Session info
diff --git a/pkgdown.yml b/pkgdown.yml
index c6d3ef2..bd41640 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7.9000
pkgdown_sha: 548a9493b72ff93d3ed8392d4ad30b77d8b15fa5
articles:
biocroxytest: biocroxytest.html
-last_built: 2024-01-17T11:01Z
+last_built: 2024-01-17T11:10Z
urls:
reference: https://xec-cm.github.io/biocroxytest/reference
article: https://xec-cm.github.io/biocroxytest/articles
diff --git a/search.json b/search.json
index 435c4c0..15fef07 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.
Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions","title":"GNU General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Automatic Licensing of Downstream Recipients","title":"GNU General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. 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Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom","title":"GNU General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_13-use-with-the-gnu-affero-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see
. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read
.","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction to biocroxytest","text":"biocroxytest package novel tool enhances efficiency test writing R, particularly Bioconductor software packages. leverages structure roxygen2 test writing, improves readability, code organization, integrates seamlessly package documentation. Bioconductor, daily tests run part nightly builds, maximum limit 40 minutes per package. tests exceed limit, developers can set “long tests” add package Bioconductor Long Tests builds. However, traditionally separating tests long tests can cumbersome. biocroxytest addresses issue introducing new roclet, @longtests, inspired roxytest. allows developers document store long tests directly within roxygen2 comments. using @longtests roclet, extensive tests run checked regularly without impacting efficiency daily build process. @longtests roclet provides dedicated space extensive tests, ensuring easily accessible well-documented. improves package’s reliability also maintainability. Thus, biocroxytest contributes creation robust, reliable, efficient Bioconductor packages.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"biocroxytest-setup","dir":"Articles","previous_headings":"","what":"biocroxytest setup","title":"Introduction to biocroxytest","text":"biocroxytest package installed, need carry two steps correctly set long tests package: Add new roclet Description file: need add biocroxytest::longtests_roclet Roxygen section Description file. enable roxygen2::roxygenize() generate long tests @longtest tag. Description file line similar : Run biocroxytest::use_longtests() function: function sets overall infrastructure long tests. run, creates longtests/testthat directory longtests/testthat.R file, necessary storing running long tests. Additionally, generates file named .BBSoptions contains RunLongTests: TRUE parameter, indicating long tests run Bioconductor servers. two steps, package set write, document, store long tests directly roxygen2 comments, improving efficiency organization test code.","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) # Create the longtests directory and .BBSoptions file biocroxytest::use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"basic-process","dir":"Articles","previous_headings":"","what":"Basic Process","title":"Introduction to biocroxytest","text":"biocroxytest package allows add extensive tests functions using @longtests tag roxygen comments. ’s detailed explanation use : Add @longtests tag function documentation: roxygen comments function, can add @longtests tag followed tests want run. tests written testthat::test_that() call. example: example, function foo() two long tests associated : expect_equal(foo(2), sqrt(2)) expect_error(foo(\"string\")). Run roxygen2::roxygenise(): adding @longtests tags functions, need run roxygen2::roxygenise(). generate new file longtests/testthat directory R script contains functions @longtests tags. generated files contain testthat::test_that() calls set long tests. instance, foo() function file named R/functions.R, roxygen2::roxygenise() generate file named longtests/test-biocroxytest-tests-functions.R following content: file contains long tests foo() function, ready run testthat.","code":"#' A function to do x #' #' @param x A number #' #' @longtests #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #' #' @return something foo <- function(x) { return(sqrt(x)) } # Generated by biocroxytest: do not edit by hand! # File R/functions.R: @longtests testthat::test_that(\"Function foo() @ L11\", { testthat::expect_equal(foo(2), sqrt(2)) testthat::expect_error(foo(\"a string\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"Introduction to biocroxytest","text":"","code":"utils::sessionInfo() #> R Under development (unstable) (2024-01-09 r85796) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.3 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> time zone: UTC #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] BiocStyle_2.31.0 jsonlite_1.8.8 compiler_4.4.0 #> [4] BiocManager_1.30.22 brio_1.1.4 xml2_1.3.6 #> [7] stringr_1.5.1 jquerylib_0.1.4 systemfonts_1.0.5 #> [10] textshaping_0.3.7 yaml_2.3.8 fastmap_1.1.1 #> [13] R6_2.5.1 knitr_1.45 desc_1.4.3 #> [16] rprojroot_2.0.4 pillar_1.9.0 bslib_0.6.1 #> [19] rlang_1.1.3 utf8_1.2.4 testthat_3.2.1 #> [22] biocroxytest_0.99.0 cachem_1.0.8 stringi_1.8.3 #> [25] roxygen2_7.3.0 xfun_0.41 fs_1.6.3 #> [28] sass_0.4.8 pkgload_1.3.4 memoise_2.0.1 #> [31] cli_3.6.2 pkgdown_2.0.7.9000 withr_3.0.0 #> [34] magrittr_2.0.3 digest_0.6.34 lifecycle_1.0.4 #> [37] waldo_0.5.2 vctrs_0.6.5 evaluate_0.23 #> [40] glue_1.7.0 ragg_1.2.7 fansi_1.0.6 #> [43] rmarkdown_2.25 purrr_1.0.2 tools_4.4.0 #> [46] htmltools_0.5.7"},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Francesc Catala-Moll. Author, maintainer.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Catala-Moll F (2024). biocroxytest: Handle Long Tests Bioconductor Packages. R package version 0.99.0, https://github.com/xec-cm/biocroxytest.","code":"@Manual{, title = {biocroxytest: Handle Long Tests in Bioconductor Packages}, author = {Francesc Catala-Moll}, year = {2024}, note = {R package version 0.99.0}, url = {https://github.com/xec-cm/biocroxytest}, }"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"biocroxytest-","dir":"","previous_headings":"","what":"Handle Long Tests in Bioconductor Packages","title":"Handle Long Tests in Bioconductor Packages","text":"biocroxytest R package inspired roxytest. specifically designed development Bioconductor packages require tests high execution times. package extends functionality roxytest introducing new roclet, @longtests. innovative feature allows developers document store long tests directly roxygen2 comments. biocroxytest, developers can now write comprehensive tests without worrying slowing daily build process. @longtests roclet provides dedicated space extensive tests, ensuring easily accessible well-documented. approach improves reliability package also enhances maintainability. Developers can easily locate, understand, update long tests needed, leading robust efficient code.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation instructions","title":"Handle Long Tests in Bioconductor Packages","text":"Get latest stable R release CRAN. install biocroxytest Bioconductor using following code: development version GitHub :","code":"# Not yet on Bioconductor # if (!requireNamespace(\"BiocManager\", quietly = TRUE)) { # install.packages(\"BiocManager\") # } # # BiocManager::install(\"biocroxytest\") BiocManager::install(\"xec-cm/biocroxytest\")"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Handle Long Tests in Bioconductor Packages","text":"can use biocroxytest create new package long tests: use package package need add additional dependencies package’s DESCRIPTION file. Simply add following lines package’s DESCRIPTION file (along Suggests: testthat): add @longtests roxygen comments functions want test. example, file R/functions.R contains code: roxygen2::roxygenise() generate (longtests_roclet roclet) file longtests/test-biocroxytest-tests-functions.R content:","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) #' A function to do x #' #' @param x A number #' #' @longtests #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #' #' @return something foo <- function(x) { return(sqrt(x)) } #' A function to do y #' #' @param x Character vector #' @param y Character vector #' #' @longtests #' expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) #' #' @export bar <- function(x, y) { paste0(x, \"/\", y) } # Generated by biocroxytest: do not edit by hand! # File R/functions.R: @longtests test_that(\"Function foo() @ L11\", { expect_equal(foo(2), sqrt(2)) expect_error(foo(\"a string\")) }) test_that(\"Function bar() @ L27\", { expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Handle Long Tests in Bioconductor Packages","text":"think encountered bug, please submit issue. Either way, learn create share reprex (minimal, reproducible example), clearly communicate code. Working first Pull Request? can learn free series Contribute Open Source Project GitHub","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Handle Long Tests in Bioconductor Packages","text":"Please note biocroxytest project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a roxygen2 block to a testthat file — block_to_testthat","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"internal function converts roxygen2 block testthat file. first checks block 'longtests' tags. , returns NULL. , extracts 'longtests' 'examples' tags block assigns 'longtests' 'examples' fields testthat file, respectively. also assigns basename block's file 'filename' field, alias block's object 'functionname' field. block's line NULL, appends 'functionname' field.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"","code":"block_to_testthat(block)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"block roxygen2 block.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"list representing testthat file, NULL block 'longtests' tags.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"internal function cleans test files generated biocroxytest. checks file provided list test files. file generated biocroxytest, removed. file generated biocroxytest, message printed inform user, file removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"","code":"internal_longtests_roclet_clean(testfiles)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"testfiles character vector representing paths test files check clean.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"invisible","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Write long test results to files — internal_longtests_roclet_output","title":"Write long test results to files — internal_longtests_roclet_output","text":"function takes three arguments: results, base_path, prefix. function iterates elements results writes content element file directory specified base_path prefix. file created biocroxytest, function informs user files removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write long test results to files — internal_longtests_roclet_output","text":"","code":"internal_longtests_roclet_output( results, base_path, prefix = \"test-biocroxytest\" )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write long test results to files — internal_longtests_roclet_output","text":"results list results. base_path base path files written. prefix prefix used name files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write long test results to files — internal_longtests_roclet_output","text":"list file paths.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"internal function processes list blocks 'longtests' roclet. first collects annotates 'rdname' blocks. , loops block converts testthat file using 'block_to_testthat' function. resulting testthat file filename contains 'longtests', added list test files. Finally, processes test files using 'process_testfiles' function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"","code":"internal_longtests_roclet_process(blocks, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"blocks list roxygen2 blocks. ... Additional arguments.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":null,"dir":"Reference","previous_headings":"","what":"Roclet for Long Tests — longtests_roclet","title":"Roclet for Long Tests — longtests_roclet","text":"roclet used identify process code blocks documentation marked @longtests. longtests_roclet function creates new roclet, plugin roxygen2 package. Roclets responsible parsing R scripts package producing relevant documentation files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"longtests_roclet()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Roclet for Long Tests — longtests_roclet","text":"roclet can used roxygen2 process code blocks marked @longtests. roclet produce set test files separate directory, can run independently rest test suite.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Roclet for Long Tests — longtests_roclet","text":"longtests_roclet specifically looks code blocks documentation annotated @longtests tag. code blocks contain tests take long time run, thus included regular test suite package. run roxygen2::roxygenise longtests_roclet, extract long tests documentation save separate directory. allows run long tests separately rest tests, example, continuous integration server set run long tests.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"# Create a new roclet longtests_roclet() #> list() #> attr(,\"class\") #> [1] \"roclet_longtests\" \"roclet\""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a file is generated by biocroxytest — made_by_biocroxytest","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"internal function checks file given path generated biocroxytest. checks file exists, name matches pattern \"test-biocroxytest-.*\\.R$\", header file starts \"Generated biocroxytest\". file exists name matches pattern header start \"Generated biocroxytest\", function return FALSE.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"","code":"made_by_biocroxytest(path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"path character string representing path file check.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"TRUE checks pass, FALSE otherwise.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":null,"dir":"Reference","previous_headings":"","what":"Process test files for 'longtests' — process_testfiles","title":"Process test files for 'longtests' — process_testfiles","text":"internal function processes list test files 'longtests'. loops test file extracts 'longtests' 'functionname' fields. prepares tests, optionally indents code, formats tests string optional 'test_that' boilerplate. function also constructs header content, including 'context' line specified. resulting content strings returned named list, names paths test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process test files for 'longtests' — process_testfiles","text":"","code":"process_testfiles( testfiles, indent_code = FALSE, add_testthat_boilerplate = FALSE, add_context_header = FALSE )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process test files for 'longtests' — process_testfiles","text":"testfiles named list test files, names paths files. indent_code logical value indicating whether indent code tests. add_testthat_boilerplate logical value indicating whether add 'test_that' boilerplate tests. add_context_header logical value indicating whether add 'context' line header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process test files for 'longtests' — process_testfiles","text":"named list content strings test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"function cleans test files 'longtests' directory given base path. first verifies 'longtests' used package calling verify_longtests_used(). , finds test files 'longtests' directory match pattern \"test-biocroxytest-.*\\.R$\". Finally, calls internal_longtests_roclet_clean(testfiles) remove test files generated biocroxytest.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_clean(x, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"x object class 'roclet_longtests'. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"Invisible NULL.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE) # Create dummy inputs obj <- longtests_roclet() # Run the roclet_output function result <- roxygen2::roclet_clean(obj, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_output(x, results, base_path, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"x object class 'roclet_longtests'. package. results list single element 'longtests', contains base_path character string representing base path ... Additional arguments passed function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\", \"testthat\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE) # Create dummy inputs obj <- longtests_roclet() results <- list(longtests = list()) # Run the roclet_output function result <- roxygen2::roclet_output(obj, results, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_process(x, blocks, env, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"x object class 'roclet_longtests'. blocks list roxygen2 blocks. env environment roxygen2 blocks parsed. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# Create a dummy block function block <- function(roclet, value) { list(roclet = roclet, value = value) } # Create a new roclet_longtests object x <- longtests_roclet() # Define some roxygen2 blocks blocks <- list( block( roclet = \"longtests\", value = list( raw = \"test_that('this is a test', { expect_equal(1, 1) })\" ) ) ) blocks <- structure(blocks, class = \"roclet_longtests\") # Define the environment and base path env <- globalenv() base_path <- tempdir() # Process the blocks roxygen2::roclet_process(x, blocks, env, base_path) #> $longtests #> list() #>"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"function parses 'roxy_tag_longtests' object. first checks object inherits 'roxy_tag_longtests' 'roxy_tag'. , aborts error message. , checks 'raw' field object empty. , returns warning value required. Finally, removes leading newline characters 'raw' field assigns result 'val' field object.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"","code":"# S3 method for roxy_tag_longtests roxy_tag_parse(x)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"x object class 'roxy_tag_longtests'.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"input object 'val' field updated.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets up overall longtests infrastructure — use_longtests","title":"Sets up overall longtests infrastructure — use_longtests","text":"Creates longtests/testthat directory longtests/testthat.R file.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets up overall longtests infrastructure — use_longtests","text":"Invisible","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"# Create the longtests directory and .BBSoptions file use_longtests() #> ✔ The .BBSoptions file has been created. #> ✔ Adding RunLongTests: TRUE to the .BBSoptions file. #> ✔ The longtests directory has been created. #> ✔ Adding testthat.R to the longtests directory. # Remove the longtests directory and .BBSoptions file unlink(file.path(\".BBSoptions\"), recursive = TRUE, force = TRUE) unlink(file.path(\"longtests\"), recursive = TRUE, force = TRUE)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if longtests are used in the package — verify_longtests_used","title":"Check if longtests are used in the package — verify_longtests_used","text":"function checks directory \"longtests\" exists current package. exist, function throw error message suggest setting using biocroxytest::use_longtests() function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if longtests are used in the package — verify_longtests_used","text":"","code":"verify_longtests_used(base_path = \".\")"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if longtests are used in the package — verify_longtests_used","text":"base_path base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if longtests are used in the package — verify_longtests_used","text":"TRUE \"longtests\" directory exists, FALSE otherwise.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"biocroxytest-0990","dir":"Changelog","previous_headings":"","what":"biocroxytest 0.99.0","title":"biocroxytest 0.99.0","text":"NEW FEATURES Added NEWS.md file track changes package. SIGNIFICANT USER-VISIBLE CHANGES main changes function foo() parameter param. BUG FIXES bug fixes. See details http://bioconductor.org/developers/package-guidelines/#news.","code":""}]
+[{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"biocroxytest-setup","dir":"Articles","previous_headings":"","what":"biocroxytest setup","title":"Introduction to biocroxytest","text":"biocroxytest package installed, need carry two steps correctly set long tests package:","code":""},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"add-the-new-roclet-to-your-description-file","dir":"Articles","previous_headings":"biocroxytest setup","what":"1 - Add the new roclet to your Description file","title":"Introduction to biocroxytest","text":"need add biocroxytest::longtests_roclet Roxygen section Description file. enable roxygen2::roxygenize() generate long tests @longtest tag. Description file line similar :","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\"))"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"run-the-biocroxytestuse_longtests-function","dir":"Articles","previous_headings":"biocroxytest setup","what":"2 - Run the biocroxytest::use_longtests() function","title":"Introduction to biocroxytest","text":"function sets overall infrastructure long tests. run, creates longtests/testthat directory longtests/testthat.R file, necessary storing running long tests. Additionally, generates file named .BBSoptions contains RunLongTests: TRUE parameter, indicating long tests run Bioconductor servers. two steps, package set write, document, store long tests directly roxygen2 comments, improving efficiency organization test code.","code":"# Create the longtests directory and .BBSoptions file biocroxytest::use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"basic-process","dir":"Articles","previous_headings":"","what":"Basic Process","title":"Introduction to biocroxytest","text":"biocroxytest package allows add extensive tests functions using @longtests tag roxygen comments. ’s detailed explanation use :","code":""},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"add-the-longtests-tag-to-your-function-documentation","dir":"Articles","previous_headings":"Basic Process","what":"1 - Add the @longtests tag to your function documentation","title":"Introduction to biocroxytest","text":"roxygen comments function, can add @longtests tag followed tests want run. tests written testthat::test_that() call. example: example, function foo() two long tests associated : expect_equal(foo(2), sqrt(2)) expect_error(foo(\"string\")).","code":"#' A function to do x #' #' @param x A number #' #' @longtests #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #' #' @return something foo <- function(x) { return(sqrt(x)) }"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"run-roxygen2roxygenise","dir":"Articles","previous_headings":"Basic Process","what":"2 - Run roxygen2::roxygenise()","title":"Introduction to biocroxytest","text":"adding @longtests tags functions, need run roxygen2::roxygenise(). generate new file longtests/testthat directory R script contains functions @longtests tags. generated files contain testthat::test_that() calls set long tests. instance, foo() function file named R/functions.R, roxygen2::roxygenise() generate file named longtests/test-biocroxytest-tests-functions.R following content: file contains long tests foo() function, ready run testthat.","code":"# Generated by biocroxytest: do not edit by hand! # File R/functions.R: @longtests testthat::test_that(\"Function foo() @ L11\", { testthat::expect_equal(foo(2), sqrt(2)) testthat::expect_error(foo(\"a string\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"Introduction to biocroxytest","text":"","code":"utils::sessionInfo() #> R Under development (unstable) (2024-01-09 r85796) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.3 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> time zone: UTC #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] BiocStyle_2.31.0 jsonlite_1.8.8 compiler_4.4.0 #> [4] BiocManager_1.30.22 brio_1.1.4 xml2_1.3.6 #> [7] stringr_1.5.1 jquerylib_0.1.4 systemfonts_1.0.5 #> [10] textshaping_0.3.7 yaml_2.3.8 fastmap_1.1.1 #> [13] R6_2.5.1 knitr_1.45 desc_1.4.3 #> [16] rprojroot_2.0.4 pillar_1.9.0 bslib_0.6.1 #> [19] rlang_1.1.3 utf8_1.2.4 testthat_3.2.1 #> [22] biocroxytest_0.99.0 cachem_1.0.8 stringi_1.8.3 #> [25] roxygen2_7.3.0 xfun_0.41 fs_1.6.3 #> [28] sass_0.4.8 pkgload_1.3.4 memoise_2.0.1 #> [31] cli_3.6.2 pkgdown_2.0.7.9000 withr_3.0.0 #> [34] magrittr_2.0.3 digest_0.6.34 lifecycle_1.0.4 #> [37] waldo_0.5.2 vctrs_0.6.5 evaluate_0.23 #> [40] glue_1.7.0 ragg_1.2.7 fansi_1.0.6 #> [43] rmarkdown_2.25 purrr_1.0.2 tools_4.4.0 #> [46] htmltools_0.5.7"},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Francesc Catala-Moll. Author, maintainer.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Catala-Moll F (2024). biocroxytest: Handle Long Tests Bioconductor Packages. R package version 0.99.0, https://github.com/xec-cm/biocroxytest.","code":"@Manual{, title = {biocroxytest: Handle Long Tests in Bioconductor Packages}, author = {Francesc Catala-Moll}, year = {2024}, note = {R package version 0.99.0}, url = {https://github.com/xec-cm/biocroxytest}, }"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"biocroxytest-","dir":"","previous_headings":"","what":"Handle Long Tests in Bioconductor Packages","title":"Handle Long Tests in Bioconductor Packages","text":"biocroxytest R package inspired roxytest. specifically designed development Bioconductor packages require tests high execution times. package extends functionality roxytest introducing new roclet, @longtests. innovative feature allows developers document store long tests directly roxygen2 comments. biocroxytest, developers can now write comprehensive tests without worrying slowing daily build process. @longtests roclet provides dedicated space extensive tests, ensuring easily accessible well-documented. approach improves reliability package also enhances maintainability. Developers can easily locate, understand, update long tests needed, leading robust efficient code.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation instructions","title":"Handle Long Tests in Bioconductor Packages","text":"Get latest stable R release CRAN. install biocroxytest Bioconductor using following code: development version GitHub :","code":"# Not yet on Bioconductor # if (!requireNamespace(\"BiocManager\", quietly = TRUE)) { # install.packages(\"BiocManager\") # } # # BiocManager::install(\"biocroxytest\") BiocManager::install(\"xec-cm/biocroxytest\")"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Handle Long Tests in Bioconductor Packages","text":"can use biocroxytest create new package long tests: use package package need add additional dependencies package’s DESCRIPTION file. Simply add following lines package’s DESCRIPTION file (along Suggests: testthat): add @longtests roxygen comments functions want test. example, file R/functions.R contains code: roxygen2::roxygenise() generate (longtests_roclet roclet) file longtests/test-biocroxytest-tests-functions.R content:","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) #' A function to do x #' #' @param x A number #' #' @longtests #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #' #' @return something foo <- function(x) { return(sqrt(x)) } #' A function to do y #' #' @param x Character vector #' @param y Character vector #' #' @longtests #' expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) #' #' @export bar <- function(x, y) { paste0(x, \"/\", y) } # Generated by biocroxytest: do not edit by hand! # File R/functions.R: @longtests test_that(\"Function foo() @ L11\", { expect_equal(foo(2), sqrt(2)) expect_error(foo(\"a string\")) }) test_that(\"Function bar() @ L27\", { expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Handle Long Tests in Bioconductor Packages","text":"think encountered bug, please submit issue. Either way, learn create share reprex (minimal, reproducible example), clearly communicate code. Working first Pull Request? can learn free series Contribute Open Source Project GitHub","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Handle Long Tests in Bioconductor Packages","text":"Please note biocroxytest project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a roxygen2 block to a testthat file — block_to_testthat","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"internal function converts roxygen2 block testthat file. first checks block 'longtests' tags. , returns NULL. , extracts 'longtests' 'examples' tags block assigns 'longtests' 'examples' fields testthat file, respectively. also assigns basename block's file 'filename' field, alias block's object 'functionname' field. block's line NULL, appends 'functionname' field.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"","code":"block_to_testthat(block)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"block roxygen2 block.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"list representing testthat file, NULL block 'longtests' tags.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"internal function cleans test files generated biocroxytest. checks file provided list test files. file generated biocroxytest, removed. file generated biocroxytest, message printed inform user, file removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"","code":"internal_longtests_roclet_clean(testfiles)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"testfiles character vector representing paths test files check clean.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"invisible","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Write long test results to files — internal_longtests_roclet_output","title":"Write long test results to files — internal_longtests_roclet_output","text":"function takes three arguments: results, base_path, prefix. function iterates elements results writes content element file directory specified base_path prefix. file created biocroxytest, function informs user files removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write long test results to files — internal_longtests_roclet_output","text":"","code":"internal_longtests_roclet_output( results, base_path, prefix = \"test-biocroxytest\" )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write long test results to files — internal_longtests_roclet_output","text":"results list results. base_path base path files written. prefix prefix used name files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write long test results to files — internal_longtests_roclet_output","text":"list file paths.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"internal function processes list blocks 'longtests' roclet. first collects annotates 'rdname' blocks. , loops block converts testthat file using 'block_to_testthat' function. resulting testthat file filename contains 'longtests', added list test files. Finally, processes test files using 'process_testfiles' function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"","code":"internal_longtests_roclet_process(blocks, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"blocks list roxygen2 blocks. ... Additional arguments.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":null,"dir":"Reference","previous_headings":"","what":"Roclet for Long Tests — longtests_roclet","title":"Roclet for Long Tests — longtests_roclet","text":"roclet used identify process code blocks documentation marked @longtests. longtests_roclet function creates new roclet, plugin roxygen2 package. Roclets responsible parsing R scripts package producing relevant documentation files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"longtests_roclet()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Roclet for Long Tests — longtests_roclet","text":"roclet can used roxygen2 process code blocks marked @longtests. roclet produce set test files separate directory, can run independently rest test suite.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Roclet for Long Tests — longtests_roclet","text":"longtests_roclet specifically looks code blocks documentation annotated @longtests tag. code blocks contain tests take long time run, thus included regular test suite package. run roxygen2::roxygenise longtests_roclet, extract long tests documentation save separate directory. allows run long tests separately rest tests, example, continuous integration server set run long tests.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"# Create a new roclet longtests_roclet() #> list() #> attr(,\"class\") #> [1] \"roclet_longtests\" \"roclet\""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a file is generated by biocroxytest — made_by_biocroxytest","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"internal function checks file given path generated biocroxytest. checks file exists, name matches pattern \"test-biocroxytest-.*\\.R$\", header file starts \"Generated biocroxytest\". file exists name matches pattern header start \"Generated biocroxytest\", function return FALSE.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"","code":"made_by_biocroxytest(path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"path character string representing path file check.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"TRUE checks pass, FALSE otherwise.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":null,"dir":"Reference","previous_headings":"","what":"Process test files for 'longtests' — process_testfiles","title":"Process test files for 'longtests' — process_testfiles","text":"internal function processes list test files 'longtests'. loops test file extracts 'longtests' 'functionname' fields. prepares tests, optionally indents code, formats tests string optional 'test_that' boilerplate. function also constructs header content, including 'context' line specified. resulting content strings returned named list, names paths test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process test files for 'longtests' — process_testfiles","text":"","code":"process_testfiles( testfiles, indent_code = FALSE, add_testthat_boilerplate = FALSE, add_context_header = FALSE )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process test files for 'longtests' — process_testfiles","text":"testfiles named list test files, names paths files. indent_code logical value indicating whether indent code tests. add_testthat_boilerplate logical value indicating whether add 'test_that' boilerplate tests. add_context_header logical value indicating whether add 'context' line header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process test files for 'longtests' — process_testfiles","text":"named list content strings test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"function cleans test files 'longtests' directory given base path. first verifies 'longtests' used package calling verify_longtests_used(). , finds test files 'longtests' directory match pattern \"test-biocroxytest-.*\\.R$\". Finally, calls internal_longtests_roclet_clean(testfiles) remove test files generated biocroxytest.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_clean(x, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"x object class 'roclet_longtests'. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"Invisible NULL.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE) # Create dummy inputs obj <- longtests_roclet() # Run the roclet_output function result <- roxygen2::roclet_clean(obj, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_output(x, results, base_path, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"x object class 'roclet_longtests'. package. results list single element 'longtests', contains base_path character string representing base path ... Additional arguments passed function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\", \"testthat\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE) # Create dummy inputs obj <- longtests_roclet() results <- list(longtests = list()) # Run the roclet_output function result <- roxygen2::roclet_output(obj, results, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_process(x, blocks, env, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"x object class 'roclet_longtests'. blocks list roxygen2 blocks. env environment roxygen2 blocks parsed. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# Create a dummy block function block <- function(roclet, value) { list(roclet = roclet, value = value) } # Create a new roclet_longtests object x <- longtests_roclet() # Define some roxygen2 blocks blocks <- list( block( roclet = \"longtests\", value = list( raw = \"test_that('this is a test', { expect_equal(1, 1) })\" ) ) ) blocks <- structure(blocks, class = \"roclet_longtests\") # Define the environment and base path env <- globalenv() base_path <- tempdir() # Process the blocks roxygen2::roclet_process(x, blocks, env, base_path) #> $longtests #> list() #>"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"function parses 'roxy_tag_longtests' object. first checks object inherits 'roxy_tag_longtests' 'roxy_tag'. , aborts error message. , checks 'raw' field object empty. , returns warning value required. Finally, removes leading newline characters 'raw' field assigns result 'val' field object.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"","code":"# S3 method for roxy_tag_longtests roxy_tag_parse(x)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"x object class 'roxy_tag_longtests'.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"input object 'val' field updated.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets up overall longtests infrastructure — use_longtests","title":"Sets up overall longtests infrastructure — use_longtests","text":"Creates longtests/testthat directory longtests/testthat.R file.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets up overall longtests infrastructure — use_longtests","text":"Invisible","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"# Create the longtests directory and .BBSoptions file use_longtests() #> ✔ The .BBSoptions file has been created. #> ✔ Adding RunLongTests: TRUE to the .BBSoptions file. #> ✔ The longtests directory has been created. #> ✔ Adding testthat.R to the longtests directory. # Remove the longtests directory and .BBSoptions file unlink(file.path(\".BBSoptions\"), recursive = TRUE, force = TRUE) unlink(file.path(\"longtests\"), recursive = TRUE, force = TRUE)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if longtests are used in the package — verify_longtests_used","title":"Check if longtests are used in the package — verify_longtests_used","text":"function checks directory \"longtests\" exists current package. exist, function throw error message suggest setting using biocroxytest::use_longtests() function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if longtests are used in the package — verify_longtests_used","text":"","code":"verify_longtests_used(base_path = \".\")"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if longtests are used in the package — verify_longtests_used","text":"base_path base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if longtests are used in the package — verify_longtests_used","text":"TRUE \"longtests\" directory exists, FALSE otherwise.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"biocroxytest-0990","dir":"Changelog","previous_headings":"","what":"biocroxytest 0.99.0","title":"biocroxytest 0.99.0","text":"NEW FEATURES Added NEWS.md file track changes package. SIGNIFICANT USER-VISIBLE CHANGES main changes function foo() parameter param. BUG FIXES bug fixes. See details http://bioconductor.org/developers/package-guidelines/#news.","code":""}]