* using log directory 'd:/RCompile/CRANincoming/R-devel/otargen.Rcheck' * using R Under development (unstable) (2024-02-08 r85876 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'otargen/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'otargen' version '1.1.1' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [14s] Note_to_CRAN_maintainers Maintainer: 'Amir Feizi ' * 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 serialization versions ... OK * checking whether package 'otargen' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 R 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 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 examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [52s] ERROR Running 'testthat.R' [52s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(otargen) > > test_check("otargen") \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [29ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [606ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [246ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [136ms] \ Downloading data for ENSG00000143001 ... v Downloading data for ENSG00000143001 ... [140ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [173ms] \ Downloading data for ENSG00000141510 ... v Downloading data for ENSG00000141510 ... [534ms] \ Downloading data for ENSG00000163946 ... | Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [195ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [140ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [49ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [145ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [53ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [48ms] \ Downloading data... v Downloading data... [46ms] \ Connecting to the Open Targets Genetics GrpahQL API... x Connecting to the Open Targets Genetics GrpahQL API... [45ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [7ms] \ Downloading data for 1_154453788_C_T ... v Downloading data for 1_154453788_C_T ... [165ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [59ms] \ Downloading data for rs55808324 ... v Downloading data for rs55808324 ... [118ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [55ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... x Downloading data... [44ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [76ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading the data... v Downloading the data... [46ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading the data... v Downloading the data... [47ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [49ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [469ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [169ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [96ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data for variant 1_55063514_G_A ... v Downloading data for variant 1_55063514_G_A ... [64ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [53ms] \ Downloading data for variant rs72698179 ... v Downloading data for variant rs72698179 ... [56ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [6ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [139ms] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [8ms] \ Downloading data for ENSG00000167207 ... v Downloading data for ENSG00000167207 ... [153ms] \ Downloading data for ENSG00000096968 ... | Downloading data for ENSG00000096968 ... v Downloading data for ENSG00000096968 ... [283ms] \ Downloading data for ENSG00000138821 ... v Downloading data for ENSG00000138821 ... [148ms] \ Downloading data for ENSG00000125255 ... v Downloading data for ENSG00000125255 ... [112ms] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [53ms] \ Downloading data for ENSG00000141510 ... v Downloading data for ENSG00000141510 ... [351ms] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [151ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [126ms] \ Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [197ms] \ Downloading data for ENSG00000141510 ... v Downloading data for ENSG00000141510 ... [374ms] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data for ENSG00000167207 ... v Downloading data for ENSG00000167207 ... [6.4s] \ Downloading data for ENSG00000096968 ... v Downloading data for ENSG00000096968 ... [5.8s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [29ms] \ Downloading data for ENSG00000167207 ... x Downloading data for ENSG00000167207 ... [10.1s] Error in test plot_l2g: Bad Gateway (HTTP 502) \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [8ms] \ Downloading data... v Downloading data... [1.1s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data for variant 14_87978408_G_A ... v Downloading data for variant 14_87978408_G_A ... [82ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [68ms] \ Downloading data for variant rs55808324 ... v Downloading data for variant rs55808324 ... [70ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [105ms] \ Connecting the database... v Connecting the database... [7ms] \ Downloading data... v Downloading data... [75ms] \ Connecting the database... v Connecting the database... [119ms] \ Downloading data... v Downloading data... [84ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [5.4s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [98ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [4.8s] \ Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [5.4s] \ Connecting to the Open Targets Genetics GrpahQL API... x Connecting to the Open Targets Genetics GrpahQL API... [50ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [206ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [7ms] \ Downloading data for GCST003044 , 14_88009660_C_T ... v Downloading data for GCST003044 , 14_88009660_C_T ... [671ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [392ms] \ Connecting the database... v Connecting the database... [7ms] \ Downloading data... v Downloading data... [181ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [7ms] \ Downloading data... v Downloading data... [74ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [7ms] \ Downloading data... v Downloading data... [69ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [64ms] \ Downloading data... v Downloading data... [135ms] [ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plot_l2g.R:23:5'): test plot_l2g works ─────────────────────── FALSE is not TRUE `actual`: FALSE `expected`: TRUE An error occurred in plotting. Backtrace: ▆ 1. └─base::tryCatch(...) at test-plot_l2g.R:3:3 2. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. └─value[[3L]](cond) 5. └─testthat::expect_true(FALSE, "An error occurred in plotting.") at test-plot_l2g.R:23:5 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ] Error: Test failures Execution halted * checking PDF version of manual ... [19s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR