Running ‘testthat.R’ [11s/20s]
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 1 | WARN 1 | SKIP 15 | PASS 30 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (15)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fetch.R:16:3'): fetchMetadata ────────────────────────────────
  `metadataObs` (`actual`) not equal to `metadataExp` (`expected`).
  
    `attr(actual, 'row.names')`: 1  
  `attr(expected, 'row.names')`: 1 2
  
  actual vs expected
                  run_accession sample_accession secondary_sample_accession sample_alias               sample_title experiment_accession study_accession                                                         fastq_md5                                                                                                                                             fastq_ftp                                                                                                                                              fastq_aspera
    actual[1, ]     SRR10876945     SAMN13836349                 SRS5984286   GSM4261292 RNAseq_Ad_lib_KO_ZT19_rep3           SRX7546518     PRJNA600892 27c572bdafa27eeb283888ddca5d8717;6c9b0c1e58a40a59db10c9f98118e6e4 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 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
  + expected[2, ]   SRR10876946     SAMN13836348                 SRS5984287   GSM4261293 RNAseq_Ad_lib_KO_ZT22_rep1           SRX7546519     PRJNA600892 6d3d27a644f3de4defce764b3542f1a9;a946383a900065e18ee27b05dd9f3d6e 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 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
  
  `actual$run_accession`:   "SRR10876945"              
  `expected$run_accession`: "SRR10876945" "SRR10876946"
  
  `actual$sample_accession`:   "SAMN13836349"               
  `expected$sample_accession`: "SAMN13836349" "SAMN13836348"
  
  `actual$secondary_sample_accession`:   "SRS5984286"             
  `expected$secondary_sample_accession`: "SRS5984286" "SRS5984287"
  
  `actual$sample_alias`:   "GSM4261292"             
  `expected$sample_alias`: "GSM4261292" "GSM4261293"
  
      actual$sample_title          | expected$sample_title           
  [1] "RNAseq_Ad_lib_KO_ZT19_rep3" | "RNAseq_Ad_lib_KO_ZT19_rep3" [1]
                                   - "RNAseq_Ad_lib_KO_ZT22_rep1" [2]
  
  `actual$experiment_accession`:   "SRX7546518"             
  `expected$experiment_accession`: "SRX7546518" "SRX7546519"
  
  `actual$study_accession`:   "PRJNA600892"              
  `expected$study_accession`: "PRJNA600892" "PRJNA600892"
  
  actual$fastq_md5 vs expected$fastq_md5
    "27c572bdafa27eeb283888ddca5d8717;6c9b0c1e58a40a59db10c9f98118e6e4"
  + "6d3d27a644f3de4defce764b3542f1a9;a946383a900065e18ee27b05dd9f3d6e"
  
  actual$fastq_ftp vs expected$fastq_ftp
    "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$fastq_aspera vs expected$fastq_aspera
    "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"
  
  [ FAIL 1 | WARN 1 | SKIP 15 | PASS 30 ]
  Error: Test failures
  Execution halted