* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/otargen.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (Debian 13.2.0-24) 13.2.0 GNU Fortran (Debian 13.2.0-24) 13.2.0 * running under: Debian GNU/Linux trixie/sid * 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 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘otargen’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/otargen-00install.html' for details. * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/3s] OK * checking whether the package can be loaded with stated dependencies ... [1s/2s] OK * checking whether the package can be unloaded cleanly ... [1s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] 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 ... [13s/15s] OK * checking Rd files ... [1s/1s] 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 ... [2s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [11s/54s] ERROR Running ‘testthat.R’ [11s/54s] 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... [68ms] \ Downloading data for ENSG00000169174 ... | Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [1.3s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [16ms] \ Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [897ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [566ms] \ Downloading data for ENSG00000143001 ... v Downloading data for ENSG00000143001 ... [478ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [310ms] \ Downloading data for ENSG00000141510 ... | Downloading data for ENSG00000141510 ... v Downloading data for ENSG00000141510 ... [1.3s] \ Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [458ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [532ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [104ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [471ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [17ms] \ Downloading data... v Downloading data... [131ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [97ms] \ Downloading data... v Downloading data... [174ms] \ Connecting to the Open Targets Genetics GrpahQL API... x Connecting to the Open Targets Genetics GrpahQL API... [143ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [14ms] \ Downloading data for 1_154453788_C_T ... v Downloading data for 1_154453788_C_T ... [487ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [160ms] \ Downloading data for rs55808324 ... v Downloading data for rs55808324 ... [409ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [14ms] \ Downloading data... v Downloading data... [135ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [20ms] \ Downloading data... x Downloading data... [207ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [41ms] \ Downloading data... v Downloading data... [427ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [31ms] \ Downloading the data... v Downloading the data... [139ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [28ms] \ Downloading the data... v Downloading the data... [219ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [26ms] \ Downloading data... v Downloading data... [174ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [24ms] \ Downloading data... v Downloading data... [1.5s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [15ms] \ Downloading data... v Downloading data... [711ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [14ms] \ Downloading data... v Downloading data... [658ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [14ms] \ Downloading data for variant 1_55063514_G_A ... v Downloading data for variant 1_55063514_G_A ... [187ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [105ms] \ Downloading data for variant rs72698179 ... v Downloading data for variant rs72698179 ... [210ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [14ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [298ms] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [14ms] \ Downloading data for ENSG00000167207 ... v Downloading data for ENSG00000167207 ... [374ms] \ Downloading data for ENSG00000096968 ... v Downloading data for ENSG00000096968 ... [893ms] \ Downloading data for ENSG00000138821 ... v Downloading data for ENSG00000138821 ... [375ms] \ Downloading data for ENSG00000125255 ... v Downloading data for ENSG00000125255 ... [459ms] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [109ms] \ Downloading data for ENSG00000141510 ... v Downloading data for ENSG00000141510 ... [1.2s] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [276ms] \ Downloading data for ENSG00000169174 ... v Downloading data for ENSG00000169174 ... [271ms] \ Downloading data for ENSG00000163946 ... | Downloading data for ENSG00000163946 ... v Downloading data for ENSG00000163946 ... [461ms] \ Downloading data for ENSG00000141510 ... v Downloading data for ENSG00000141510 ... [1.1s] Selecting by Trait_reported_trimmed \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [13ms] \ 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... [14ms] \ Downloading data... v Downloading data... [3s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [14ms] \ Downloading data for variant 14_87978408_G_A ... v Downloading data for variant 14_87978408_G_A ... [211ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [138ms] \ Downloading data for variant rs55808324 ... v Downloading data for variant rs55808324 ... [219ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [30ms] \ Downloading data... v Downloading data... [320ms] \ Connecting the database... v Connecting the database... [17ms] \ Downloading data... v Downloading data... [183ms] \ Connecting the database... v Connecting the database... [205ms] \ Downloading data... v Downloading data... [190ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [18ms] \ Downloading data for ENSG00000169174 ... x Downloading data for ENSG00000169174 ... [10.1s] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [15ms] \ Downloading data... v Downloading data... [131ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [14ms] \ Downloading data for GCST003044 , 14_88009660_C_T ... v Downloading data for GCST003044 , 14_88009660_C_T ... [896ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [31ms] \ Downloading data... v Downloading data... [1.6s] \ Connecting the database... v Connecting the database... [22ms] \ Downloading data... v Downloading data... [270ms] \ Connecting to the Open Targets Genetics GrpahQL API... v Connecting to the Open Targets Genetics GrpahQL API... [15ms] \ Downloading data... v Downloading data... [182ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [19ms] \ Downloading data... v Downloading data... [140ms] \ Connecting to the Open Targets Genetics GraphQL API... v Connecting to the Open Targets Genetics GraphQL API... [113ms] \ Downloading data... v Downloading data... [152ms] [ FAIL 2 | WARN 0 | SKIP 0 | PASS 74 ] ══ 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 ── Error ('test-studiesAndLeadVariantsForGeneByL2G.R:2:3'): test studiesAndLeadVariantsForGeneByL2G works ── Error: Bad Gateway (HTTP 502) Backtrace: ▆ 1. └─otargen::studiesAndLeadVariantsForGeneByL2G(gene = "ENSG00000169174") at test-studiesAndLeadVariantsForGeneByL2G.R:2:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 74 ] Error: Test failures Execution halted * checking PDF version of manual ... [6s/7s] OK * checking HTML version of manual ... [2s/3s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR