list(old = list(structure(list(stdout = "* using log directory ‘/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/old/gwasrapidd.Rcheck’\n* using R Under development (unstable) (2022-10-19 r83129)\n* using platform: x86_64-pc-linux-gnu (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘gwasrapidd/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘gwasrapidd’ version ‘0.99.13’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘gwasrapidd’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking R/sysdata.rda ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n Running ‘spelling.R’\n Running ‘testthat.R’\n OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n ‘bmi_variants.Rmd’ using ‘UTF-8’... OK\n ‘faq.Rmd’ using ‘UTF-8’... OK\n ‘gwasrapidd.Rmd’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n",
stderr = "", status = 0L, duration = 57.0786, timeout = FALSE,
rversion = list(), platform = "x86_64-pc-linux-gnu", errors = character(0),
warnings = character(0), notes = character(0), description = "Package: gwasrapidd\nType: Package\nTitle: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog\nVersion: 0.99.13\nAuthors@R: c(\n person(given = \"Ramiro\", family = \"Magno\", email = \"ramiro.magno@gmail.com\",\n role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5226-3441\")),\n person(given = \"Ana-Teresa\", family = \"Maia\",\n email = \"maia.anateresa@gmail.com\", role = \"aut\", \n comment = c(ORCID = \"0000-0002-0454-9207\")),\n person(\"CINTESIS\",\n role = c(\"cph\", \"fnd\"))\n )\nDescription: 'GWAS' R 'API' Data Download.\n This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by\n accessing the 'REST' 'API' .\nDepends: R (>= 3.2.3)\nLicense: MIT + file LICENSE\nURL: https://github.com/ramiromagno/gwasrapidd\nBugReports: https://github.com/ramiromagno/gwasrapidd/issues\nEncoding: UTF-8\nLanguage: en-US\nLazyData: true\nRoxygenNote: 7.2.1\nImports: magrittr, httr, urltools, pingr, stringr, concatenate, dplyr,\n jsonlite, purrr, tibble, glue, tidyr (> 0.8.99), assertthat,\n rlang, methods, lubridate, plyr, testthat, utils, progress\nSuggests: httptest, spelling, covr, knitr, rmarkdown\nCollate: 'browser.R' 'class-associations.R' 'class-studies.R'\n 'class-traits.R' 'class-variants.R' 'data.R' 'ebi_server.R'\n 'generics.R' 'get_associations.R' 'get_metadata.R'\n 'get_studies.R' 'get_traits.R' 'get_variants.R'\n 'gwasrapidd-package.R' 'id_mapping.R' 'list_joins.R'\n 'missing.R' 'parse-associations.R' 'parse-studies.R'\n 'parse-traits.R' 'parse-utils.R' 'parse-variants.R'\n 'post-studies.R' 'post-traits.R' 'post-variants.R'\n 'recursive_apply.R' 'request.R' 's4-utils.R' 'sure.R' 'tests.R'\n 'utils-pipe.R' 'utils.R'\nVignetteBuilder: knitr\nbiocViews: ThirdPartyClient, BiomedicalInformatics,\n GenomeWideAssociation, SNP\nNeedsCompilation: no\nPackaged: 2022-08-11 22:04:08 UTC; rmagno\nAuthor: Ramiro Magno [aut, cre] (),\n Ana-Teresa Maia [aut] (),\n CINTESIS [cph, fnd]\nMaintainer: Ramiro Magno \nRepository: CRAN\nDate/Publication: 2022-08-11 22:20:02 UTC",
package = "gwasrapidd", version = "0.99.13", cran = TRUE,
bioc = TRUE, checkdir = "/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/old/gwasrapidd.Rcheck",
test_fail = structure(list(), names = character(0)), test_output = list(
spelling = "> if(requireNamespace('spelling', quietly=TRUE))\n+ spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)\nNULL\n> \n> proc.time()\n user system elapsed \n 0.132 0.021 0.145 \n",
testthat = "> library(testthat)\n> library(gwasrapidd)\n> \n> test_check(\"gwasrapidd\")\n[ FAIL 0 | WARN 2 | SKIP 1 | PASS 721 ]\n\n══ Skipped tests ═══════════════════════════════════════════════════════════════\n• empty test (1)\n\n[ FAIL 0 | WARN 2 | SKIP 1 | PASS 721 ]\n> \n> proc.time()\n user system elapsed \n 22.043 0.240 24.273 \n"),
install_out = "* installing *source* package ‘gwasrapidd’ ...\n** package ‘gwasrapidd’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (gwasrapidd)\n"), class = "rcmdcheck")),
new = structure(list(stdout = "* using log directory ‘/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/new/gwasrapidd.Rcheck’\n* using R Under development (unstable) (2022-10-19 r83129)\n* using platform: x86_64-pc-linux-gnu (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘gwasrapidd/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘gwasrapidd’ version ‘0.99.13’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘gwasrapidd’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking R/sysdata.rda ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... ERROR\nRunning examples in ‘gwasrapidd-Ex.R’ failed\nThe error most likely occurred in:\n\n> ### Name: get_variants\n> ### Title: Get GWAS Catalog variants\n> ### Aliases: get_variants\n> \n> ### ** Examples\n> \n> # Get variants by study identifier\n> get_variants(study_id = 'GCST001085', warnings = FALSE)\nError in if (is.numeric(x) && any(x > 1900)) { : \n missing value where TRUE/FALSE needed\nCalls: get_variants ... -> .parse_xxx_hms -> unlist -> lapply -> FUN\nExecution halted\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n Running ‘spelling.R’\n Running ‘testthat.R’\n ERROR\nRunning the tests in ‘tests/testthat.R’ failed.\nLast 13 lines of output:\n } else {\n as.character(x)\n }`: missing value where TRUE/FALSE needed\n Backtrace:\n ▆\n 1. └─gwasrapidd:::empty_to_na(empty_date) at test-utils.R:38:2\n 2. └─lubridate::ymd_hms(NA_real_)\n 3. └─lubridate:::.parse_xxx_hms(...)\n 4. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 5. └─base::lapply(list(...), .num_to_date)\n 6. └─lubridate (local) FUN(X[[i]], ...)\n \n [ FAIL 43 | WARN 2 | SKIP 1 | PASS 642 ]\n Error: Test failures\n Execution halted\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n ‘bmi_variants.Rmd’ using ‘UTF-8’... OK\n ‘faq.Rmd’ using ‘UTF-8’... OK\n ‘gwasrapidd.Rmd’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: 2 ERRORs\nSee\n ‘/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/new/gwasrapidd.Rcheck/00check.log’\nfor details.\n\n\n",
stderr = "", status = 1L, duration = 47.7099, timeout = FALSE,
rversion = list(), platform = "x86_64-pc-linux-gnu",
errors = c("checking examples ... ERROR\nRunning examples in ‘gwasrapidd-Ex.R’ failed\nThe error most likely occurred in:\n\n> ### Name: get_variants\n> ### Title: Get GWAS Catalog variants\n> ### Aliases: get_variants\n> \n> ### ** Examples\n> \n> # Get variants by study identifier\n> get_variants(study_id = 'GCST001085', warnings = FALSE)\nError in if (is.numeric(x) && any(x > 1900)) { : \n missing value where TRUE/FALSE needed\nCalls: get_variants ... -> .parse_xxx_hms -> unlist -> lapply -> FUN\nExecution halted",
"checking tests ...\n Running ‘spelling.R’\n Running ‘testthat.R’\n ERROR\nRunning the tests in ‘tests/testthat.R’ failed.\nLast 13 lines of output:\n } else {\n as.character(x)\n }`: missing value where TRUE/FALSE needed\n Backtrace:\n ▆\n 1. └─gwasrapidd:::empty_to_na(empty_date) at test-utils.R:38:2\n 2. └─lubridate::ymd_hms(NA_real_)\n 3. └─lubridate:::.parse_xxx_hms(...)\n 4. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 5. └─base::lapply(list(...), .num_to_date)\n 6. └─lubridate (local) FUN(X[[i]], ...)\n \n [ FAIL 43 | WARN 2 | SKIP 1 | PASS 642 ]\n Error: Test failures\n Execution halted"
), warnings = character(0), notes = character(0), description = "Package: gwasrapidd\nType: Package\nTitle: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog\nVersion: 0.99.13\nAuthors@R: c(\n person(given = \"Ramiro\", family = \"Magno\", email = \"ramiro.magno@gmail.com\",\n role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5226-3441\")),\n person(given = \"Ana-Teresa\", family = \"Maia\",\n email = \"maia.anateresa@gmail.com\", role = \"aut\", \n comment = c(ORCID = \"0000-0002-0454-9207\")),\n person(\"CINTESIS\",\n role = c(\"cph\", \"fnd\"))\n )\nDescription: 'GWAS' R 'API' Data Download.\n This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by\n accessing the 'REST' 'API' .\nDepends: R (>= 3.2.3)\nLicense: MIT + file LICENSE\nURL: https://github.com/ramiromagno/gwasrapidd\nBugReports: https://github.com/ramiromagno/gwasrapidd/issues\nEncoding: UTF-8\nLanguage: en-US\nLazyData: true\nRoxygenNote: 7.2.1\nImports: magrittr, httr, urltools, pingr, stringr, concatenate, dplyr,\n jsonlite, purrr, tibble, glue, tidyr (> 0.8.99), assertthat,\n rlang, methods, lubridate, plyr, testthat, utils, progress\nSuggests: httptest, spelling, covr, knitr, rmarkdown\nCollate: 'browser.R' 'class-associations.R' 'class-studies.R'\n 'class-traits.R' 'class-variants.R' 'data.R' 'ebi_server.R'\n 'generics.R' 'get_associations.R' 'get_metadata.R'\n 'get_studies.R' 'get_traits.R' 'get_variants.R'\n 'gwasrapidd-package.R' 'id_mapping.R' 'list_joins.R'\n 'missing.R' 'parse-associations.R' 'parse-studies.R'\n 'parse-traits.R' 'parse-utils.R' 'parse-variants.R'\n 'post-studies.R' 'post-traits.R' 'post-variants.R'\n 'recursive_apply.R' 'request.R' 's4-utils.R' 'sure.R' 'tests.R'\n 'utils-pipe.R' 'utils.R'\nVignetteBuilder: knitr\nbiocViews: ThirdPartyClient, BiomedicalInformatics,\n GenomeWideAssociation, SNP\nNeedsCompilation: no\nPackaged: 2022-08-11 22:04:08 UTC; rmagno\nAuthor: Ramiro Magno [aut, cre] (),\n Ana-Teresa Maia [aut] (),\n CINTESIS [cph, fnd]\nMaintainer: Ramiro Magno \nRepository: CRAN\nDate/Publication: 2022-08-11 22:20:02 UTC",
package = "gwasrapidd", version = "0.99.13", cran = TRUE,
bioc = TRUE, checkdir = "/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/new/gwasrapidd.Rcheck",
test_fail = list(testthat = "> library(testthat)\n> library(gwasrapidd)\n> \n> test_check(\"gwasrapidd\")\n[ FAIL 43 | WARN 2 | SKIP 1 | PASS 642 ]\n\n══ Skipped tests ═══════════════════════════════════════════════════════════════\n• empty test (1)\n\n══ Failed tests ════════════════════════════════════════════════════════════════\n── Error ('test-generics.R:89'): n(): empty_variants ───────────────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd:::variants() at test-generics.R:89:2\n 2. │ ├─methods::new(...)\n 3. │ │ ├─methods::initialize(value, ...)\n 4. │ │ └─methods::initialize(value, ...)\n 5. │ └─gwasrapidd:::variants_tbl()\n 6. │ └─tibble::tibble(...)\n 7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 8. │ └─rlang::eval_tidy(xs[[j]], mask)\n 9. └─gwasrapidd:::empty_to_na(last_update_date)\n 10. └─lubridate::ymd_hms(NA_real_)\n 11. └─lubridate:::.parse_xxx_hms(...)\n 12. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 13. └─base::lapply(list(...), .num_to_date)\n 14. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-generics.R:113'): n(): 2 variants: ────────────────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = variant_ids) at test-generics.R:113:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-generics.R:244'): subsetting variants with `[` ─────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = c(\"rs3798440\", \"rs7329174\")) at test-generics.R:244:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-generics.R:329'): set operations on S4 variants ────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = \"rs3798440\") at test-generics.R:329:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-generics.R:417'): bind S4 variants ─────────────────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = \"rs3798440\") at test-generics.R:417:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:25'): get_variants: GCST002420 ──────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(study_id = \"GCST002420\") at test-get_variants.R:25:4\n 2. │ └─gwasrapidd:::get_variants_by_study_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:36'): get_variants: by association id ───────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(association_id = \"15608\") at test-get_variants.R:36:4\n 2. │ └─gwasrapidd:::get_variants_by_association_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:47'): get_variants: by variant id ───────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = c(\"rs3798440\", \"rs7329174\")) at test-get_variants.R:47:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:57'): get_variants: variants that also map to scaffolds other than the normal chromosomes ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(...) at test-get_variants.R:57:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:65'): get_variants: variants that also map to scaffolds other than the normal chromosomes ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(...) at test-get_variants.R:65:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:78'): get_variants: by efo id ───────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(efo_id = \"EFO_0004291\") at test-get_variants.R:78:4\n 2. │ └─gwasrapidd:::get_variants_by_efo_id(...)\n 3. │ └─gwasrapidd:::get_variants_by_efo_trait(...)\n 4. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:88'): get_variants: by pubmed id ────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(pubmed_id = \"24882193\") at test-get_variants.R:88:4\n 2. │ └─gwasrapidd:::get_variants_by_pubmed_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:98'): get_variants: by genomic range ────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(...) at test-get_variants.R:98:4\n 2. │ └─gwasrapidd:::get_variants_by_genomic_range(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:108'): get_variants: by cytogenetic band ────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(cytogenetic_band = \"3p21.32\") at test-get_variants.R:108:4\n 2. │ └─gwasrapidd:::get_variants_by_cytogenetic_band(...)\n 3. │ └─gwasrapidd:::get_variants_by_genomic_range(...)\n 4. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:119'): get_variants: by gene name ───────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(gene_name = \"AGKP1\") at test-get_variants.R:119:4\n 2. │ └─gwasrapidd:::get_variants_by_gene_name(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:129'): get_variants: by efo_trait ───────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(efo_trait = \"braces\") at test-get_variants.R:129:4\n 2. │ └─gwasrapidd:::get_variants_by_efo_trait(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:148'): get_variants: by genomic range ───────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(...) at test-get_variants.R:148:4\n 2. │ └─gwasrapidd:::get_variants_by_genomic_range(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:154'): get_variants: by genomic range, exceptions ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(...) at test-get_variants.R:154:2\n 2. │ └─gwasrapidd:::get_variants_by_genomic_range(...)\n 3. │ └─gwasrapidd:::variants()\n 4. │ ├─methods::new(...)\n 5. │ │ ├─methods::initialize(value, ...)\n 6. │ │ └─methods::initialize(value, ...)\n 7. │ └─gwasrapidd:::variants_tbl()\n 8. │ └─tibble::tibble(...)\n 9. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 10. │ └─rlang::eval_tidy(xs[[j]], mask)\n 11. └─gwasrapidd:::empty_to_na(last_update_date)\n 12. └─lubridate::ymd_hms(NA_real_)\n 13. └─lubridate:::.parse_xxx_hms(...)\n 14. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 15. └─base::lapply(list(...), .num_to_date)\n 16. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:160'): get_variants_by_study_id: study_id is NULL ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(get_variants_by_study_id(), variants()) at test-get_variants.R:160:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_study_id()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error (???): get_variants_by_study_id: status code is not 200 ───────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...)\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_study_id(study_id = \"GCST002420\")\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:169'): get_variants_by_association_id: association_id is NULL ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...) at test-get_variants.R:169:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_association_id()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error (???): get_variants_by_association_id: status code is not 200 ─────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...)\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd::get_variants(association_id = c(\"15608\", \"24299710\"))\n 5. │ └─gwasrapidd:::get_variants_by_association_id(...)\n 6. │ └─gwasrapidd:::variants()\n 7. │ ├─methods::new(...)\n 8. │ │ ├─methods::initialize(value, ...)\n 9. │ │ └─methods::initialize(value, ...)\n 10. │ └─gwasrapidd:::variants_tbl()\n 11. │ └─tibble::tibble(...)\n 12. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 13. │ └─rlang::eval_tidy(xs[[j]], mask)\n 14. └─gwasrapidd:::empty_to_na(last_update_date)\n 15. └─lubridate::ymd_hms(NA_real_)\n 16. └─lubridate:::.parse_xxx_hms(...)\n 17. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 18. └─base::lapply(list(...), .num_to_date)\n 19. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:178'): get_variants_by_variant_id: variant_id is NULL ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(get_variants_by_variant_id(), variants()) at test-get_variants.R:178:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_variant_id()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error (???): get_variants_by_variant_id: status code is not 200 ─────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...)\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd::get_variants(variant_id = c(\"rs3798440\", \"rs7329174\"))\n 5. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 6. │ └─gwasrapidd:::variants()\n 7. │ ├─methods::new(...)\n 8. │ │ ├─methods::initialize(value, ...)\n 9. │ │ └─methods::initialize(value, ...)\n 10. │ └─gwasrapidd:::variants_tbl()\n 11. │ └─tibble::tibble(...)\n 12. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 13. │ └─rlang::eval_tidy(xs[[j]], mask)\n 14. └─gwasrapidd:::empty_to_na(last_update_date)\n 15. └─lubridate::ymd_hms(NA_real_)\n 16. └─lubridate:::.parse_xxx_hms(...)\n 17. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 18. └─base::lapply(list(...), .num_to_date)\n 19. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:188'): get_variants_by_efo_id: efo_id is NULL ───\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(get_variants_by_efo_id(), variants()) at test-get_variants.R:188:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_efo_id()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:193'): get_variants_by_pubmed_id: pubmed is NULL ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(get_variants_by_pubmed_id(), variants()) at test-get_variants.R:193:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_pubmed_id()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error (???): get_variants_by_pubmed_id: status code is not 200 ──────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...)\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd::get_variants(pubmed_id = c(\"21626137\", \"25890600\"))\n 5. │ └─gwasrapidd:::get_variants_by_pubmed_id(...)\n 6. │ └─gwasrapidd:::variants()\n 7. │ ├─methods::new(...)\n 8. │ │ ├─methods::initialize(value, ...)\n 9. │ │ └─methods::initialize(value, ...)\n 10. │ └─gwasrapidd:::variants_tbl()\n 11. │ └─tibble::tibble(...)\n 12. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 13. │ └─rlang::eval_tidy(xs[[j]], mask)\n 14. └─gwasrapidd:::empty_to_na(last_update_date)\n 15. └─lubridate::ymd_hms(NA_real_)\n 16. └─lubridate:::.parse_xxx_hms(...)\n 17. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 18. └─base::lapply(list(...), .num_to_date)\n 19. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:202'): get_variants_by_efo_trait: efo_trait is NULL ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(get_variants_by_efo_trait(), variants()) at test-get_variants.R:202:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_efo_trait()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error (???): get_variants_by_efo_trait: status code is not 200 ──────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...)\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd::get_variants(...)\n 5. │ └─gwasrapidd:::get_variants_by_efo_trait(...)\n 6. │ └─gwasrapidd:::variants()\n 7. │ ├─methods::new(...)\n 8. │ │ ├─methods::initialize(value, ...)\n 9. │ │ └─methods::initialize(value, ...)\n 10. │ └─gwasrapidd:::variants_tbl()\n 11. │ └─tibble::tibble(...)\n 12. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 13. │ └─rlang::eval_tidy(xs[[j]], mask)\n 14. └─gwasrapidd:::empty_to_na(last_update_date)\n 15. └─lubridate::ymd_hms(NA_real_)\n 16. └─lubridate:::.parse_xxx_hms(...)\n 17. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 18. └─base::lapply(list(...), .num_to_date)\n 19. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-get_variants.R:211'): get_variants_by_reported_trait: reported_trait is NULL ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...) at test-get_variants.R:211:2\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd:::get_variants_by_reported_trait()\n 5. │ └─gwasrapidd:::variants()\n 6. │ ├─methods::new(...)\n 7. │ │ ├─methods::initialize(value, ...)\n 8. │ │ └─methods::initialize(value, ...)\n 9. │ └─gwasrapidd:::variants_tbl()\n 10. │ └─tibble::tibble(...)\n 11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 12. │ └─rlang::eval_tidy(xs[[j]], mask)\n 13. └─gwasrapidd:::empty_to_na(last_update_date)\n 14. └─lubridate::ymd_hms(NA_real_)\n 15. └─lubridate:::.parse_xxx_hms(...)\n 16. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 17. └─base::lapply(list(...), .num_to_date)\n 18. └─lubridate (local) FUN(X[[i]], ...)\n── Error (???): get_variants_by_reported_trait: status code is not 200 ─────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_identical(...)\n 2. │ └─testthat::quasi_label(enquo(object), label, arg = \"object\")\n 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))\n 4. ├─gwasrapidd::get_variants(...)\n 5. │ └─gwasrapidd:::get_variants_by_reported_trait(...)\n 6. │ └─gwasrapidd:::variants()\n 7. │ ├─methods::new(...)\n 8. │ │ ├─methods::initialize(value, ...)\n 9. │ │ └─methods::initialize(value, ...)\n 10. │ └─gwasrapidd:::variants_tbl()\n 11. │ └─tibble::tibble(...)\n 12. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 13. │ └─rlang::eval_tidy(xs[[j]], mask)\n 14. └─gwasrapidd:::empty_to_na(last_update_date)\n 15. └─lubridate::ymd_hms(NA_real_)\n 16. └─lubridate:::.parse_xxx_hms(...)\n 17. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 18. └─base::lapply(list(...), .num_to_date)\n 19. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:33'): study_to_variant: normal usage ──────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::study_to_variant(c(\"GCST001084\", \"GCST001085\")) at test-id_mapping.R:33:4\n 2. │ └─purrr::map_dfr(...)\n 3. │ └─purrr::map(.x, .f, ...)\n 4. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 5. │ └─gwasrapidd::get_variants(study_id = .x, verbose = verbose, warnings = warnings)\n 6. │ └─gwasrapidd:::get_variants_by_study_id(...)\n 7. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 8. │ └─gwasrapidd:::variants()\n 9. │ ├─methods::new(...)\n 10. │ │ ├─methods::initialize(value, ...)\n 11. │ │ └─methods::initialize(value, ...)\n 12. │ └─gwasrapidd:::variants_tbl()\n 13. │ └─tibble::tibble(...)\n 14. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 15. │ └─rlang::eval_tidy(xs[[j]], mask)\n 16. └─gwasrapidd:::empty_to_na(last_update_date)\n 17. └─lubridate::ymd_hms(NA_real_)\n 18. └─lubridate:::.parse_xxx_hms(...)\n 19. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 20. └─base::lapply(list(...), .num_to_date)\n 21. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:43'): study_to_variant: verbose ───────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_message(...) at test-id_mapping.R:43:4\n 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)\n 3. │ ├─testthat (local) .capture(...)\n 4. │ │ └─base::withCallingHandlers(...)\n 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))\n 6. ├─gwasrapidd::study_to_variant(c(\"GCST001084\"), verbose = TRUE)\n 7. │ └─purrr::map_dfr(...)\n 8. │ └─purrr::map(.x, .f, ...)\n 9. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 10. │ └─gwasrapidd::get_variants(study_id = .x, verbose = verbose, warnings = warnings)\n 11. │ └─gwasrapidd:::get_variants_by_study_id(...)\n 12. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 13. │ └─gwasrapidd:::variants()\n 14. │ ├─methods::new(...)\n 15. │ │ ├─methods::initialize(value, ...)\n 16. │ │ └─methods::initialize(value, ...)\n 17. │ └─gwasrapidd:::variants_tbl()\n 18. │ └─tibble::tibble(...)\n 19. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 20. │ └─rlang::eval_tidy(xs[[j]], mask)\n 21. └─gwasrapidd:::empty_to_na(last_update_date)\n 22. └─lubridate::ymd_hms(NA_real_)\n 23. └─lubridate:::.parse_xxx_hms(...)\n 24. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 25. └─base::lapply(list(...), .num_to_date)\n 26. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:49'): study_to_variant: warnings ──────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_warning(...) at test-id_mapping.R:49:2\n 2. │ └─testthat:::quasi_capture(...)\n 3. │ ├─testthat (local) .capture(...)\n 4. │ │ └─base::withCallingHandlers(...)\n 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))\n 6. ├─gwasrapidd::study_to_variant(c(\"GCST0\"), warnings = TRUE)\n 7. │ └─purrr::map_dfr(...)\n 8. │ └─purrr::map(.x, .f, ...)\n 9. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 10. │ └─gwasrapidd::get_variants(study_id = .x, verbose = verbose, warnings = warnings)\n 11. │ └─gwasrapidd:::get_variants_by_study_id(...)\n 12. │ └─gwasrapidd:::variants()\n 13. │ ├─methods::new(...)\n 14. │ │ ├─methods::initialize(value, ...)\n 15. │ │ └─methods::initialize(value, ...)\n 16. │ └─gwasrapidd:::variants_tbl()\n 17. │ └─tibble::tibble(...)\n 18. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 19. │ └─rlang::eval_tidy(xs[[j]], mask)\n 20. └─gwasrapidd:::empty_to_na(last_update_date)\n 21. └─lubridate::ymd_hms(NA_real_)\n 22. └─lubridate:::.parse_xxx_hms(...)\n 23. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 24. └─base::lapply(list(...), .num_to_date)\n 25. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:111'): association_to_variant: normal usage ───────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::association_to_variant(c(\"24300097\", \"24299759\")) at test-id_mapping.R:111:4\n 2. │ └─purrr::map_dfr(...)\n 3. │ └─purrr::map(.x, .f, ...)\n 4. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 5. │ └─gwasrapidd::get_variants(...)\n 6. │ └─gwasrapidd:::get_variants_by_association_id(...)\n 7. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 8. │ └─gwasrapidd:::variants()\n 9. │ ├─methods::new(...)\n 10. │ │ ├─methods::initialize(value, ...)\n 11. │ │ └─methods::initialize(value, ...)\n 12. │ └─gwasrapidd:::variants_tbl()\n 13. │ └─tibble::tibble(...)\n 14. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 15. │ └─rlang::eval_tidy(xs[[j]], mask)\n 16. └─gwasrapidd:::empty_to_na(last_update_date)\n 17. └─lubridate::ymd_hms(NA_real_)\n 18. └─lubridate:::.parse_xxx_hms(...)\n 19. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 20. └─base::lapply(list(...), .num_to_date)\n 21. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:126'): association_to_variant: warnings ───────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_warning(...) at test-id_mapping.R:126:4\n 2. │ └─testthat:::quasi_capture(...)\n 3. │ ├─testthat (local) .capture(...)\n 4. │ │ └─base::withCallingHandlers(...)\n 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))\n 6. ├─gwasrapidd::association_to_variant(c(\"0\"), warnings = TRUE)\n 7. │ └─purrr::map_dfr(...)\n 8. │ └─purrr::map(.x, .f, ...)\n 9. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 10. │ └─gwasrapidd::get_variants(...)\n 11. │ └─gwasrapidd:::get_variants_by_association_id(...)\n 12. │ └─gwasrapidd:::variants()\n 13. │ ├─methods::new(...)\n 14. │ │ ├─methods::initialize(value, ...)\n 15. │ │ └─methods::initialize(value, ...)\n 16. │ └─gwasrapidd:::variants_tbl()\n 17. │ └─tibble::tibble(...)\n 18. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 19. │ └─rlang::eval_tidy(xs[[j]], mask)\n 20. └─gwasrapidd:::empty_to_na(last_update_date)\n 21. └─lubridate::ymd_hms(NA_real_)\n 22. └─lubridate:::.parse_xxx_hms(...)\n 23. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 24. └─base::lapply(list(...), .num_to_date)\n 25. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:312'): trait_to_variant: verbose ──────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_message(...) at test-id_mapping.R:312:4\n 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)\n 3. │ ├─testthat (local) .capture(...)\n 4. │ │ └─base::withCallingHandlers(...)\n 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))\n 6. ├─gwasrapidd::trait_to_variant(c(\"EFO_0005108\"), verbose = TRUE)\n 7. │ └─purrr::map_dfr(...)\n 8. │ └─purrr::map(.x, .f, ...)\n 9. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 10. │ └─gwasrapidd::get_variants(efo_id = .x, verbose = verbose, warnings = warnings)\n 11. │ └─gwasrapidd:::get_variants_by_efo_id(...)\n 12. │ └─gwasrapidd:::get_variants_by_efo_trait(...)\n 13. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 14. │ └─gwasrapidd:::variants()\n 15. │ ├─methods::new(...)\n 16. │ │ ├─methods::initialize(value, ...)\n 17. │ │ └─methods::initialize(value, ...)\n 18. │ └─gwasrapidd:::variants_tbl()\n 19. │ └─tibble::tibble(...)\n 20. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 21. │ └─rlang::eval_tidy(xs[[j]], mask)\n 22. └─gwasrapidd:::empty_to_na(last_update_date)\n 23. └─lubridate::ymd_hms(NA_real_)\n 24. └─lubridate:::.parse_xxx_hms(...)\n 25. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 26. └─base::lapply(list(...), .num_to_date)\n 27. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-id_mapping.R:318'): trait_to_variant: warnings ─────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─testthat::expect_warning(...) at test-id_mapping.R:318:2\n 2. │ └─testthat:::quasi_capture(...)\n 3. │ ├─testthat (local) .capture(...)\n 4. │ │ └─base::withCallingHandlers(...)\n 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))\n 6. ├─gwasrapidd::trait_to_variant(c(\"EFO_0000000\"), warnings = TRUE)\n 7. │ └─purrr::map_dfr(...)\n 8. │ └─purrr::map(.x, .f, ...)\n 9. │ └─gwasrapidd (local) .f(.x[[i]], ...)\n 10. │ └─gwasrapidd::get_variants(efo_id = .x, verbose = verbose, warnings = warnings)\n 11. │ └─gwasrapidd:::get_variants_by_efo_id(...)\n 12. │ └─gwasrapidd:::get_variants_by_efo_trait(...)\n 13. │ └─gwasrapidd:::variants()\n 14. │ ├─methods::new(...)\n 15. │ │ ├─methods::initialize(value, ...)\n 16. │ │ └─methods::initialize(value, ...)\n 17. │ └─gwasrapidd:::variants_tbl()\n 18. │ └─tibble::tibble(...)\n 19. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 20. │ └─rlang::eval_tidy(xs[[j]], mask)\n 21. └─gwasrapidd:::empty_to_na(last_update_date)\n 22. └─lubridate::ymd_hms(NA_real_)\n 23. └─lubridate:::.parse_xxx_hms(...)\n 24. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 25. └─base::lapply(list(...), .num_to_date)\n 26. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-parse-variants.R:9'): filter_variants_by_standard_chromosomes: no non-standard locations ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = c(\"rs3798440\", \"rs7329174\")) at test-parse-variants.R:9:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-parse-variants.R:18'): filter_variants_by_standard_chromosomes: mitochondrial locations ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = c(\"rs147903261\", \"rs267606894\")) at test-parse-variants.R:18:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-parse-variants.R:29'): filter_variants_by_standard_chromosomes: drop mitochondrial locations ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = c(\"rs147903261\", \"rs267606894\")) at test-parse-variants.R:29:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-parse-variants.R:42'): filter_variants_by_standard_chromosomes: non-standard locations are dropped ──\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. ├─gwasrapidd::get_variants(variant_id = c(\"rs10910092\", \"rs570398477\")) at test-parse-variants.R:42:4\n 2. │ └─gwasrapidd:::get_variants_by_variant_id(...)\n 3. │ └─gwasrapidd:::v_obj_to_variants(obj)\n 4. │ └─gwasrapidd:::variants()\n 5. │ ├─methods::new(...)\n 6. │ │ ├─methods::initialize(value, ...)\n 7. │ │ └─methods::initialize(value, ...)\n 8. │ └─gwasrapidd:::variants_tbl()\n 9. │ └─tibble::tibble(...)\n 10. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)\n 11. │ └─rlang::eval_tidy(xs[[j]], mask)\n 12. └─gwasrapidd:::empty_to_na(last_update_date)\n 13. └─lubridate::ymd_hms(NA_real_)\n 14. └─lubridate:::.parse_xxx_hms(...)\n 15. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 16. └─base::lapply(list(...), .num_to_date)\n 17. └─lubridate (local) FUN(X[[i]], ...)\n── Error ('test-utils.R:38'): empty_to_na: dates ───────────────────────────────\nError in `if (is.numeric(x) && any(x > 1900)) {\n out <- rep.int(as.character(NA), length(x))\n nnas <- !is.na(x)\n x <- format(x[nnas], scientific = FALSE, trim = TRUE)\n x <- paste(ifelse(nchar(x)%%2 == 1, \"0\", \"\"), x, sep = \"\")\n out[nnas] <- x\n out\n} else {\n as.character(x)\n}`: missing value where TRUE/FALSE needed\nBacktrace:\n ▆\n 1. └─gwasrapidd:::empty_to_na(empty_date) at test-utils.R:38:2\n 2. └─lubridate::ymd_hms(NA_real_)\n 3. └─lubridate:::.parse_xxx_hms(...)\n 4. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 5. └─base::lapply(list(...), .num_to_date)\n 6. └─lubridate (local) FUN(X[[i]], ...)\n\n[ FAIL 43 | WARN 2 | SKIP 1 | PASS 642 ]\nError: Test failures\nExecution halted\n"),
test_output = list(spelling = "> if(requireNamespace('spelling', quietly=TRUE))\n+ spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)\nNULL\n> \n> proc.time()\n user system elapsed \n 0.132 0.021 0.144 \n"),
install_out = "* installing *source* package ‘gwasrapidd’ ...\n** package ‘gwasrapidd’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (gwasrapidd)\n"), class = "rcmdcheck"))