nil # nil ((2577 0 "- " nil nil nil 2741) (2741 0 "- " nil nil nil 2857)) #47] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2579 2579 2579 2741 2741 0 nil nil nil nil nil nil nil nil # nil nil #50]) (link (:standard-properties [2579 nil nil nil 2652 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2" :application nil :search-option nil)) #(":\n Contains the python2 version of gn2. Don't use this. Please use the\n python3 image!\n" 0 89 (:parent #53)))) (item (:standard-properties [2741 2741 2743 2857 2857 0 (:tag) item nil nil nil nil nil nil # nil ((2577 0 "- " nil nil nil 2741) (2741 0 "- " nil nil nil 2857)) #47] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2743 2743 2743 2857 2857 0 nil nil nil nil nil nil nil nil # nil nil #51]) (link (:standard-properties [2743 nil nil nil 2816 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "https" :type-explicit-p t :path "//hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2" :format plain :raw-link "https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2" :application nil :search-option nil)) #(":\n Contains the python3 version of gn2.\n" 0 41 (:parent #54))))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil 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