* using log directory 'd:/RCompile/CRANincoming/R-devel/ieugwasr.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86457 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'ieugwasr/DESCRIPTION' ... OK * this is package 'ieugwasr' version '1.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Gibran Hemani ' Found the following (possibly) invalid URLs: URL: https://api.opengwas.io/profile From: inst/doc/guide.html Status: 404 Message: Not Found URL: https://mygene.info/ From: inst/doc/guide.html Status: 204 Message: No Content * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'ieugwasr' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... NONE * checking for unstated dependencies in 'tests' ... OK * checking tests ... [17s] ERROR Running 'testthat.R' [16s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(ieugwasr) OpenGWAS updates: Date: 2024-03-07 [>] There is exceptional load on the OpenGWAS servers. [>] Urgent infrastructure development being performed. [>] See local options for analysis: https://mrcieu.github.io/gwasvcf/. > > test_check("ieugwasr") [ FAIL 19 | WARN 0 | SKIP 3 | PASS 15 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test_query.r:104:2' • Server issues (2): 'test_ld.r:7:1', 'test_query.r:63:2' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_afl2.r:19:2'): ancestry ──────────────────────────────────────── Error in `auto_copy(x, y, copy = copy)`: `x` and `y` must share the same src. ℹ `x` is a object. ℹ `y` is a object. ℹ Set `copy = TRUE` if `y` can be copied to the same source as `x` (may be slow). Backtrace: ▆ 1. ├─ieugwasr::infer_ancestry(a, snpinfo1) at test_afl2.r:19:9 2. │ └─snpinfo %>% dplyr::inner_join(., d, by = "rsid") 3. ├─dplyr::inner_join(., d, by = "rsid") 4. └─dplyr:::inner_join.data.frame(., d, by = "rsid") 5. └─dplyr::auto_copy(x, y, copy = copy) 6. └─rlang::abort(bullets) ── Failure ('test_afl2.r:25:2'): chrpos ──────────────────────────────────────── nrow(a) > 100 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_afl2.r:30:2'): rsid ────────────────────────────────────────── nrow(a) == 2 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_query.r:16:2'): gwasinfo ───────────────────────────────────── ... == 1 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_query.r:19:2'): gwasinfo ───────────────────────────────────── nrow(...) not equal to 2. target is NULL, current is numeric ── Error ('test_query.r:23:2'): gwasinfo ─────────────────────────────────────── Error in `dplyr::bind_rows(out)`: Argument 1 must be a data frame or a named atomic vector. Backtrace: ▆ 1. ├─testthat::expect_gt(nrow(gwasinfo()), 100) at test_query.r:23:9 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(gwasinfo()) 5. ├─ieugwasr::gwasinfo() 6. │ ├─dplyr::bind_rows(out) %>% ... 7. │ └─dplyr::bind_rows(out) 8. │ └─rlang::abort(glue("Argument {i} must be a data frame or a named atomic vector.")) 9. └─dplyr::select(., "id", "trait", dplyr::everything()) ── Error ('test_query.r:30:2'): gwasinfo without token ───────────────────────── Error in `dplyr::bind_rows(out)`: Argument 1 must be a data frame or a named atomic vector. Backtrace: ▆ 1. ├─ieugwasr::gwasinfo("ieu-a-2", opengwas_jwt = "") at test_query.r:30:9 2. │ ├─dplyr::bind_rows(out) %>% ... 3. │ └─dplyr::bind_rows(out) 4. │ └─rlang::abort(glue("Argument {i} must be a data frame or a named atomic vector.")) 5. └─dplyr::select(., "id", "trait", dplyr::everything()) ── Failure ('test_query.r:38:2'): associations ───────────────────────────────── ... == 2 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_query.r:42:2'): associations ───────────────────────────────── ... == 1 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_query.r:46:2'): associations ───────────────────────────────── ... > 10000 is not TRUE `actual`: `expected`: TRUE ── Error ('test_query.r:54:2'): fill_n ───────────────────────────────────────── Error in `dplyr::bind_rows(out)`: Argument 1 must be a data frame or a named atomic vector. Backtrace: ▆ 1. ├─associations(c("rs12759473"), "bbj-a-10") %>% fill_n at test_query.r:54:9 2. ├─ieugwasr::fill_n(.) 3. │ └─ieugwasr::gwasinfo(id, opengwas_jwt = opengwas_jwt) 4. │ ├─dplyr::bind_rows(out) %>% ... 5. │ └─dplyr::bind_rows(out) 6. │ └─rlang::abort(glue("Argument {i} must be a data frame or a named atomic vector.")) 7. └─dplyr::select(., "id", "trait", dplyr::everything()) ── Failure ('test_query.r:82:2'): phewas ─────────────────────────────────────── nrow(a) > 10 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_query.r:88:2'): tophits ────────────────────────────────────── nrow(tophits("ieu-a-2")) not equal to 79. target is NULL, current is numeric ── Failure ('test_query.r:89:2'): tophits ────────────────────────────────────── nrow(tophits("ieu-a-2", clump = 0)) > 79 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_variants.r:13:2'): genes ───────────────────────────────────── nrow(o1) is not strictly more than 0. Difference: 0 ── Failure ('test_variants.r:14:2'): genes ───────────────────────────────────── nrow(o2) is not strictly more than nrow(o1). Difference: 0 ── Failure ('test_variants.r:21:2'): chrpos ──────────────────────────────────── nrow(o) > 1 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_variants.r:24:2'): chrpos ──────────────────────────────────── nrow(o) == 1 is not TRUE `actual`: `expected`: TRUE ── Failure ('test_variants.r:43:2'): conversion ──────────────────────────────── length(o) == 2 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 19 | WARN 0 | SKIP 3 | PASS 15 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE