Last updated on 2024-09-28 03:50:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 8.18 | 178.51 | 186.69 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 5.68 | 113.61 | 119.29 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 318.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 304.25 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 9.00 | 285.00 | 294.00 | ERROR | |
| r-patched-linux-x86_64 | 2.0.1 | 7.73 | 85.99 | 93.72 | ERROR | |
| r-release-linux-x86_64 | 2.0.1 | 7.40 | 166.36 | 173.76 | OK | |
| r-release-macos-arm64 | 2.0.1 | 261.00 | OK | |||
| r-release-macos-x86_64 | 2.1 | 218.00 | OK | |||
| r-release-windows-x86_64 | 2.1 | 14.00 | 269.00 | 283.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 414.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.1 | 221.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.0.1 | 12.00 | 433.00 | 445.00 | ERROR |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' using rmarkdown
--- finished re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd'
--- re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd' using rmarkdown
--- finished re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd'
--- re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' using rmarkdown
Quitting from lines 251-258 [get_aids_by_formula] (Working_with_PubChemR_to_Access_Chemical_Data.Rmd)
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
<text>:1:9: unexpected symbol
1: Request timed
^
--- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
SUMMARY: processing the following file failed:
'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Enhancing_Chemical_Data_Access_with_PubChemR.Rmd’ using rmarkdown
--- finished re-building ‘Enhancing_Chemical_Data_Access_with_PubChemR.Rmd’
--- re-building ‘Exploring_Chemical_Data_with_PubChemR.Rmd’ using rmarkdown
--- finished re-building ‘Exploring_Chemical_Data_with_PubChemR.Rmd’
--- re-building ‘Working_with_PubChemR_to_Access_Chemical_Data.Rmd’ using rmarkdown
Quitting from lines 251-258 [get_aids_by_formula] (Working_with_PubChemR_to_Access_Chemical_Data.Rmd)
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
<text>:1:10: unexpected symbol
1: MFSearch failed
^
--- failed re-building ‘Working_with_PubChemR_to_Access_Chemical_Data.Rmd’
SUMMARY: processing the following file failed:
‘Working_with_PubChemR_to_Access_Chemical_Data.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.0.1
Check: examples
Result: ERROR
Running examples in 'PubChemR-Ex.R' failed
The error most likely occurred in:
> ### Name: AIDs-SIDs-CIDs
> ### Title: Assay, Compound, and Substance Identifiers
> ### Aliases: AIDs-SIDs-CIDs AIDs CIDs SIDs AIDs.PubChemInstance_AIDs
> ### CIDs.PubChemInstance_CIDs SIDs.PubChemInstance_SIDs
>
> ### ** Examples
>
> # Retrieve Assay IDs
> aids <- get_aids(identifier = c("aspirin", "caffeine"), namespace = "name")
Error in parse(text = command_string) : <text>:1:9: unexpected symbol
1: Timeout was
^
Calls: get_aids -> lapply -> FUN -> get_json -> eval -> parse
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 2.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [88s]
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 'D:\temp\RtmpwTLbYM/aspirin.json'
The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.json'
The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.json'
The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.json'
The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.sdf'
Error in parse(text = command_string) : <text>:1:9: unexpected symbol
1: Timeout was
^
Error in UseMethod("retrieve") :
no applicable method for 'retrieve' applied to an object of class "character"
trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF'
downloaded 3641 bytes
trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF'
downloaded 3641 bytes
trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF'
downloaded 3641 bytes
SDF file to save --> 'aspirin_2024-09-27_08_45_41.100472.sdf'
Saved into folder --> D:\temp\RtmpwTLbYM
Completed options
trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF'
downloaded 3641 bytes
SDF file to save --> 'file.sdf'
Saved into folder --> D:\temp\RtmpwTLbYM
Completed options
'path' is not specified. Saving files into a temporary folder.
trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF'
downloaded 3641 bytes
SDF file to save --> 'file.sdf'
Saved into folder --> D:\temp\RtmpwTLbYM
Completed options
Error in parse(text = command_string) : <text>:1:9: unexpected symbol
1: Timeout was
^
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 5 | WARN 1 | SKIP 0 | PASS 176 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get_cids.R:19:3'): (code run outside of `test_that()`) ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `object[["request_args"]]`: subscript out of bounds
Backtrace:
▆
1. └─PubChemR (local) test1(cids) at test-get_cids.R:33:1
2. ├─testthat::test_that(...) at test-get_cids.R:19:3
3. │ └─testthat:::check_string(desc)
4. │ └─testthat:::.rlang_check_is_string(...)
5. │ └─rlang::is_string(x)
6. ├─base::paste0(...)
7. └─PubChemR::request_args(object, "namespace")
── Failure ('test-get_compounds.R:44:3'): instance() returns an object of class 'PubChemInstance' ──
"PubChemInstance" %in% class(instance(compounds)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_compounds.R:45:3'): instance() returns an object of class 'PubChemInstance' ──
`print\(instance\(compounds\)\)` does not match "An object of class 'PubChemInstance'".
Actual value: "NULL"
Backtrace:
▆
1. └─testthat::expect_output(print(instance(compounds)), "An object of class 'PubChemInstance'") at test-get_compounds.R:45:3
2. └─testthat::expect_match(...)
3. └─testthat:::expect_match_(...)
── Error ('test-get_compounds.R:50:3'): retrieve() returns selected slots as expected for a compound ──
Error in `UseMethod("retrieve")`: no applicable method for 'retrieve' applied to an object of class "character"
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-get_compounds.R:50:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─PubChemR::retrieve(...)
5. └─PubChemR:::retrieve.PubChemInstanceList(...)
6. ├─base::do.call("retrieve", args)
7. └─PubChemR::retrieve(.slot = "id", .to.data.frame = TRUE, .combine.all = FALSE)
── Error ('test-get_sids.R:19:3'): (code run outside of `test_that()`) ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `object[["request_args"]]`: subscript out of bounds
Backtrace:
▆
1. └─PubChemR (local) test1(sids) at test-get_sids.R:33:1
2. ├─testthat::test_that(...) at test-get_sids.R:19:3
3. │ └─testthat:::check_string(desc)
4. │ └─testthat:::.rlang_check_is_string(...)
5. │ └─rlang::is_string(x)
6. ├─base::paste0(...)
7. └─PubChemR::request_args(object, "namespace")
[ FAIL 5 | WARN 1 | SKIP 0 | PASS 176 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' using rmarkdown
--- finished re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd'
--- re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd' using rmarkdown
--- finished re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd'
--- re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' using rmarkdown
Quitting from lines 357-364 [get_cids_by_formula] (Working_with_PubChemR_to_Access_Chemical_Data.Rmd)
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
<text>:1:9: unexpected symbol
1: Request timed
^
--- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
SUMMARY: processing the following file failed:
'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64