* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/ptm.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘ptm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ptm’ version ‘0.2.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ptm’ can be installed ... [33s/44s] OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [56s/86s] OK
* checking Rd files ... NOTE
checkRd: (-1) imutant.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ptm.plot.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:47: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... [8s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [35s/58s]
 [35s/58s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 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 1 | WARN 5 | SKIP 54 | PASS 190 ]
  
  ══ 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_metosite.R:57:5'): meto.scan() works properly ────────────────
  file.exists("report_scan_P01009.txt") is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 5 | SKIP 54 | PASS 190 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [10s/15s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/ptm.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:41.98, 260.30 + 25.00