Running ‘testthat.R’ [17s/163s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(seeker)
  > 
  > test_check('seeker')
  qs 0.25.5
  reading in files with read_tsv
  1 2 
  transcripts missing from tx2gene: 116471
  summarizing abundance
  summarizing counts
  summarizing length
  [ FAIL 2 | WARN 1 | SKIP 15 | PASS 29 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (15)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fetch.R:13:3'): fetchMetadata ────────────────────────────────
  `metadataObs` (`actual`) not equal to `metadataExp` (`expected`).
  
  `actual` is length 1
  `expected` is length 10
  
      names(actual)     | names(expected)                  
  [1] "<!doctype html>" - "run_accession"              [1] 
                        - "sample_accession"           [2] 
                        - "secondary_sample_accession" [3] 
                        - "sample_alias"               [4] 
                        - "sample_title"               [5] 
                        - "experiment_accession"       [6] 
                        - "study_accession"            [7] 
                        - "fastq_md5"                  [8] 
                        - "fastq_ftp"                  [9] 
                        - "fastq_aspera"               [10]
  
    `attr(actual, 'row.names')`:    
  `attr(expected, 'row.names')`: 1 2
  
  `actual$<!doctype html>` is a character vector ()
  `expected$<!doctype html>` is absent
  
  `actual$run_accession` is absent
  `expected$run_accession` is a character vector ('SRR10876945', 'SRR10876946')
  
  `actual$sample_accession` is absent
  `expected$sample_accession` is a character vector ('SAMN13836349', 'SAMN13836348')
  
  `actual$secondary_sample_accession` is absent
  `expected$secondary_sample_accession` is a character vector ('SRS5984286', 'SRS5984287')
  
  `actual$sample_alias` is absent
  `expected$sample_alias` is a character vector ('GSM4261292', 'GSM4261293')
  
  `actual$sample_title` is absent
  `expected$sample_title` is a character vector ('RNAseq_Ad_lib_KO_ZT19_rep3', 'RNAseq_Ad_lib_KO_ZT22_rep1')
  
  `actual$experiment_accession` is absent
  `expected$experiment_accession` is a character vector ('SRX7546518', 'SRX7546519')
  
  `actual$study_accession` is absent
  `expected$study_accession` is a character vector ('PRJNA600892', 'PRJNA600892')
  
  `actual$fastq_md5` is absent
  `expected$fastq_md5` is a character vector ('27c572bdafa27eeb283888ddca5d8717;6c9b0c1e58a40a59db10c9f98118e6e4', '6d3d27a644f3de4defce764b3542f1a9;a946383a900065e18ee27b05dd9f3d6e')
  
  `actual$fastq_ftp` is absent
  `expected$fastq_ftp` is a character vector ('ftp.sra.ebi.ac.uk/vol1/fastq/SRR108/045/SRR10876945/SRR10876945_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR108/045/SRR10876945/SRR10876945_2.fastq.gz', 'ftp.sra.ebi.ac.uk/vol1/fastq/SRR108/046/SRR10876946/SRR10876946_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR108/046/SRR10876946/SRR10876946_2.fastq.gz')
  
  `actual$fastq_aspera` is absent
  `expected$fastq_aspera` is a character vector ('fasp.sra.ebi.ac.uk:/vol1/fastq/SRR108/045/SRR10876945/SRR10876945_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR108/045/SRR10876945/SRR10876945_2.fastq.gz', 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR108/046/SRR10876946/SRR10876946_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR108/046/SRR10876946/SRR10876946_2.fastq.gz')
  ── Failure ('test-fetch.R:26:3'): fetchMetadata ────────────────────────────────
  `metadataObs2` (`actual`) not equal to `metadataExp2` (`expected`).
  
  `actual` is length 1
  `expected` is length 10
  
      names(actual)     | names(expected)                  
  [1] "<!doctype html>" - "run_accession"              [1] 
                        - "sample_accession"           [2] 
                        - "secondary_sample_accession" [3] 
                        - "sample_alias"               [4] 
                        - "sample_title"               [5] 
                        - "experiment_accession"       [6] 
                        - "study_accession"            [7] 
                        - "fastq_md5"                  [8] 
                        - "fastq_ftp"                  [9] 
                        - "fastq_aspera"               [10]
  
    `attr(actual, 'row.names')`:    
  `attr(expected, 'row.names')`: 1 2
  
  `actual$<!doctype html>` is a character vector ()
  `expected$<!doctype html>` is absent
  
  `actual$run_accession` is absent
  `expected$run_accession` is a character vector ('SRR12782103', 'SRR12782104')
  
  `actual$sample_accession` is absent
  `expected$sample_accession` is a character vector ('SAMN16382905', 'SAMN16382904')
  
  `actual$secondary_sample_accession` is absent
  `expected$secondary_sample_accession` is a character vector ('SRS7484120', 'SRS7484121')
  
  `actual$sample_alias` is absent
  `expected$sample_alias` is a character vector ('GSM4820121', 'GSM4820122')
  
  `actual$sample_title` is absent
  `expected$sample_title` is a character vector ('252_albcre_DF_20A', '252_albcre_DF_20B')
  
  `actual$experiment_accession` is absent
  `expected$experiment_accession` is a character vector ('SRX9251666', 'SRX9251667')
  
  `actual$study_accession` is absent
  `expected$study_accession` is a character vector ('PRJNA667743', 'PRJNA667743')
  
  `actual$fastq_md5` is absent
  `expected$fastq_md5` is a character vector ('33383cbef5b2980f4eb19e0519952d07', '33f0ad9e6eba3cd14339f1c7234bb881')
  
  `actual$fastq_ftp` is absent
  `expected$fastq_ftp` is a character vector ('ftp.sra.ebi.ac.uk/vol1/fastq/SRR127/003/SRR12782103/SRR12782103.fastq.gz', 'ftp.sra.ebi.ac.uk/vol1/fastq/SRR127/004/SRR12782104/SRR12782104.fastq.gz')
  
  `actual$fastq_aspera` is absent
  `expected$fastq_aspera` is a character vector ('fasp.sra.ebi.ac.uk:/vol1/fastq/SRR127/003/SRR12782103/SRR12782103.fastq.gz', 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR127/004/SRR12782104/SRR12782104.fastq.gz')
  
  [ FAIL 2 | WARN 1 | SKIP 15 | PASS 29 ]
  Error: Test failures
  Execution halted