- 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 the install log 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