Running 'testthat.R' [10m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ptm)
  > 
  > test_check("ptm")
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
     PDB has ALT records, taking A only, rm.alt=TRUE
    Note: Accessing on-line PDB file
    Note: Accessing on-line PDB file
  [ FAIL 21 | WARN 3 | SKIP 54 | PASS 169 ]
  
  ══ Skipped tests (54) ══════════════════════════════════════════════════════════
  • On CRAN (54): 'test_aa.R:9:3', 'test_aa.R:24:3', 'test_aa.R:53:3',
    'test_aa.R:89:3', 'test_aa.R:116:3', 'test_aa.R:147:3', 'test_aa.R:169:3',
    'test_abundance.R:9:3', 'test_accdpx.R:10:3', 'test_accdpx.R:60:3',
    'test_accdpx.R:138:3', 'test_accdpx.R:180:3', 'test_accdpx.R:211:3',
    'test_accdpx.R:242:3', 'test_accdpx.R:281:3', 'test_ddG.R:9:3',
    'test_ddG.R:57:3', 'test_ddG.R:91:3', 'test_ddG.R:110:3', 'test_ddG.R:131:3',
    'test_ddG.R:154:3', 'test_environment.R:9:3', 'test_environment.R:88:3',
    'test_evolutionary.R:9:3', 'test_getseq.R:9:3', 'test_getseq.R:32:3',
    'test_getseq.R:52:3', 'test_getseq.R:92:3', 'test_getseq.R:134:3',
    'test_getseq.R:150:3', 'test_getseq.R:186:3', 'test_getseq.R:209:3',
    'test_getseq.R:230:3', 'test_getseq.R:251:3', 'test_getseq.R:306:3',
    'test_getseq.R:347:3', 'test_getseq.R:369:3', 'test_getseq.R:390:3',
    'test_getseq.R:405:3', 'test_getseq.R:420:3', 'test_getseq.R:443:3',
    'test_getseq.R:467:3', 'test_getseq.R:496:3', 'test_getseq.R:521:3',
    'test_go.R:9:3', 'test_go.R:39:3', 'test_go.R:72:3', 'test_go.R:111:3',
    'test_go.R:137:3', 'test_go.R:173:3', 'test_gracefully.R:9:3',
    'test_ptmScan.R:139:3', 'test_ptmScan.R:212:3', 'test_ptmplot.R:10:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_saromatic.R:14:3'): saro.dist() works properly ───────────────
  typeof(a) not equal to "list".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "list"
  ── Failure ('test_saromatic.R:15:3'): saro.dist() works properly ───────────────
  class(a[[1]]) not equal to "data.frame".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "data.frame"
  ── Failure ('test_saromatic.R:16:3'): saro.dist() works properly ───────────────
  nrow(a[[1]]) not equal to 9.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:17:3'): saro.dist() works properly ───────────────
  ncol(a[[1]]) not equal to 10.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:18:3'): saro.dist() works properly ───────────────
  class(a[[2]]) not equal to "data.frame".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "data.frame"
  ── Failure ('test_saromatic.R:19:3'): saro.dist() works properly ───────────────
  nrow(a[[2]]) not equal to 9.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:21:3'): saro.dist() works properly ───────────────
  typeof(b) not equal to "list".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "list"
  ── Failure ('test_saromatic.R:22:3'): saro.dist() works properly ───────────────
  class(b) not equal to "data.frame".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "data.frame"
  ── Failure ('test_saromatic.R:23:3'): saro.dist() works properly ───────────────
  nrow(b) not equal to 3.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:24:3'): saro.dist() works properly ───────────────
  ncol(b) not equal to 10.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:25:3'): saro.dist() works properly ───────────────
  is.na(b$Wd[1]) is not TRUE
  
  `actual`:       
  `expected`: TRUE
  ── Failure ('test_saromatic.R:57:3'): saro.geometry() works properly ───────────
  typeof(c) not equal to "list".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "list"
  ── Failure ('test_saromatic.R:58:3'): saro.geometry() works properly ───────────
  class(c) not equal to "data.frame".
  1/1 mismatches
  x[1]: "NULL"
  y[1]: "data.frame"
  ── Failure ('test_saromatic.R:59:3'): saro.geometry() works properly ───────────
  nrow(c) not equal to 2.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:60:3'): saro.geometry() works properly ───────────
  ncol(c) not equal to 8.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:61:3'): saro.geometry() works properly ───────────
  c$resid[1] not equal to "MET".
  target is NULL, current is character
  ── Failure ('test_saromatic.R:62:3'): saro.geometry() works properly ───────────
  c$resid[2] not equal to "TYR".
  target is NULL, current is character
  ── Error ('test_saromatic.R:63:3'): saro.geometry() works properly ─────────────
  Error in `expect_compare("<", act, exp)`: Result of comparison must be a single logical value
  Backtrace:
      ▆
   1. └─testthat::expect_lt(c$length[2], 7) at test_saromatic.R:63:3
   2.   └─testthat:::expect_compare("<", act, exp)
   3.     └─rlang::abort("Result of comparison must be a single logical value")
  ── Failure ('test_saromatic.R:87:3'): saro.motif() works properly ──────────────
  `c` inherits from `'NULL'` not `'character'`.
  ── Failure ('test_saromatic.R:88:3'): saro.motif() works properly ──────────────
  nrow(c) not equal to 0.
  target is NULL, current is numeric
  ── Failure ('test_saromatic.R:89:3'): saro.motif() works properly ──────────────
  ncol(c) not equal to 4.
  target is NULL, current is numeric
  
  [ FAIL 21 | WARN 3 | SKIP 54 | PASS 169 ]
  Error: Test failures
  Execution halted