Running ‘testthat.R’ [18s/584s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ptm)
  > 
  > test_check("ptm")
  ── Skip (test_aa.R:66:3): the function renum.pdb() works properly ──────────────
  Reason: On CRAN
  
  ── Skip (test_aa.R:90:3): the function renum.meto() works properly ─────────────
  Reason: On CRAN
  
  ── Skip (test_aa.R:109:3): renum() works properly ──────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_accdpx.R:9:3): acc.dssp() works properly ─────────────────────────
  Reason: On CRAN
  
  ── Skip (test_accdpx.R:75:3): get.area() works properly ────────────────────────
  Reason: On CRAN
  
  ── Warning (test_accdpx.R:99:1): (code run outside of `test_that()`) ───────────
  cannot remove file './pdb/1U8F_getarea.Rda', reason 'No such file or directory'
  
  ── Warning (test_accdpx.R:100:1): (code run outside of `test_that()`) ──────────
  cannot remove file './pdb/1U8F_getarea.txt', reason 'No such file or directory'
  
  ── Skip (test_accdpx.R:108:3): dpx() works properly ────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_accdpx.R:132:3): atom.dpx() works properly ───────────────────────
  Reason: On CRAN
  
  ── Skip (test_accdpx.R:154:3): res.dpx() works properly ────────────────────────
  Reason: On CRAN
  
  ── Skip (test_accdpx.R:182:3): stru.part() works properly ──────────────────────
  Reason: On CRAN
  
  ── Skip (test_ddG.R:9:3): imutant() works properly ─────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_ddG.R:54:3): foldx.mut() works properly ──────────────────────────
  Reason: On CRAN
  
  ── Skip (test_ddG.R:81:3): foldx.stab() works properly ─────────────────────────
  Reason: On CRAN
  
  ── Skip (test_ddG.R:96:3): foldx.assembly() works properly ─────────────────────
  Reason: On CRAN
  
  ── Skip (test_ddG.R:113:3): ddG.profile() works properly ───────────────────────
  Reason: On CRAN
  
  ── Skip (test_ddG.R:129:3): ddG.ptm() works properly ───────────────────────────
  Reason: On CRAN
  
  ── Skip (test_distances.R:26:3): res.dist() works properly ─────────────────────
  Reason: On CRAN
  
  ── Skip (test_distances.R:80:3): dist2closest() works properly ─────────────────
  Reason: On CRAN
  
  ── Skip (test_distances.R:101:3): ball() works properly ────────────────────────
  Reason: On CRAN
  
  ── Skip (test_dssp.R:10:3): parse.dssp() works properly ────────────────────────
  Reason: On CRAN
  
  ── Skip (test_dssp.R:29:3): compute.dssp() works properly ──────────────────────
  Reason: On CRAN
  
  ── Skip (test_dssp.R:47:3): mkdssp() works properly ────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_environment.R:9:3): env.extract() works properly ─────────────────
  Reason: On CRAN
  
  ── Skip (test_environment.R:74:3): env.extract() works properly ────────────────
  Reason: On CRAN
  
  ── Skip (test_evolutionary.R:9:3): msa() works properly ────────────────────────
  Reason: On CRAN
  
  ── Skip (test_evolutionary.R:35:3): custom.aln() works properly ────────────────
  Reason: On CRAN
  
  ── Skip (test_evolutionary.R:71:3): list.hom() works properly ──────────────────
  Reason: On CRAN
  
  ── Skip (test_evolutionary.R:111:3): parse.hssp() works properly ───────────────
  Reason: On CRAN
  
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_insertions.Rda', reason 'No such file or directory'
  
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_aln.Rda', reason 'No such file or directory'
  
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_profile.Rda', reason 'No such file or directory'
  
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_seq_list.Rda', reason 'No such file or directory'
  
  ── Skip (test_evolutionary.R:134:3): get.hssp() works properly ─────────────────
  Reason: On CRAN
  
  ── Skip (test_evolutionary.R:159:3): shannon() works properly ──────────────────
  Reason: On CRAN
  
  ── Skip (test_evolutionary.R:192:3): site.type() works properly ────────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:9:3): get.seq() works properly with UniProt ─────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:24:3): get.seq() works properly with MetOSite ───────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:39:3): get.seq() works properly with PDB ────────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:64:3): get.seq() works properly with KEGG ───────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:92:3): prot2codon() works properly ──────────────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:131:3): id.mapping() works properly when pdb -> uniprot ─
  Reason: On CRAN
  
  ── Skip (test_getseq.R:146:3): id.mapping() works properly when up -> pdb ──────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:161:3): id.mapping() works properly when up -> kegg ─────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:172:3): id.mapping() works properly when kegg -> up ─────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:185:3): id.mapping() works properly when pdb -> kegg ────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:202:3): id.mapping() works properly when kegg <- pdb ────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:220:3): id.features() works properly ────────────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:239:3): species.mapping works properly ──────────────────
  Reason: On CRAN
  
  ── Skip (test_getseq.R:256:3): species.kegg works properly ─────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:9:3): search.go() works properly ────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:26:3): term.go() works properly ─────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:52:3): get.go() works properly ──────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:88:3): bg.go() works properly ───────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:111:3):  hdfisher.go() works properly ───────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:130:3): net.go() works properly ─────────────────────────────
  Reason: On CRAN
  
  ── Skip (test_go.R:166:3): gorila() works properly ─────────────────────────────
  Reason: On CRAN
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 3
   $ out.width: chr "50px"
   $ fig.align: chr "left"
   $ echo     : logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-2 (with options) 
  List of 1
   $ echo: logi FALSE
  
  label: unnamed-chunk-3 (with options) 
  List of 1
   $ echo: logi FALSE
  
  label: unnamed-chunk-4 (with options) 
  List of 1
   $ echo: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-5 (with options) 
  List of 1
   $ echo: logi FALSE
  
  ── Skip (test_pdb_ancillary.R:9:3): pdb.quaternary works properly ──────────────
  Reason: On CRAN
  
  ── Skip (test_pdb_ancillary.R:24:3): pdb.quaternary works properly ─────────────
  Reason: On CRAN
  
  ── Warning (test_pdb_ancillary.R:47:1): (code run outside of `test_that()`) ────
  cannot remove file '2hhb.fa', reason 'No such file or directory'
  
  ── Skip (test_pdb_ancillary.R:55:3): pdb.chain works properly ──────────────────
  Reason: On CRAN
  
  ── Skip (test_pdb_ancillary.R:78:3): pdb2uniprot works properly ────────────────
  Reason: On CRAN
  
  ── Skip (test_pdb_ancillary.R:94:3): uniprot2pdb works properly ────────────────
  Reason: On CRAN
  
  ── Skip (test_pdb_ancillary.R:109:3): pdb.res() works properly ─────────────────
  Reason: On CRAN
  
  ── Skip (test_pdb_ancillary.R:125:3): pdb.pep() works properly ─────────────────
  Reason: On CRAN
  
  ── Skip (test_pdb_ancillary.R:142:3): pdb.select works properly ────────────────
  Reason: On CRAN
  
  
  MUSCLE v3.8.31 by Robert C. Edgar
  
  http://www.drive5.com/muscle
  This software is donated to the public domain.
  Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
  
  file4e605739de8 2 seqs, max length 418, avg  length 406
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node       
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node
  100 MB(20%)00:00:00                Iter   1   50.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  file4e6032b75f21 2 seqs, max length 418, avg  length 406
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node       
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node
  100 MB(20%)00:00:00                Iter   1   50.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  file4e60d041ad6 2 seqs, max length 418, avg  length 406
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node       
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node
  100 MB(20%)00:00:00                Iter   1   50.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  file4e60ff66653 2 seqs, max length 418, avg  length 406
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node       
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node
  100 MB(20%)00:00:00                Iter   1   50.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  file4e6066e04821 2 seqs, max length 418, avg  length 406
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node       
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node
  100 MB(20%)00:00:00                Iter   1   50.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  file4e607059231 2 seqs, max length 476, avg  length 476
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  100 MB(20%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node       
  100 MB(20%)00:00:00                Iter   1  100.00%  Align node
  100 MB(20%)00:00:00                Iter   1   50.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  100 MB(20%)00:00:00                Iter   1  100.00%  Root alignment
  ── ERROR (test_ptmScan.R:114:3): ptm.scan() works properly ─────────────────────
  Error: replacement has 2 rows, data has 1
  Backtrace:
      █
   1. ├─base::suppressWarnings(ptm.scan("Q15796")) test_ptmScan.R:114:2
   2. │ └─base::withCallingHandlers(...)
   3. └─ptm::ptm.scan("Q15796")
   4.   ├─base::`$<-`(`*tmp*`, "p", value = c(NA, TRUE))
   5.   └─base::`$<-.data.frame`(`*tmp*`, "p", value = c(NA, TRUE))
  
  ── Skip (test_ptmplot.R:10:3): ptm.plot() works properly ───────────────────────
  Reason: On CRAN
  
  ── Skip (test_saromatic.R:9:3): saro.dist() works properly ─────────────────────
  Reason: On CRAN
  
  ── Skip (test_saromatic.R:36:3): saro.geometry() works properly ────────────────
  Reason: On CRAN
  
  ── Skip (test_saromatic.R:74:3): saro.motif() works properly ───────────────────
  Reason: On CRAN
  
  ── Skipped tests  ──────────────────────────────────────────────────────────────
  ● On CRAN (63)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  Warning (test_accdpx.R:99:1): (code run outside of `test_that()`)
  Warning (test_accdpx.R:100:1): (code run outside of `test_that()`)
  Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`)
  Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`)
  Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`)
  Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`)
  Warning (test_pdb_ancillary.R:47:1): (code run outside of `test_that()`)
  ERROR (test_ptmScan.R:114:3): ptm.scan() works properly
  
  [ FAIL 1 | WARN 7 | SKIP 63 | PASS 182 ]
  Error: Test failures
  Execution halted