Last updated on 2025-04-26 07:52:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.4 | 8.81 | 178.59 | 187.40 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.4 | 5.92 | 68.36 | 74.28 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.4 | 295.12 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.4 | 294.17 | OK | |||
| r-devel-windows-x86_64 | 2.1.4 | 10.00 | 373.00 | 383.00 | ERROR | |
| r-patched-linux-x86_64 | 2.1.4 | 9.44 | 171.27 | 180.71 | OK | |
| r-release-linux-x86_64 | 2.1.4 | 8.01 | 169.53 | 177.54 | OK | |
| r-release-macos-arm64 | 2.1.4 | 326.00 | OK | |||
| r-release-macos-x86_64 | 2.1.4 | 283.00 | OK | |||
| r-release-windows-x86_64 | 2.1.4 | 11.00 | 1089.00 | 1100.00 | ERROR | |
| r-oldrel-macos-arm64 | 2.1.4 | 221.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.1.4 | 312.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.4 | 13.00 | 1064.00 | 1077.00 | ERROR |
Version: 2.1.4
Check: examples
Result: ERROR
Running examples in ‘PubChemR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download
> ### Title: Download Content from PubChem and Save to a File
> ### Aliases: download
>
> ### ** Examples
>
> # Download JSON file for the compound "aspirin" into "Aspirin.JSON"
> # A folder named "Compound" will be created under current directory"
> download(
+ filename = "Aspirin",
+ outformat = "json",
+ path = "./Compound",
+ identifier = "aspirin",
+ namespace = "name",
+ domain = "compound",
+ overwrite = TRUE
+ )
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Calls: download -> get_pubchem
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AIDs-SIDs-CIDs 0.304 0.009 114.416
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/171s]
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")
+ }
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in file(con, "r") : cannot open the connection
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")
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")
Request failed [504]. Retrying in 1.5 seconds...
Request failed [503]. Retrying in 6.7 seconds...
Request failed [400]. Retrying in 2.8 seconds...
Request failed [400]. Retrying in 1.7 seconds...
Request failed [504]. Retrying in 1.8 seconds...
Request failed [504]. Retrying in 1 seconds...
Request failed [503]. Retrying in 1.8 seconds...
Request failed [503]. Retrying in 2.7 seconds...
Request failed [503]. Retrying in 1 seconds...
Request failed [503]. Retrying in 6.6 seconds...
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
'path' is not specified. Saving files into a temporary folder.
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
[ FAIL 36 | WARN 43 | SKIP 0 | PASS 134 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-download.R:51:5'): overwrite file if it already exists. ──────
identical(ctime, mtime) is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-download.R:119:3'): create 'path' if it does not exist. ──────
all(file.exists(json_file), file.exists(sdf_file)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_all_sources.R:9:3'): get all sources for 'substance' ─────
inherits(tmp, "try-error") is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-get_all_sources.R:10:3'): get all sources for 'substance' ────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_all_sources.R:20:3'): get all sources for 'assay' ────────
inherits(tmp, "try-error") is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-get_all_sources.R:21:3'): get all sources for 'assay' ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:5:1'): pulling via 'aid' is succesfull ──────────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ──
`retrieve(assay, .slot = "comment", .verbose = TRUE)` produced no output
── Failure ('test-get_assays.R:62:3'): checking the effect of '.verbose' argument in retrieve() function ──
retrieve(assay, .slot = "comment", .verbose = TRUE, .combine.all = TRUE) returns visibly, not invisibly.
── Failure ('test-get_cids.R:20:5'): pulling cids via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:20:5'): pulling cids via 'smiles' is succesfull ───
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ──
cids$result[[1]]$success is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:12:1'): pulling via 'cid' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ──
all(propNamesRequested %in% propNamesReturned) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ──
(all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ───────────
is.array(pubChemData(tmp)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ────────
all(tmp$success, is.array(tmp$result)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:51:3'): test for PNG output successful ────────
all(tmp2$success, is.array(tmp$result)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ────────
{
...
} is not TRUE
`actual`:
`expected`: TRUE
── Error ('test-get_sdf.R:14:3'): pulling SDFs via 'name' is succesful ─────────
Error in `file.exists(tmp)`: invalid 'file' argument
Backtrace:
▆
1. ├─testthat::expect_true(file.exists(tmp)) at test-get_sdf.R:14:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::file.exists(tmp)
── Failure ('test-get_sdf.R:30:3'): pulling SDFs via 'cid' is succesful ────────
file.exists(file.path(temp_dir, "file.sdf")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sdf.R:60:3'): save SDF files to temporary working directory when path is not specified. ──
file.exists(file.path(default_path, "file.sdf")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'cid' is succesfull ──────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'smiles' is succesfull ───
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ──
sids$result[[1]]$success is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ──
all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:35:3'): '.verbose' works as expected ────────
retrieve(...) returns visibly, not invisibly.
── Failure ('test-get_substances.R:38:3'): '.verbose' works as expected ────────
retrieve(...) returns visibly, not invisibly.
── Failure ('test-get_substances.R:50:3'): return error for unavailable substance idx. ──
`retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 66666)` did not throw the expected error.
── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:10:3'): synonyms returns list or data.frame correctly ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:41:3'): pulling synonyms via 'name' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:50:3'): pulling synonyms via 'cid' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 36 | WARN 43 | SKIP 0 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.4
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 Working_with_PubChemR_to_Access_Chemical_Data.Rmd:955-961 [get_all_sources_substance]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
---
Backtrace:
▆
1. └─PubChemR::get_all_sources(domain = "substance")
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
--- 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-linux-x86_64-debian-gcc
Version: 2.1.4
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘Compound’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.4
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 Working_with_PubChemR_to_Access_Chemical_Data.Rmd:1038-1048 [download_jsson]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Could not connect to server [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 9929 ms: Could not connect to server
---
Backtrace:
▆
1. ├─PubChemR::download(...)
2. │ └─PubChemR:::get_pubchem(...)
3. │ └─httr::GET(...)
4. │ └─httr:::request_perform(req, hu$handle$handle)
5. │ ├─httr:::request_fetch(req$output, req$url, handle)
6. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. │ └─curl::curl_fetch_memory(url, handle = handle)
8. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
Could not connect to server [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 9929 ms: Could not connect to server
--- 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: 2.1.4
Check: examples
Result: ERROR
Running examples in 'PubChemR-Ex.R' failed
The error most likely occurred in:
> ### Name: download
> ### Title: Download Content from PubChem and Save to a File
> ### Aliases: download
>
> ### ** Examples
>
> # Download JSON file for the compound "aspirin" into "Aspirin.JSON"
> # A folder named "Compound" will be created under current directory"
> download(
+ filename = "Aspirin",
+ outformat = "json",
+ path = "./Compound",
+ identifier = "aspirin",
+ namespace = "name",
+ domain = "compound",
+ overwrite = TRUE
+ )
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Calls: download -> get_pubchem
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 2.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [479s]
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")
+ }
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.Timeout", Message = "Request timed out")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in file(con, "r") : cannot open the connection
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")
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")
Request failed [503]. Retrying in 3.1 seconds...
Request failed [503]. Retrying in 4.2 seconds...
Request failed [503]. Retrying in 1.3 seconds...
Request failed [400]. Retrying in 4.7 seconds...
Request failed [504]. Retrying in 1 seconds...
Request failed [504]. Retrying in 5.1 seconds...
Request failed [504]. Retrying in 2 seconds...
Request failed [504]. Retrying in 5.2 seconds...
Request failed [503]. Retrying in 2.9 seconds...
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
'path' is not specified. Saving files into a temporary folder.
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
[ FAIL 35 | WARN 34 | SKIP 0 | PASS 135 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-download.R:51:5'): overwrite file if it already exists. ──────
identical(ctime, mtime) is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-download.R:119:3'): create 'path' if it does not exist. ──────
all(file.exists(json_file), file.exists(sdf_file)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_all_sources.R:9:3'): get all sources for 'substance' ─────
inherits(tmp, "try-error") is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-get_all_sources.R:10:3'): get all sources for 'substance' ────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_all_sources.R:20:3'): get all sources for 'assay' ────────
inherits(tmp, "try-error") is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-get_all_sources.R:21:3'): get all sources for 'assay' ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:5:1'): pulling via 'aid' is succesfull ──────────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:20:5'): pulling cids via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:20:5'): pulling cids via 'smiles' is succesfull ───
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ──
cids$result[[1]]$success is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:12:1'): pulling via 'cid' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ──
all(propNamesRequested %in% propNamesReturned) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ──
(all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ───────────
is.array(pubChemData(tmp)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:28:3'): tests for SDF output successful ───────
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:32:3'): tests for SDF output successful ───────
all(is.list(pubChemData(tmp)), length(pubChemData(tmp)) == 0) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ────────
all(tmp$success, is.array(tmp$result)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:51:3'): test for PNG output successful ────────
all(tmp2$success, is.array(tmp$result)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ────────
{
...
} is not TRUE
`actual`:
`expected`: TRUE
── Error ('test-get_sdf.R:14:3'): pulling SDFs via 'name' is succesful ─────────
Error in `file.exists(tmp)`: invalid 'file' argument
Backtrace:
▆
1. ├─testthat::expect_true(file.exists(tmp)) at test-get_sdf.R:14:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::file.exists(tmp)
── Failure ('test-get_sdf.R:30:3'): pulling SDFs via 'cid' is succesful ────────
file.exists(file.path(temp_dir, "file.sdf")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sdf.R:60:3'): save SDF files to temporary working directory when path is not specified. ──
file.exists(file.path(default_path, "file.sdf")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'cid' is succesfull ──────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ──
sids$result[[1]]$success is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ──
all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:35:3'): '.verbose' works as expected ────────
retrieve(...) returns visibly, not invisibly.
── Failure ('test-get_substances.R:38:3'): '.verbose' works as expected ────────
retrieve(...) returns visibly, not invisibly.
── Failure ('test-get_substances.R:50:3'): return error for unavailable substance idx. ──
`retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 66666)` did not throw the expected error.
── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:10:3'): synonyms returns list or data.frame correctly ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:41:3'): pulling synonyms via 'name' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:50:3'): pulling synonyms via 'cid' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 35 | WARN 34 | SKIP 0 | PASS 135 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 2.1.4
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 Working_with_PubChemR_to_Access_Chemical_Data.Rmd:955-961 [get_all_sources_substance]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
---
Backtrace:
▆
1. └─PubChemR::get_all_sources(domain = "substance")
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
--- 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
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 2.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [254s]
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")
+ }
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in get_pubchem(identifier, namespace, domain, operation, outformat, :
c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Error in file(con, "r") : cannot open the connection
Request failed [503]. Retrying in 2.9 seconds...
Request failed [503]. Retrying in 7.5 seconds...
Request failed [503]. Retrying in 1 seconds...
Request failed [503]. Retrying in 6.4 seconds...
Request failed [400]. Retrying in 3.2 seconds...
Request failed [503]. Retrying in 1 seconds...
Request failed [503]. Retrying in 2.7 seconds...
Request failed [504]. Retrying in 7.6 seconds...
Request failed [504]. Retrying in 2.1 seconds...
Request failed [504]. Retrying in 4.5 seconds...
Request failed [503]. Retrying in 1 seconds...
Request failed [503]. Retrying in 1 seconds...
Request failed [503]. Retrying in 1 seconds...
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
'path' is not specified. Saving files into a temporary folder.
Error: Received no content to write to the SDF file. URL may be invalid or the content is missing.
[ FAIL 35 | WARN 47 | SKIP 0 | PASS 135 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-download.R:51:5'): overwrite file if it already exists. ──────
identical(ctime, mtime) is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-download.R:119:3'): create 'path' if it does not exist. ──────
all(file.exists(json_file), file.exists(sdf_file)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:5:1'): pulling via 'aid' is succesfull ──────────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ──
`retrieve(assay, .slot = "comment", .verbose = TRUE)` produced no output
── Failure ('test-get_assays.R:62:3'): checking the effect of '.verbose' argument in retrieve() function ──
retrieve(assay, .slot = "comment", .verbose = TRUE, .combine.all = TRUE) returns visibly, not invisibly.
── Failure ('test-get_cids.R:20:5'): pulling cids via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:20:5'): pulling cids via 'smiles' is succesfull ───
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ──
cids$result[[1]]$success is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:12:1'): pulling via 'cid' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ──
all(propNamesRequested %in% propNamesReturned) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ──
(all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ───────────
is.array(pubChemData(tmp)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:28:3'): tests for SDF output successful ───────
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:32:3'): tests for SDF output successful ───────
all(is.list(pubChemData(tmp)), length(pubChemData(tmp)) == 0) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:35:3'): tests for SDF output successful ───────
file.exists(file.path(tmp2$fileDetails$Path, tmp2$fileDetails$Name)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ────────
all(tmp$success, is.array(tmp$result)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:51:3'): test for PNG output successful ────────
all(tmp2$success, is.array(tmp$result)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ────────
{
...
} is not TRUE
`actual`:
`expected`: TRUE
── Error ('test-get_sdf.R:14:3'): pulling SDFs via 'name' is succesful ─────────
Error in `file.exists(tmp)`: invalid 'file' argument
Backtrace:
▆
1. ├─testthat::expect_true(file.exists(tmp)) at test-get_sdf.R:14:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::file.exists(tmp)
── Failure ('test-get_sdf.R:30:3'): pulling SDFs via 'cid' is succesful ────────
file.exists(file.path(temp_dir, "file.sdf")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sdf.R:60:3'): save SDF files to temporary working directory when path is not specified. ──
file.exists(file.path(default_path, "file.sdf")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'cid' is succesfull ──────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:20:5'): pulling sids via 'smiles' is succesfull ───
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ──
sids$result[[1]]$success is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ──
all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:35:3'): '.verbose' works as expected ────────
retrieve(...) returns visibly, not invisibly.
── Failure ('test-get_substances.R:38:3'): '.verbose' works as expected ────────
retrieve(...) returns visibly, not invisibly.
── Failure ('test-get_substances.R:50:3'): return error for unavailable substance idx. ──
`retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 66666)` did not throw the expected error.
── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:10:3'): synonyms returns list or data.frame correctly ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:41:3'): pulling synonyms via 'name' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:50:3'): pulling synonyms via 'cid' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 35 | WARN 47 | SKIP 0 | PASS 135 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64