search

ropensci / onekp

Access sequences from the 1000 Plant Initiative (1KP)
https://docs.ropensci.org/onekp
Other
12 stars 4 forks source link

test failures #8

Open maelle opened 1 year ago

maelle commented 1 year ago 
�*!�*�\�EܑN$�JÀcurl -Lb onekp_test/nuc/cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' onekp_test/nuc/cookie`&id=17-T5vBegJopiqiR9Wr0pQSYXEFQwg0rn" -o onekp_test/nuc/LJQF.fna.tar.bz2  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:28 --:--:--     0
100 1811k  100 1811k    0     0  64418      0  0:00:28  0:00:28 --:--:-- 3398k
✖ | 1 20     5 | download [741.5s]            
──────────────────────────────────────────────
Error (test-download.R:11): Can download protein sequence
Error in `curl::curl_download(db_url, db_path_file, quiet = TRUE)`: Failed to connect to ftp.ncbi.nih.gov port 21: Connection refused
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:11:2
  7. onekp::filter_by_clade(onekp, "Brassicaceae")
  8. taxizedb::name2taxid(clade)
       at onekp/R/filter.R:39:4
  9. taxizedb:::ap_vector_dispatch(...)
 10. taxizedb:::run_with_db(...)
 14. taxizedb::db_download_ncbi(verbose = FALSE)
 15. curl::curl_download(db_url, db_path_file, quiet = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
  1. testthat::expect_equal(...)
       at test-download.R:31:2
  4. onekp::download_nucleotides(...)
       at test-download.R:33:6
  5. onekp:::.download(...)
       at onekp/R/download.R:152:2
  6. base::apply(...)
       at onekp/R/download.R:41:2
  7. onekp (local) FUN(newX[, i], ...)
  8. onekp (local) unwrap(path)
       at onekp/R/download.R:64:6
 10. utils::untar(path, compressed = "bzip2", list = TRUE)

Warning (test-download.R:31): Can download nucleotide sequence
untar(compressed=) is deprecated
Backtrace:
 1. testthat::expect_equal(...)
      at test-download.R:31:2
 4. onekp::download_nucleotides(...)
      at test-download.R:33:6
 5. onekp:::.download(...)
      at onekp/R/download.R:152:2
 6. base::apply(...)
      at onekp/R/download.R:41:2
 7. onekp (local) FUN(newX[, i], ...)
 8. onekp (local) unwrap(path)
      at onekp/R/download.R:64:6
 9. utils::untar(path, compressed = "bzip2", exdir = dir)
      at onekp/R/download.R:114:2
──────────────────────────────────────────────
✔ |         9 | filter [0.4s]                 
✖ | 1       2 | retrieval [8.4s]              
──────────────────────────────────────────────
Failure (test-retrieval.R:8): The cached metadata is the same as the online data
retrieve_onekp() not equal to `onekp`.
Attributes: < Component “table”: Attributes: < Component “class”: Lengths (3, 1) differ (string compare on first 1) > >
Attributes: < Component “table”: Attributes: < Component “class”: 1 string mismatch > >
Attributes: < Component “table”: Component “tax_id”: 'is.NA' value mismatch: 99 in current 95 in target >
──────────────────────────────────────────────

══ Results ═══════════════════════════════════
Duration: 751.3 s

[ FAIL 2 | WARN 20 | SKIP 0 | PASS 16 ]