* using log directory 'd:/Rcompile/CRANpkg/local/4.7/ptm.Rcheck'
* using R Under development (unstable) (2026-10-24 r90762 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-10-26 00:40:23 UTC
* checking for file 'ptm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ptm' version '1.0.1'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ptm' can be installed ... OK
* checking installed package size ... 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 ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] 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 ... [6s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 ... [1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... [4s] ERROR
Running examples in 'ptm-Ex.R' failed
The error most likely occurred in:

> ### Name: meto.list
> ### Title: List Proteins Found in MetOSite Matching a Keyword
> ### Aliases: meto.list
> 
> ### ** Examples
> 
> meto.list('inhibitor')
No encoding supplied: defaulting to UTF-8.
Error: lexical error: invalid char in json text.
                                       <html>   <head>     <title>Univ
                     (right here) ------^
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [4s] ERROR
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ptm)
  > 
  > test_check("ptm")
  Saving _problems/test_metosite-37.R
  Saving _problems/test_metosite-68.R
  [ FAIL 2 | WARN 1 | SKIP 11 | PASS 5 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test_aa.R:8:3', 'test_aa.R:23:3', 'test_aa.R:52:3',
    'test_aa.R:88:3', 'test_getseq.R:8:3', 'test_getseq.R:31:3',
    'test_gracefully.R:8:3', 'test_saromatic.R:9:3', 'test_saromatic.R:38:3',
    'test_saromatic.R:78:3'
  • empty test (1): 'test_metosite.R:7:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_metosite.R:37:3'): meto.scan() works properly ──────────────────
  Error: lexical error: invalid char in json text.
                                         <html>   <head>     <title>Univ
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─ptm::meto.scan("P01009") at test_metosite.R:37:3
   2.   └─jsonlite::fromJSON(output, flatten = TRUE)
   3.     └─jsonlite:::parse_and_simplify(...)
   4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   5.         └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test_metosite.R:68:3'): meto.list() works properly ──────────────────
  Error: lexical error: invalid char in json text.
                                         <html>   <head>     <title>Univ
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─ptm::meto.list("calcium") at test_metosite.R:68:3
   2.   └─jsonlite::fromJSON(entries, flatten = TRUE)
   3.     └─jsonlite:::parse_and_simplify(...)
   4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   5.         └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 2 | WARN 1 | SKIP 11 | PASS 5 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [26s] OK
* checking HTML version of manual ... [1s] OK
* DONE
Status: 2 ERRORs