Last updated on 2025-09-12 01:53:37 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| fastml | 13 | ||
| genSEIR | 13 | ||
| MVN | 13 | ||
| PubChemR | 1 | 3 | 9 |
| rPDBapi | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 3, OK: 9
Version: 2.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/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/RtmpXS3j1w/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpXS3j1w/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpXS3j1w/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpXS3j1w/aspirin.json'
Error in file(con, "r") : cannot open the connection
Request failed [400]. Retrying in 2.4 seconds...
Request failed [400]. Retrying in 7.6 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250908_190721.sdf'
Saved at: /home/hornik/tmp/scratch/RtmpXS3j1w
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/RtmpXS3j1w
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/RtmpXS3j1w
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 1 | SKIP 0 | PASS 169 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── 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
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 169 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.5
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 4.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 2.1.1
Check: examples
Result: ERROR
Running examples in 'rPDBapi-Ex.R' failed
The error most likely occurred in:
> ### Name: get_fasta_from_rcsb_entry
> ### Title: Retrieve FASTA Sequence from PDB Entry or Specific Chain
> ### Aliases: get_fasta_from_rcsb_entry
>
> ### ** Examples
>
> # Example 1: Retrieve all FASTA sequences for the entry 4HHB
> all_sequences <- get_fasta_from_rcsb_entry("4HHB", verbosity = TRUE)
Querying RCSB for the '4HHB' FASTA file.
Error in value[[3L]](cond) :
Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10008 milliseconds
Calls: get_fasta_from_rcsb_entry ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 2.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rPDBapi)
>
> test_check("rPDBapi")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 65 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_get_fasta_from_rcsb_entry.R:5:3'): get_fasta_from_rcsb_entry returns correct FASTA sequences ──
Error in `value[[3L]](cond)`: Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10012 milliseconds
Backtrace:
▆
1. └─rPDBapi::get_fasta_from_rcsb_entry("4HHB") at test_get_fasta_from_rcsb_entry.R:5:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_get_fasta_from_rcsb_entry.R:13:3'): get_fasta_from_rcsb_entry returns correct chain sequence ──
Error in `value[[3L]](cond)`: Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10014 milliseconds
Backtrace:
▆
1. └─rPDBapi::get_fasta_from_rcsb_entry("4HHB", chain_id = "A") at test_get_fasta_from_rcsb_entry.R:13:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_get_pdb_file.R:3:3'): get_pdb_file downloads and parses the PDB file correctly ──
Error in `value[[3L]](cond)`: API Error: Failed to retrieve data for PDB ID '4HHB'. Error: HTTP Error: Request to https://files.rcsb.org/download/4HHB.pdb.gz failed with status: - Server error: (503) Service Unavailable
Backtrace:
▆
1. └─rPDBapi::get_pdb_file("4HHB", filetype = "pdb", save = FALSE) at test_get_pdb_file.R:3:3
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 3 | WARN 0 | SKIP 0 | PASS 65 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64