diff --git a/DESCRIPTION b/DESCRIPTION index 92134eb..09adced 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drugfindR Title: Investigate iLINCS for candidate repurposable drugs -Version: 0.99.980 +Version: 0.99.986 Authors@R: c( person(given = c("Ali", "Sajid"), family = "Imami", @@ -34,10 +34,9 @@ URL: https://github.com/CogDisResLab/drugfindR BugReports: https://github.com/CogDisResLab/drugfindR/issues LazyData: false Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 biocViews: FunctionalPrediction, DifferentialExpression, GeneSetEnrichment Imports: - httr, magrittr, tibble, rlang, @@ -47,7 +46,9 @@ Imports: stringr, stats, lifecycle, - S4Vectors + S4Vectors, + httr2, + curl Depends: R (>= 4.4.0) Suggests: diff --git a/NAMESPACE b/NAMESPACE index 5770a15..ebb7e55 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -9,6 +9,7 @@ export(investigateTarget) export(prepareSignature) import(lifecycle) importFrom(S4Vectors,DataFrame) +importFrom(curl,form_file) importFrom(dplyr,across) importFrom(dplyr,any_of) importFrom(dplyr,arrange) @@ -22,10 +23,15 @@ importFrom(dplyr,rename) importFrom(dplyr,rename_with) importFrom(dplyr,select) importFrom(dplyr,ungroup) -importFrom(httr,POST) -importFrom(httr,content) -importFrom(httr,status_code) -importFrom(httr,upload_file) +importFrom(httr2,req_method) +importFrom(httr2,req_perform) +importFrom(httr2,req_url_path_append) +importFrom(httr2,req_url_query) +importFrom(httr2,req_user_agent) +importFrom(httr2,request) +importFrom(httr2,resp_body_json) +importFrom(httr2,resp_body_string) +importFrom(httr2,resp_status) importFrom(lifecycle,deprecated) importFrom(magrittr,"%>%") importFrom(purrr,flatten_dfr) @@ -35,6 +41,7 @@ importFrom(purrr,map_dfr) importFrom(readr,write_tsv) importFrom(rlang,.data) importFrom(stats,quantile) +importFrom(stringr,str_glue) importFrom(stringr,str_to_lower) importFrom(tibble,as_tibble) importFrom(tibble,tibble) diff --git a/R/getConcordants.R b/R/getConcordants.R index 8b3662e..1372265 100644 --- a/R/getConcordants.R +++ b/R/getConcordants.R @@ -16,12 +16,13 @@ #' @export #' #' @importFrom readr write_tsv -#' @importFrom httr POST status_code content upload_file +#' @importFrom httr2 request req_method req_url_query req_user_agent req_url_path_append req_perform resp_status resp_body_json resp_body_string #' @importFrom purrr map flatten_dfr #' @importFrom dplyr select any_of mutate filter #' @importFrom tibble tibble #' @importFrom rlang .data -#' @importFrom magrittr %>% +#' @importFrom stringr str_glue +#' @importFrom curl form_file #' #' @examples #' # Get the L1000 signature for LINCSKD_28 @@ -37,7 +38,7 @@ getConcordants <- function(signature, ilincsLibrary = "CP") { stop("signature must be a data frame or data frame like object") } else { signatureFile <- tempfile(pattern = "ilincs_sig", fileext = ".xls") - signature %>% + signature |> readr::write_tsv(signatureFile) } @@ -55,24 +56,25 @@ getConcordants <- function(signature, ilincsLibrary = "CP") { CP = "LIB_5" ) - if (!ilincsLibrary %in% c("OE", "KD", "CP")) { - stop("library must be one of 'OE', 'KD' or 'CP'") - } - - url <- "http://www.ilincs.org/api/SignatureMeta/uploadAndAnalyze" - query <- list(lib = libMap[ilincsLibrary]) - body <- list(file = httr::upload_file(signatureFile)) + stopIfInvalidLibraries(ilincsLibrary) - request <- httr::POST(url, query = query, body = body) + request <- httr2::request(.ilincsBaseUrl()) |> + httr2::req_url_path_append("SignatureMeta") |> + httr2::req_url_path_append("uploadAndAnalyze") |> + httr2::req_url_query(lib = libMap[ilincsLibrary]) |> + httr2::req_body_multipart(file = curl::form_file(signatureFile)) |> + httr2::req_method("POST") |> + httr2::req_user_agent(stringr::str_glue("drugfindR/v{packageVersion('drugfindR')}; https://github.com/CogDisResLab/drugfindR")) |> + httr2::req_perform() - if (httr::status_code(request) == 200L) { - concordants <- httr::content(request) %>% - purrr::map("concordanceTable") %>% - purrr::flatten_dfr() %>% + if (httr2::resp_status(request) == 200L) { + concordants <- httr2::resp_body_json(request) |> + purrr::map("concordanceTable") |> + purrr::flatten_dfr() |> dplyr::select(dplyr::any_of(c( "signatureid", "compound", "treatment", "concentration", "time", "cellline", "similarity", "pValue" - ))) %>% + ))) |> dplyr::mutate( similarity = round(.data[["similarity"]], 8L), pValue = round(.data[["pValue"]], 20L), @@ -80,6 +82,6 @@ getConcordants <- function(signature, ilincsLibrary = "CP") { ) return(concordants) } else { - httr::stop_for_status(request, "get concardant signatures") + stop(httr2::resp_status(request), " ", httr2::resp_body_string(request)) } } diff --git a/R/getSignature.R b/R/getSignature.R index d82006a..84e289a 100644 --- a/R/getSignature.R +++ b/R/getSignature.R @@ -16,9 +16,8 @@ #' @return a tibble with the L1000 Signature #' @export #' -#' @importFrom httr POST content status_code +#' @importFrom httr2 request req_method req_url_query req_user_agent req_url_path_append req_perform resp_status resp_body_json resp_body_string #' @importFrom tibble tibble as_tibble -#' @importFrom magrittr %>% #' @importFrom rlang .data #' @importFrom dplyr select #' @importFrom purrr map_dfr @@ -28,32 +27,32 @@ #' # Get the L1000 signature for LINCSKD_28 #' kdSignature <- getSignature("LINCSKD_28") getSignature <- function(sigId, l1000 = TRUE) { - url <- "http://www.ilincs.org/api/ilincsR/downloadSignature" - if (l1000) { numGenes <- 978L } else { numGenes <- Inf } - query <- list(sigID = sigId, noOfTopGenes = numGenes) + request <- httr2::request(.ilincsBaseUrl()) |> + httr2::req_url_path_append("ilincsR") |> + httr2::req_url_path_append("downloadSignature") |> + httr2::req_url_query(sigID = sigId, noOfTopGenes = numGenes) |> + httr2::req_method("POST") |> + httr2::req_user_agent("drugfindR/v0.99.980; https://github.com/CogDisResLab/drugfindR") |> + httr2::req_perform() - request <- httr::POST(url, query = query) - if (httr::status_code(request) == 200L) { - signature <- httr::content(request) %>% - purrr::map("signature") %>% - purrr::flatten_dfr() %>% - dplyr::select(-"PROBE") %>% + if (httr2::resp_status(request) == 200L) { + signature <- httr2::resp_body_json(request) |> + purrr::map("signature") |> + purrr::flatten_dfr() |> + dplyr::select(-"PROBE") |> dplyr::mutate( ID_geneid = as.character(.data[["ID_geneid"]]), Value_LogDiffExp = round(.data[["Value_LogDiffExp"]], 12L), Significance_pvalue = round(.data[["Significance_pvalue"]], 12L) ) - signature %>% - S4Vectors::DataFrame() %>% - as_tibble() } else { - stop(httr::status_code(request), " ", httr::content(request)) + stop(httr2::resp_status(request), " ", httr2::resp_body_string(request)) } } diff --git a/R/utilities.R b/R/utilities.R index 5ed1e73..998d5cb 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -21,6 +21,14 @@ targetRename <- function(inputNames) { } } +#' Parameterize the base URL for the iLINCS API +#' +#' +#' @return a fixed string URL +.ilincsBaseUrl <- function() { + "http://www.ilincs.org/api" +} + #' Check if the library is valid #' #' @param lib a string of libraries @@ -69,3 +77,21 @@ loadMetadata <- function(lib) { stop("Invalid library") } } + + +#' Return the internal iLINCS Library ID for a given library +#' +#' @param lib A library name. Can be one of "OE", "KD" or "CP" +#' +#' @return A string with the associated library ID +.return_library <- function(lib) { + stopIfInvalidLibraries(lib) + + libMap <- c( + OE = "LIB_11", + KD = "LIB_6", + CP = "LIB_5" + ) + + libMap[lib] +} diff --git a/VERSION.txt b/VERSION.txt deleted file mode 100644 index 100f7f0..0000000 --- a/VERSION.txt +++ /dev/null @@ -1 +0,0 @@ -0.99.662 diff --git a/codemeta.json b/codemeta.json index 399a8d1..8c53b02 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,7 +7,7 @@ "codeRepository": "https://github.com/CogDisResLab/drugfindR", "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.99.980", + "version": "0.99.986", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -203,18 +203,6 @@ ], "softwareRequirements": { "1": { - "@type": "SoftwareApplication", - "identifier": "httr", - "name": "httr", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=httr" - }, - "2": { "@type": "SoftwareApplication", "identifier": "magrittr", "name": "magrittr", @@ -226,7 +214,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=magrittr" }, - "3": { + "2": { "@type": "SoftwareApplication", "identifier": "tibble", "name": "tibble", @@ -238,7 +226,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=tibble" }, - "4": { + "3": { "@type": "SoftwareApplication", "identifier": "rlang", "name": "rlang", @@ -250,7 +238,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=rlang" }, - "5": { + "4": { "@type": "SoftwareApplication", "identifier": "dplyr", "name": "dplyr", @@ -262,7 +250,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=dplyr" }, - "6": { + "5": { "@type": "SoftwareApplication", "identifier": "purrr", "name": "purrr", @@ -274,7 +262,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=purrr" }, - "7": { + "6": { "@type": "SoftwareApplication", "identifier": "readr", "name": "readr", @@ -286,7 +274,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=readr" }, - "8": { + "7": { "@type": "SoftwareApplication", "identifier": "stringr", "name": "stringr", @@ -298,12 +286,12 @@ }, "sameAs": "https://CRAN.R-project.org/package=stringr" }, - "9": { + "8": { "@type": "SoftwareApplication", "identifier": "stats", "name": "stats" }, - "10": { + "9": { "@type": "SoftwareApplication", "identifier": "lifecycle", "name": "lifecycle", @@ -315,7 +303,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=lifecycle" }, - "11": { + "10": { "@type": "SoftwareApplication", "identifier": "S4Vectors", "name": "S4Vectors", @@ -327,7 +315,31 @@ }, "sameAs": "https://bioconductor.org/packages/release/bioc/html/S4Vectors.html" }, + "11": { + "@type": "SoftwareApplication", + "identifier": "httr2", + "name": "httr2", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=httr2" + }, "12": { + "@type": "SoftwareApplication", + "identifier": "curl", + "name": "curl", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=curl" + }, + "13": { "@type": "SoftwareApplication", "identifier": "R", "name": "R", @@ -338,7 +350,7 @@ "applicationCategory": "Genomics", "isPartOf": "https://bioconductor.org", "keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"], - "fileSize": "2083.425KB", + "fileSize": "2085.479KB", "releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md", "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md", "contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"], diff --git a/man/dot-ilincsBaseUrl.Rd b/man/dot-ilincsBaseUrl.Rd new file mode 100644 index 0000000..6aa1baa --- /dev/null +++ b/man/dot-ilincsBaseUrl.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utilities.R +\name{.ilincsBaseUrl} +\alias{.ilincsBaseUrl} +\title{Parameterize the base URL for the iLINCS API} +\usage{ +.ilincsBaseUrl() +} +\value{ +a fixed string URL +} +\description{ +Parameterize the base URL for the iLINCS API +} diff --git a/man/dot-return_library.Rd b/man/dot-return_library.Rd new file mode 100644 index 0000000..e983258 --- /dev/null +++ b/man/dot-return_library.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utilities.R +\name{.return_library} +\alias{.return_library} +\title{Return the internal iLINCS Library ID for a given library} +\usage{ +.return_library(lib) +} +\arguments{ +\item{lib}{A library name. Can be one of "OE", "KD" or "CP"} +} +\value{ +A string with the associated library ID +} +\description{ +Return the internal iLINCS Library ID for a given library +} diff --git a/renv.lock b/renv.lock index ce2fa63..d5c706b 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.0", + "Version": "4.4.1", "Repositories": [ { "Name": "BioCsoft", @@ -81,17 +81,17 @@ }, "BiocManager": { "Package": "BiocManager", - "Version": "1.30.23", + "Version": "1.30.25", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "47e968dfe563c1b22c2e20a067ec21d5" + "Hash": "3aec5928ca10897d7a0a1205aae64627" }, "BiocStyle": { "Package": "BiocStyle", - "Version": "2.32.0", + "Version": "2.32.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -103,7 +103,7 @@ "utils", "yaml" ], - "Hash": "d93773e50f3776f134734d8320bec61f" + "Hash": "beadb5ac6d6b64dc6153cb300dd063ef" }, "BiocVersion": { "Package": "BiocVersion", @@ -117,7 +117,7 @@ }, "Biostrings": { "Package": "Biostrings", - "Version": "2.72.0", + "Version": "2.72.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -133,22 +133,22 @@ "stats", "utils" ], - "Hash": "48618c7c7b90b503837824ebcfee6363" + "Hash": "886ff0ed958d6f839ed2e0d01f6853b3" }, "DBI": { "Package": "DBI", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "164809cd72e1d5160b4cb3aa57f510fe" + "Hash": "065ae649b05f1ff66bb0c793107508f5" }, "GenomeInfoDb": { "Package": "GenomeInfoDb", - "Version": "1.40.0", + "Version": "1.40.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -163,7 +163,7 @@ "stats4", "utils" ], - "Hash": "614124bc9fb80d222cfa0d2e3e76c339" + "Hash": "171e9becd9bb948b9e64eb3759208c94" }, "GenomeInfoDbData": { "Package": "GenomeInfoDbData", @@ -176,7 +176,7 @@ }, "IRanges": { "Package": "IRanges", - "Version": "2.38.0", + "Version": "2.38.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -188,11 +188,11 @@ "stats4", "utils" ], - "Hash": "836770692f7c8401090519228b93af32" + "Hash": "066f3c5d6b022ed62c91ce49e4d8f619" }, "KEGGREST": { "Package": "KEGGREST", - "Version": "1.44.0", + "Version": "1.44.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -202,13 +202,13 @@ "methods", "png" ], - "Hash": "05ef9fd9aa613310e060ddd93a0c8571" + "Hash": "017f19c09477c0473073518db9076ac1" }, "MASS": { "Package": "MASS", - "Version": "7.3-60.2", + "Version": "7.3-61", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -217,7 +217,7 @@ "stats", "utils" ], - "Hash": "2f342c46163b0b54d7b64d1f798e2c78" + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "Matrix": { "Package": "Matrix", @@ -258,7 +258,7 @@ }, "RSQLite": { "Package": "RSQLite", - "Version": "2.3.6", + "Version": "2.3.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -273,22 +273,22 @@ "plogr", "rlang" ], - "Hash": "ae4a925e0f6bb1b7e5fa96b739c5221a" + "Hash": "46b45a4dd7bb0e0f4e3fc22245817240" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + "Hash": "f27411eb6d9c3dada5edd444b8416675" }, "S4Vectors": { "Package": "S4Vectors", - "Version": "0.42.0", + "Version": "0.42.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -299,7 +299,7 @@ "stats4", "utils" ], - "Hash": "245ac721ca6088200392ea5251db9e3c" + "Hash": "86398fc7c5f6be4ba29fe23ed08c2da6" }, "UCSC.utils": { "Package": "UCSC.utils", @@ -344,13 +344,13 @@ }, "backports": { "Package": "backports", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" + "Hash": "e1e1b9d75c37401117b636b7ae50827a" }, "base64enc": { "Package": "base64enc", @@ -400,7 +400,7 @@ }, "bookdown": { "Package": "bookdown", - "Version": "0.39", + "Version": "0.40", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -413,7 +413,7 @@ "xfun", "yaml" ], - "Hash": "cb4f7066855b6f936e8d25edc9a9cff9" + "Hash": "896a79478a50c78fb035a37148638f4e" }, "brew": { "Package": "brew", @@ -434,14 +434,13 @@ }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -451,11 +450,11 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", - "Version": "0.7.0", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -473,18 +472,18 @@ "rlang", "sass" ], - "Hash": "8644cc53f43828f19133548195d7e59e" + "Hash": "b299c6741ca9746fb227debcb0f9fb6c" }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", @@ -513,14 +512,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.2", + "Version": "3.6.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" + "Hash": "b21916dd77a27642b447374a5d30ecf3" }, "clipr": { "Package": "clipr", @@ -534,7 +533,7 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.1-0", + "Version": "2.1-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -544,7 +543,7 @@ "methods", "stats" ], - "Hash": "f20c47fd52fae58b4e377c37bb8c335b" + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" }, "commonmark": { "Package": "commonmark", @@ -568,17 +567,17 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.7", + "Version": "0.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://cran.r-project.org", "Requirements": [ "R" ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" + "Hash": "91570bba75d0c9d3f1040c835cee8fba" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -586,7 +585,7 @@ "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "credentials": { "Package": "credentials", @@ -604,9 +603,9 @@ }, "crul": { "Package": "crul", - "Version": "1.4.2", + "Version": "1.5.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R6", "curl", @@ -615,28 +614,28 @@ "mime", "urltools" ], - "Hash": "5685d2603020d0f879a147ba23d51292" + "Hash": "22e70c5046981d39b7bf7af74433e396" }, "curl": { "Package": "curl", - "Version": "5.2.1", + "Version": "5.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://cran.r-project.org", "Requirements": [ "R" ], - "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" + "Hash": "8f27335f2bcff4d6035edcc82d7d46de" }, "data.table": { "Package": "data.table", - "Version": "1.15.4", + "Version": "1.16.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e" + "Hash": "fb24e05d4a91d8b1c7ff8e284bde834a" }, "dbplyr": { "Package": "dbplyr", @@ -730,18 +729,18 @@ }, "digest": { "Package": "digest", - "Version": "0.6.35", + "Version": "0.6.37", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31" + "Hash": "33698c4b3127fc9f506654607fb73676" }, "downlit": { "Package": "downlit", - "Version": "0.4.3", + "Version": "0.4.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -757,7 +756,7 @@ "withr", "yaml" ], - "Hash": "14fa1f248b60ed67e1f5418391a17b14" + "Hash": "45a6a596bf0108ee1ff16a040a2df897" }, "dplyr": { "Package": "dplyr", @@ -814,14 +813,13 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "R", - "methods" + "R" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "6b567375113ceb7d9f800de4dd42218e" }, "fansi": { "Package": "fansi", @@ -837,17 +835,17 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Repository": "https://cran.r-project.org", + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fauxpas": { "Package": "fauxpas", @@ -935,7 +933,7 @@ }, "gert": { "Package": "gert", - "Version": "2.0.1", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -946,7 +944,7 @@ "sys", "zip" ], - "Hash": "f70d3fe2d9e7654213a946963d1591eb" + "Hash": "ab2ca7d6bd706ed218d096b7b16d7233" }, "ggplot2": { "Package": "ggplot2", @@ -1196,7 +1194,7 @@ }, "httr2": { "Package": "httr2", - "Version": "1.0.1", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1213,7 +1211,7 @@ "vctrs", "withr" ], - "Hash": "03d741c92fda96d98c3a3f22494e3b4a" + "Hash": "836e9564fbeca3bb390bb429a53cd401" }, "ids": { "Package": "ids", @@ -1266,7 +1264,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.47", + "Version": "1.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1278,7 +1276,7 @@ "xfun", "yaml" ], - "Hash": "7c99b2d55584b982717fcc0950378612" + "Hash": "acf380f300c721da9fde7df115a5f86f" }, "labeling": { "Package": "labeling", @@ -1434,7 +1432,7 @@ }, "nlme": { "Package": "nlme", - "Version": "3.1-164", + "Version": "3.1-166", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1444,17 +1442,17 @@ "stats", "utils" ], - "Hash": "a623a2239e642806158bc4dc3f51565d" + "Hash": "ccbb8846be320b627e6aa2b4616a2ded" }, "openssl": { "Package": "openssl", - "Version": "2.1.2", + "Version": "2.2.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "https://cran.r-project.org", "Requirements": [ "askpass" ], - "Hash": "ea2475b073243d9d338aa8f086ce973e" + "Hash": "c62edf62de70cadf40553e10c739049d" }, "org.Hs.eg.db": { "Package": "org.Hs.eg.db", @@ -1511,9 +1509,9 @@ }, "pkgdown": { "Package": "pkgdown", - "Version": "2.0.9", + "Version": "2.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "bslib", @@ -1522,11 +1520,11 @@ "desc", "digest", "downlit", + "fontawesome", "fs", - "httr", + "httr2", "jsonlite", - "magrittr", - "memoise", + "openssl", "purrr", "ragg", "rlang", @@ -1537,28 +1535,29 @@ "xml2", "yaml" ], - "Hash": "8bf1151ed1a48328d71b937e651117a6" + "Hash": "df2912d5873422b55a13002510f02c9f" }, "pkgload": { "Package": "pkgload", - "Version": "1.3.4", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", - "crayon", "desc", "fs", "glue", + "lifecycle", "methods", "pkgbuild", + "processx", "rlang", "rprojroot", "utils", "withr" ], - "Hash": "876c618df5ae610be84356d5d7a5d124" + "Hash": "2ec30ffbeec83da57655b850cf2d3e0e" }, "plogr": { "Package": "plogr", @@ -1654,14 +1653,14 @@ }, "ps": { "Package": "ps", - "Version": "1.7.6", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "dd2b9319ee0656c8acf45c7f40c59de7" + "Hash": "4b9c8485b0c7eecdf0a9ba5132a45576" }, "purrr": { "Package": "purrr", @@ -1680,14 +1679,14 @@ }, "ragg": { "Package": "ragg", - "Version": "1.3.0", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "082e1a198e3329d571f4448ef0ede4bc" + "Hash": "0595fe5e47357111f29ad19101c7d271" }, "rappdirs": { "Package": "rappdirs", @@ -1802,9 +1801,9 @@ }, "reprex": { "Package": "reprex", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "callr", @@ -1820,7 +1819,7 @@ "utils", "withr" ], - "Hash": "1425f91b4d5d9a8f25352c44a3d914ed" + "Hash": "97b1d5361a24d9fb588db7afe3e5bcbf" }, "rlang": { "Package": "rlang", @@ -1835,7 +1834,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.28", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1854,11 +1853,11 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "062470668513dcda416927085ee9bdc7" }, "roxygen2": { "Package": "roxygen2", - "Version": "7.3.1", + "Version": "7.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1880,7 +1879,7 @@ "withr", "xml2" ], - "Hash": "c25fe7b2d8cba73d1b63c947bf7afdb9" + "Hash": "6ee25f9054a70f44d615300ed531ba8d" }, "rprojroot": { "Package": "rprojroot", @@ -1992,7 +1991,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.8.1.1", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2021,7 +2020,7 @@ "withr", "xtable" ], - "Hash": "54b26646816af9960a4c64d8ceec75d6" + "Hash": "6a293995a66e12c48d13aa1f957d09c7" }, "sourcetools": { "Package": "sourcetools", @@ -2035,16 +2034,16 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://cran.r-project.org", "Requirements": [ "R", "stats", "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -2072,14 +2071,15 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "6d538cff441f0f1f36db2209ac7495ac" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "testthat": { "Package": "testthat", @@ -2112,15 +2112,16 @@ }, "textshaping": { "Package": "textshaping", - "Version": "0.3.7", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11", + "lifecycle", "systemfonts" ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "tibble": { "Package": "tibble", @@ -2233,13 +2234,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.50", + "Version": "0.53", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "be7a76845222ad20adb761f462eed3ea" + "Hash": "9db859e8aabbb474293dde3097839420" }, "triebeard": { "Package": "triebeard", @@ -2291,7 +2292,7 @@ }, "usethis": { "Package": "usethis", - "Version": "2.2.3", + "Version": "3.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2318,7 +2319,7 @@ "withr", "yaml" ], - "Hash": "d524fd42c517035027f866064417d7e6" + "Hash": "b2fbf93c2127bedd2cbe9b799530d5d2" }, "utf8": { "Package": "utf8", @@ -2332,17 +2333,17 @@ }, "uuid": { "Package": "uuid", - "Version": "1.2-0", + "Version": "1.2-1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "303c19bfd970bece872f93a824e323d9" + "Hash": "34e965e62a41fcafb1ca60e9b142085b" }, "vcr": { "Package": "vcr", - "Version": "1.2.2", + "Version": "1.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2350,12 +2351,13 @@ "base64enc", "crul", "httr", + "httr2", "rprojroot", "urltools", "webmockr", "yaml" ], - "Hash": "7cb7298ab402fca46f635fb5c9304c14" + "Hash": "03d6a34785bc21c75fc85bcdf1fbf701" }, "vctrs": { "Package": "vctrs", @@ -2409,25 +2411,24 @@ }, "waldo": { "Package": "waldo", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", "diffobj", - "fansi", "glue", "methods", "rematch2", "rlang", "tibble" ], - "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6" + "Hash": "16aa934a49658677d8041df9017329b9" }, "webmockr": { "Package": "webmockr", - "Version": "0.9.0", + "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2440,7 +2441,7 @@ "magrittr", "urltools" ], - "Hash": "2f97808043100cbe30e3cbb1e751f8db" + "Hash": "9065629eb730d8d7636c5ec05602ff42" }, "whisker": { "Package": "whisker", @@ -2451,27 +2452,28 @@ }, "withr": { "Package": "withr", - "Version": "3.0.0", + "Version": "3.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", "graphics" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "Hash": "07909200e8bbe90426fbfeb73e1e27aa" }, "xfun": { "Package": "xfun", - "Version": "0.44", + "Version": "0.47", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "grDevices", "stats", "tools" ], - "Hash": "317a0538d32f4a009658bcedb7923f4b" + "Hash": "36ab21660e2d095fef0d83f689e0477c" }, "xml2": { "Package": "xml2", @@ -2511,10 +2513,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" }, "zip": { "Package": "zip", diff --git a/tests/testthat/test-get_concordants.R b/tests/testthat/test-get_concordants.R index 639c647..664001a 100644 --- a/tests/testthat/test-get_concordants.R +++ b/tests/testthat/test-get_concordants.R @@ -17,9 +17,9 @@ test_that("Function errors if it receives an error response", { "post", "http://www.ilincs.org/api/SignatureMeta/uploadAndAnalyze" ) |> webmockr::to_return(status = 500L) - webmockr::httr_mock() + webmockr::httr2_mock() expect_error(getConcordants(exampleSignature())) - webmockr::httr_mock(FALSE) + webmockr::httr2_mock(FALSE) })