Last updated on 2024-06-16 11:58:16 CEST.
| Package | ERROR | OK |
|---|---|---|
| otargen | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/62s]
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... [117ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [1.2s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [39ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [346ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [280ms]
\ Downloading data for ENSG00000143001 ...
v Downloading data for ENSG00000143001 ... [396ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [235ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [613ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [320ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [266ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [89ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [237ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [37ms]
\ Downloading data...
v Downloading data... [133ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [81ms]
\ Downloading data...
v Downloading data... [119ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [114ms]
\ 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 ... [415ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [94ms]
\ Downloading data for rs55808324 ...
v Downloading data for rs55808324 ... [310ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
\ 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... [155ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
\ Downloading data...
v Downloading data... [108ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [23ms]
\ Downloading the data...
v Downloading the data... [104ms]
\ 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... [103ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [31ms]
\ Downloading data...
v Downloading data... [113ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [20ms]
\ Downloading data...
v Downloading data... [1.2s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data...
v Downloading data... [309ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [13ms]
\ Downloading data...
v Downloading data... [196ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [25ms]
\ Downloading data for variant 1_55063514_G_A ...
v Downloading data for variant 1_55063514_G_A ... [136ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [99ms]
\ Downloading data for variant rs72698179 ...
x Downloading data for variant rs72698179 ... [74ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [263ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [193ms]
\ Downloading data for ENSG00000096968 ...
| Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [341ms]
\ Downloading data for ENSG00000138821 ...
v Downloading data for ENSG00000138821 ... [233ms]
\ Downloading data for ENSG00000125255 ...
v Downloading data for ENSG00000125255 ... [228ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [118ms]
\ Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [591ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [247ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [243ms]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [324ms]
\ Downloading data for ENSG00000141510 ...
| Downloading data for ENSG00000141510 ...
v Downloading data for ENSG00000141510 ... [624ms]
Selecting by Trait_reported_trimmed
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [44ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [6.2s]
\ Downloading data for ENSG00000096968 ...
v Downloading data for ENSG00000096968 ... [5.2s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data for ENSG00000167207 ...
v Downloading data for ENSG00000167207 ... [5.2s]
\ 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... [11ms]
\ Downloading data...
v Downloading data... [842ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [21ms]
\ Downloading data for variant 14_87978408_G_A ...
v Downloading data for variant 14_87978408_G_A ... [146ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [106ms]
\ Downloading data for variant rs55808324 ...
v Downloading data for variant rs55808324 ... [140ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
\ Downloading data...
v Downloading data... [133ms]
\ Connecting the database...
v Connecting the database... [11ms]
\ Downloading data...
v Downloading data... [133ms]
\ Connecting the database...
v Connecting the database... [174ms]
\ Downloading data...
v Downloading data... [158ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [5.2s]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [159ms]
\ Downloading data for ENSG00000169174 ...
v Downloading data for ENSG00000169174 ... [5.1s]
\ Downloading data for ENSG00000163946 ...
v Downloading data for ENSG00000163946 ... [5.1s]
\ Connecting to the Open Targets Genetics GrpahQL API...
x Connecting to the Open Targets Genetics GrpahQL API... [100ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
\ Downloading data...
v Downloading data... [109ms]
\ 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 ... [771ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [30ms]
\ Downloading data...
v Downloading data... [362ms]
\ Connecting the database...
v Connecting the database... [36ms]
\ Downloading data...
v Downloading data... [165ms]
\ Connecting to the Open Targets Genetics GrpahQL API...
v Connecting to the Open Targets Genetics GrpahQL API... [27ms]
\ Downloading data...
v Downloading data... [120ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [26ms]
\ Downloading data...
v Downloading data... [131ms]
\ Connecting to the Open Targets Genetics GraphQL API...
v Connecting to the Open Targets Genetics GraphQL API... [86ms]
\ Downloading data...
v Downloading data... [161ms]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pheWAS.R:3:3'): test phewas works ──────────────────────────────
Error: variable `variantId` is null or not found in variables
Backtrace:
▆
1. └─otargen::pheWAS(variant_id = "rs72698179") at test-pheWAS.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 79 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc