Last updated on 2024-12-18 19:49:46 CET.
| Package | ERROR | OK |
|---|---|---|
| fastml | 13 | |
| genSEIR | 13 | |
| MVN | 13 | |
| PubChemR | 4 | 9 |
| rPDBapi | 13 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 4, OK: 9
Version: 2.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/53s]
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/Rtmp94JpzK/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.sdf'
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 5.1 seconds...
SDF file saved successfully:
File Name: 'aspirin_20241216_182515.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp94JpzK
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp94JpzK
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp94JpzK
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 1 | WARN 0 | SKIP 1 | PASS 201 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-00_globals.R:21:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_substances.R:45:3'): NULL returns for unknown/empty slots. ──
retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 132) is not NULL
`actual` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`expected` is NULL
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 201 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/52s]
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/Rtmp95nJAz/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp95nJAz/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp95nJAz/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp95nJAz/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp95nJAz/aspirin.sdf'
Request failed [400]. Retrying in 3.5 seconds...
Request failed [400]. Retrying in 1 seconds...
SDF file saved successfully:
File Name: 'aspirin_20241214_182214.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp95nJAz
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp95nJAz
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp95nJAz
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 1 | WARN 0 | SKIP 1 | PASS 201 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-00_globals.R:21:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_substances.R:45:3'): NULL returns for unknown/empty slots. ──
retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 132) is not NULL
`actual` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`expected` is NULL
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 201 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [57s]
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\2024_12_08_01_50_01_8405\Rtmp4MpHat/aspirin.json'
The file has been saved to 'D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat/aspirin.json'
The file has been saved to 'D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat/aspirin.json'
The file has been saved to 'D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat/aspirin.json'
The file has been saved to 'D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat/aspirin.sdf'
Request failed [400]. Retrying in 1.2 seconds...
Request failed [400]. Retrying in 4.3 seconds...
SDF file saved successfully:
File Name: 'aspirin_20241208_092738.sdf'
Saved at: D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2024_12_08_01_50_01_8405\Rtmp4MpHat
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 1 | WARN 0 | SKIP 0 | PASS 204 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_substances.R:45:3'): NULL returns for unknown/empty slots. ──
retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 132) is not NULL
`actual` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`expected` is NULL
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 204 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 2.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [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 'D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN/aspirin.json'
The file has been saved to 'D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN/aspirin.json'
The file has been saved to 'D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN/aspirin.json'
The file has been saved to 'D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN/aspirin.json'
The file has been saved to 'D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN/aspirin.sdf'
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 2.3 seconds...
SDF file saved successfully:
File Name: 'aspirin_20241216_095837.sdf'
Saved at: D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2024_12_16_01_50_00_4579\Rtmpig4osN
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 1 | WARN 0 | SKIP 1 | PASS 201 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-00_globals.R:21:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_substances.R:45:3'): NULL returns for unknown/empty slots. ──
retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 132) is not NULL
`actual` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`expected` is NULL
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 201 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 13