Last updated on 2024-05-15 18:56:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 7.74 | 83.67 | 91.41 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 6.64 | 61.05 | 67.69 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 117.68 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 108.21 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.1 | 10.00 | 123.00 | 133.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 5.86 | 78.99 | 84.85 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 5.07 | 79.04 | 84.11 | OK | |
| r-release-macos-arm64 | 1.1.1 | 99.00 | OK | |||
| r-release-macos-x86_64 | 1.1.1 | 143.00 | OK | |||
| r-release-windows-x86_64 | 1.1.1 | 10.00 | 124.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | 109.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.1.1 | 139.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1.1 | 11.00 | 138.00 | 149.00 | OK |
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/108s]
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... [152ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [2.1s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [54ms]
\ Downloading data for ENSG00000163946 ...
| Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [1.2s]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [407ms]
\ Downloading data for ENSG00000143001 ...
v Downloading data for ENSG00000143001 ... [627ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [9.3s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [82ms]
\ Downloading data...
v Downloading data... [324ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [4.7s]
\ Downloading data...
v Downloading data... [426ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [223ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [90ms]
\ Downloading data for 1_154453788_C_T ...
v Downloading data for 1_154453788_C_T ... [1.3s]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [187ms]
\ Downloading data for rs55808324 ...
v Downloading data for rs55808324 ... [680ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [50ms]
\ Downloading data...
v Downloading data... [213ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [69ms]
\ Downloading data...
x Downloading data... [291ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [57ms]
\ Downloading data...
v Downloading data... [4.8s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [98ms]
\ Downloading the data...
v Downloading the data... [276ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [74ms]
\ Downloading the data...
v Downloading the data... [4.1s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [51ms]
\ Downloading data...
v Downloading data... [558ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [70ms]
\ Downloading data...
v Downloading data... [2.8s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [63ms]
\ Downloading data...
v Downloading data... [765ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ Downloading data...
v Downloading data... [2.4s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [73ms]
\ Downloading data for variant 1_55063514_G_A ...
v Downloading data for variant 1_55063514_G_A ... [408ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [204ms]
\ Downloading data for variant rs72698179 ...
v Downloading data for variant rs72698179 ... [605ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [17ms]
\ Downloading data for ENSG00000169174 ...
| Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [1.6s]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [69ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [541ms]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [835ms]
\ Downloading data for ENSG00000138821 ...
| Downloading data for ENSG00000138821 ...
v Downloading data for ENSG00000138821 ... [730ms]
\ Downloading data for ENSG00000125255 ...
v Downloading data for ENSG00000125255 ... [494ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [140ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [1s]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [231ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [298ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [626ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [785ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [6s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [5.7s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [39ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [5.7s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [5.5s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [47ms]
\ Downloading data...
v Downloading data... [2.4s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
\ Downloading data for variant 14_87978408_G_A ...
v Downloading data for variant 14_87978408_G_A ... [265ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [131ms]
\ Downloading data for variant rs55808324 ...
v Downloading data for variant rs55808324 ... [197ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
\ Downloading data...
v Downloading data... [148ms]
\ Connecting the database...
v Connecting the database... [17ms]
\ Downloading data...
v Downloading data... [104ms]
\ Connecting the database...
v Connecting the database... [186ms]
\ Downloading data...
v Downloading data... [120ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
\ 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... [37ms]
\ Downloading data...
v Downloading data... [184ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [37ms]
\ Downloading data for GCST003044 , 14_88009660_C_T ...
v Downloading data for GCST003044 , 14_88009660_C_T ... [752ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [24ms]
\ Downloading data...
v Downloading data... [236ms]
\ Connecting the database...
v Connecting the database... [17ms]
\ Downloading data...
v Downloading data... [259ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [39ms]
\ Downloading data...
v Downloading data... [160ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [35ms]
\ Downloading data...
v Downloading data... [151ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [119ms]
\ Downloading data...
v Downloading data... [221ms]
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 70 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-colocalisationsForGene.R:4:3'): test colocalisationsForGene works ──
Error: Bad Gateway (HTTP 502)
Backtrace:
▆
1. └─otargen::colocalisationsForGene(genes = c("TP53", "TASOR", "PCSK9")) at test-colocalisationsForGene.R:4:3
2. ├─jsonlite::fromJSON(...)
3. └─con$exec(qry$queries$gene2ensembl, variables)
4. ├─ghql:::cont(gh_POST(self$url, body, self$headers, ...), encoding = encoding)
5. └─ghql:::gh_POST(self$url, body, self$headers, ...)
6. └─res$raise_for_status()
── 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 70 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/71s]
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... [224ms]
\ Downloading data for ENSG00000169174 ...
| Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [1.5s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [21ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [437ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [324ms]
\ Downloading data for ENSG00000143001 ...
v Downloading data for ENSG00000143001 ... [484ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [242ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [794ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [312ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [339ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [65ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [262ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [38ms]
\ Downloading data...
v Downloading data... [176ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [83ms]
\ Downloading data...
v Downloading data... [144ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [105ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [43ms]
\ Downloading data for 1_154453788_C_T ...
v Downloading data for 1_154453788_C_T ... [669ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [141ms]
\ Downloading data for rs55808324 ...
v Downloading data for rs55808324 ... [386ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [27ms]
\ Downloading data...
v Downloading data... [135ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [35ms]
\ Downloading data...
x Downloading data... [412ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [20ms]
\ Downloading data...
v Downloading data... [150ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
\ Downloading the data...
v Downloading the data... [111ms]
\ 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... [180ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [30ms]
\ Downloading data...
v Downloading data... [128ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [43ms]
\ Downloading data...
v Downloading data... [1.8s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [117ms]
\ Downloading data...
v Downloading data... [640ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [44ms]
\ Downloading data...
v Downloading data... [674ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [34ms]
\ Downloading data for variant 1_55063514_G_A ...
v Downloading data for variant 1_55063514_G_A ... [198ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [134ms]
\ Downloading data for variant rs72698179 ...
v Downloading data for variant rs72698179 ... [247ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [32ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [309ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [34ms]
\ Downloading data for ENSG00000167207 ...
| Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [290ms]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [789ms]
\ Downloading data for ENSG00000138821 ...
v Downloading data for ENSG00000138821 ... [318ms]
\ Downloading data for ENSG00000125255 ...
v Downloading data for ENSG00000125255 ... [327ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [80ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [717ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [275ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [294ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [316ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [699ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [27ms]
\ 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... [18ms]
\ Downloading data...
v Downloading data... [1.6s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [65ms]
\ Downloading data for variant 14_87978408_G_A ...
v Downloading data for variant 14_87978408_G_A ... [309ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [135ms]
\ Downloading data for variant rs55808324 ...
v Downloading data for variant rs55808324 ... [202ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ Downloading data...
v Downloading data... [160ms]
\ Connecting the database...
v Connecting the database... [33ms]
\ Downloading data...
v Downloading data... [208ms]
\ Connecting the database...
v Connecting the database... [155ms]
\ Downloading data...
v Downloading data... [158ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [9.7s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [185ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [5.2s]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [7.9s]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [121ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data...
v Downloading data... [106ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [27ms]
\ Downloading data for GCST003044 , 14_88009660_C_T ...
v Downloading data for GCST003044 , 14_88009660_C_T ... [1s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [37ms]
\ Downloading data...
v Downloading data... [1.7s]
\ Connecting the database...
v Connecting the database... [32ms]
\ Downloading data...
v Downloading data... [189ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [30ms]
\ Downloading data...
v Downloading data... [161ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [28ms]
\ Downloading data...
v Downloading data... [151ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [107ms]
\ Downloading data...
v Downloading data... [169ms]
[ 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
Flavor: r-devel-linux-x86_64-fedora-gcc