R Under development (unstable) (2024-05-06 r86526 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(ptm)
> 
> test_check("ptm")
  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
  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 0 | WARN 3 | SKIP 54 | PASS 187 ]

══ 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'

[ FAIL 0 | WARN 3 | SKIP 54 | PASS 187 ]
> 
> proc.time()
   user  system elapsed 
  19.06    0.71   35.93