Last updated on 2024-06-03 09:56:46 CEST.
Package | ERROR | OK |
---|---|---|
otargen | 2 | 11 |
Current CRAN status: ERROR: 2, OK: 11
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/68s]
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... [85ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [1s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [580ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [243ms]
\ Downloading data for ENSG00000143001 ...
v Downloading data for ENSG00000143001 ... [339ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [311ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [489ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [300ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [344ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [106ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [281ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [17ms]
\ Downloading data...
v Downloading data... [117ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [135ms]
\ Downloading data...
v Downloading data... [162ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [137ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [19ms]
\ Downloading data for 1_154453788_C_T ...
v Downloading data for 1_154453788_C_T ... [358ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [108ms]
\ Downloading data for rs55808324 ...
v Downloading data for rs55808324 ... [401ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading data...
v Downloading data... [129ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ Downloading data...
x Downloading data... [154ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data...
v Downloading data... [146ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading the data...
v Downloading the data... [108ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ Downloading the data...
v Downloading the data... [118ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data...
v Downloading data... [129ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading data...
v Downloading data... [1.3s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading data...
v Downloading data... [310ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
\ Downloading data...
v Downloading data... [226ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [33ms]
\ Downloading data for variant 1_55063514_G_A ...
v Downloading data for variant 1_55063514_G_A ... [130ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [97ms]
\ Downloading data for variant rs72698179 ...
v Downloading data for variant rs72698179 ... [132ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [258ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [24ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [261ms]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [361ms]
\ Downloading data for ENSG00000138821 ...
v Downloading data for ENSG00000138821 ... [267ms]
\ Downloading data for ENSG00000125255 ...
v Downloading data for ENSG00000125255 ... [253ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [108ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [561ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [272ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [250ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [304ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [569ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [4.6s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [4.9s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [27ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [5s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [4.7s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data...
v Downloading data... [801ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading data for variant 14_87978408_G_A ...
v Downloading data for variant 14_87978408_G_A ... [136ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [119ms]
\ Downloading data for variant rs55808324 ...
v Downloading data for variant rs55808324 ... [208ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading data...
v Downloading data... [323ms]
\ Connecting the database...
v Connecting the database... [20ms]
\ Downloading data...
v Downloading data... [150ms]
\ Connecting the database...
v Connecting the database... [235ms]
\ Downloading data...
v Downloading data... [190ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [15ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [6.1s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [199ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [5s]
\ Downloading data for ENSG00000163946 ...
x Downloading data for ENSG00000163946 ... [10.2s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [20ms]
\ Downloading data...
v Downloading data... [166ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [32ms]
\ Downloading data for GCST003044 , 14_88009660_C_T ...
v Downloading data for GCST003044 , 14_88009660_C_T ... [1.3s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [16ms]
\ Downloading data...
v Downloading data... [546ms]
\ Connecting the database...
v Connecting the database... [33ms]
\ Downloading data...
v Downloading data... [227ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [33ms]
\ Downloading data...
v Downloading data... [200ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [33ms]
\ Downloading data...
v Downloading data... [179ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [132ms]
\ Downloading data...
v Downloading data... [173ms]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-studiesAndLeadVariantsForGeneByL2G.R:3:3'): test studiesAndLeadVariantsForGeneByL2G works ──
Error: Bad Gateway (HTTP 502)
Backtrace:
▆
1. └─otargen::studiesAndLeadVariantsForGeneByL2G(...) at test-studiesAndLeadVariantsForGeneByL2G.R:3:3
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 1 | WARN 0 | SKIP 0 | PASS 78 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [49s]
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... [41ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [682ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [300ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [182ms]
\ Downloading data for ENSG00000143001 ...
v Downloading data for ENSG00000143001 ... [154ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [163ms]
\ Downloading data for ENSG00000141510 ...
| Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [549ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [257ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [161ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [56ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [170ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [7ms]
\ Downloading data...
v Downloading data... [56ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [54ms]
\ Downloading data...
v Downloading data... [76ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [57ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [11ms]
\ Downloading data for 1_154453788_C_T ...
v Downloading data for 1_154453788_C_T ... [210ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [62ms]
\ Downloading data for rs55808324 ...
v Downloading data for rs55808324 ... [134ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
\ Downloading data...
v Downloading data... [65ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
\ Downloading data...
x Downloading data... [58ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
\ Downloading data...
v Downloading data... [89ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading the data...
v Downloading the data... [52ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
\ Downloading the data...
v Downloading the data... [56ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
\ Downloading data...
v Downloading data... [76ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data...
v Downloading data... [577ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data...
v Downloading data... [190ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data...
v Downloading data... [139ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
\ Downloading data for variant 1_55063514_G_A ...
v Downloading data for variant 1_55063514_G_A ... [77ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [56ms]
\ Downloading data for variant rs72698179 ...
v Downloading data for variant rs72698179 ... [76ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [179ms]
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 ... [164ms]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [316ms]
\ Downloading data for ENSG00000138821 ...
v Downloading data for ENSG00000138821 ... [173ms]
\ Downloading data for ENSG00000125255 ...
v Downloading data for ENSG00000125255 ... [123ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [64ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [457ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [161ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [163ms]
\ Downloading data for ENSG00000163946 ...
| Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [240ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [463ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [4.7s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [4.7s]
\ 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 ... [6s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [6.3s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
\ Downloading data...
v Downloading data... [822ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data for variant 14_87978408_G_A ...
v Downloading data for variant 14_87978408_G_A ... [101ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [67ms]
\ Downloading data for variant rs55808324 ...
v Downloading data for variant rs55808324 ... [83ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data...
v Downloading data... [129ms]
\ Connecting the database...
v Connecting the database... [9ms]
\ Downloading data...
v Downloading data... [90ms]
\ Connecting the database...
v Connecting the database... [111ms]
\ Downloading data...
v Downloading data... [94ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ 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... [11ms]
\ Downloading data...
v Downloading data... [56ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [8ms]
\ Downloading data for GCST003044 , 14_88009660_C_T ...
v Downloading data for GCST003044 , 14_88009660_C_T ... [1.6s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data...
v Downloading data... [585ms]
\ Connecting the database...
v Connecting the database... [11ms]
\ Downloading data...
v Downloading data... [184ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data...
v Downloading data... [116ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [13ms]
\ Downloading data...
v Downloading data... [102ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [77ms]
\ Downloading data...
v Downloading data... [87ms]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── 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 1 | WARN 0 | SKIP 0 | PASS 78 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64