Last updated on 2025-11-28 02:51:16 CET.
| Package | ERROR | OK |
|---|---|---|
| fastml | 13 | |
| genSEIR | 13 | |
| MVN | 13 | |
| PubChemR | 2 | 11 |
| rPDBapi | 13 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, OK: 11
Version: 2.1.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/167s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PubChemR)
>
> # Functions used globally in package tests (testthat) ----
> allSuccess <- function(object){
+ all(unlist(lapply(object$result, "[[", "success")))
+ }
>
> testRequest <- function(object, ...){
+ test_that(paste0("pulling via '", request_args(object, "namespace"), "' is succesfull"), {
+ expect_true(allSuccess(object))
+ })
+
+ test_that("prints output to the R Console", {
+ expect_output(print(object))
+ })
+ }
>
> # Set 'skipTests' FALSE to run test codes. This is set TRUE to skip
> # all tests on GitHub actions since some of PubChem requests were incomplete due to
> # timeout and/or API related issues. BUILD & CHECK actions on GitHub returns error
> # even if all tests were passed on local installations of R.
> skipTests <- FALSE
>
> if (!skipTests){
+ test_check("PubChemR")
+ }
The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json'
The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json'
The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json'
The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json'
The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.sdf'
Request failed [400]. Retrying in 3.4 seconds...
Request failed [400]. Retrying in 5.3 seconds...
Request failed [504]. Retrying in 2.5 seconds...
Saving _problems/test-get_sids-20.R
Saving _problems/test-get_sids-53.R
PubChem Substance Details (comment)
Same as: <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=7847177">D00109</a>
Is a reactant of enzyme EC: 3.1.1.55
PubChem Substance Details (comment)
Same as: <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=7847177">D00109</a>
Is a reactant of enzyme EC: 3.1.1.55
Saving _problems/test-get_synonyms-6.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 158 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ─────
Expected `allSuccess(object)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ──
Expected `sids$result[[1]]$success` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
Expected `allSuccess(object)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 158 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.1.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PubChemR)
>
> # Functions used globally in package tests (testthat) ----
> allSuccess <- function(object){
+ all(unlist(lapply(object$result, "[[", "success")))
+ }
>
> testRequest <- function(object, ...){
+ test_that(paste0("pulling via '", request_args(object, "namespace"), "' is succesfull"), {
+ expect_true(allSuccess(object))
+ })
+
+ test_that("prints output to the R Console", {
+ expect_output(print(object))
+ })
+ }
>
> # Set 'skipTests' FALSE to run test codes. This is set TRUE to skip
> # all tests on GitHub actions since some of PubChem requests were incomplete due to
> # timeout and/or API related issues. BUILD & CHECK actions on GitHub returns error
> # even if all tests were passed on local installations of R.
> skipTests <- FALSE
>
> if (!skipTests){
+ test_check("PubChemR")
+ }
The file has been saved to '/home/hornik/tmp/scratch/Rtmpyxuqqe/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmpyxuqqe/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmpyxuqqe/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmpyxuqqe/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmpyxuqqe/aspirin.sdf'
Error in value[[3L]](cond) :
Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Saving _problems/test-get_all_sources-9.R
Saving _problems/test-get_all_sources-10.R
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 1 seconds...
PubChem Substance Details (comment)
Same as: <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=7847177">D00109</a>
Is a reactant of enzyme EC: 3.1.1.55
PubChem Substance Details (comment)
Same as: <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=7847177">D00109</a>
Is a reactant of enzyme EC: 3.1.1.55
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 159 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_all_sources.R:9:3'): get all sources for 'substance' ─────
Expected `inherits(tmp, "try-error")` to be FALSE.
Differences:
`actual`: TRUE
`expected`: FALSE
── Failure ('test-get_all_sources.R:10:3'): get all sources for 'substance' ────
Expected `all(...)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 159 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Current CRAN status: OK: 13