* using log directory 'd:/RCompile/CRANincoming/R-devel/Deduplicator1.Rcheck'
* using R Under development (unstable) (2023-12-04 r85659 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'Deduplicator1/DESCRIPTION' ... OK
* this is package 'Deduplicator1' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Chaitanya Patange <cpatange@purdue.edu>'

New submission

Non-FOSS package license (`use_mit_license()`, `use_gpl3_license()` or friends to pick a
license)

Possibly misspelled words in DESCRIPTION:
  Deduplication (2:27)
  Endnote (2:19)
  chaipat (7:48)
  dedup (7:56, 7:71, 7:86, 7:103, 7:121, 7:143)
  endnote (7:78)
  ris (7:117, 7:178)

The Title field should be in title case. Current version is:
'Automating Endnote Deduplication process'
In title case that is:
'Automating Endnote Deduplication Process'
* 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 serialization versions ... OK
* checking whether package 'Deduplicator1' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  `use_mit_license()`, `use_gpl3_license()` or friends to pick a
  license
Standardizable: FALSE
Authors@R field gives no person with name and author role
Authors@R field gives persons with invalid ORCID identifiers:
  Chaitanya Patange <cpatange@purdue.edu> [cre] (YOUR-ORCID-ID)
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... WARNING
'::' or ':::' import not declared from: 'dplyr'
'library' or 'require' calls not declared from:
  'revtools' 'tidyverse'
'library' or 'require' calls in package code:
  'revtools' 'tidyverse'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chaipat.dedup : <anonymous>: no visible global function definition for
  'read_bibliography'
chaipat.dedup: no visible global function definition for '%>%'
chaipat.dedup: no visible global function definition for 'mutate'
chaipat.dedup: no visible global function definition for 'row_number'
chaipat.dedup: no visible global function definition for 'mutate_all'
chaipat.dedup: no visible global function definition for 'separate'
chaipat.dedup: no visible binding for global variable 'pages'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'select'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for '%>%'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'mutate'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'across'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'everything'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'filter_all'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'any_vars'
chaipat.dedup : dedup_checks_4: no visible binding for global variable
  '.'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'drop_na'
chaipat.dedup : dedup_checks_4: no visible global function definition
  for 'distinct'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'select'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for '%>%'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'mutate'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'across'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'everything'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'filter_all'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'any_vars'
chaipat.dedup : dedup_checks_3: no visible binding for global variable
  '.'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'drop_na'
chaipat.dedup : dedup_checks_3: no visible global function definition
  for 'distinct'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'select'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for '%>%'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'mutate'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'across'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'everything'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'filter_all'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'any_vars'
chaipat.dedup : dedup_checks_2: no visible binding for global variable
  '.'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'drop_na'
chaipat.dedup : dedup_checks_2: no visible global function definition
  for 'distinct'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'select'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for '%>%'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'mutate'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'across'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'everything'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'filter_all'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'any_vars'
chaipat.dedup : dedup_checks_1: no visible binding for global variable
  '.'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'drop_na'
chaipat.dedup : dedup_checks_1: no visible global function definition
  for 'distinct'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'select'
endnote.dedup : dedup_checks_4: no visible global function definition
  for '%>%'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'mutate'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'across'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'everything'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'filter_all'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'any_vars'
endnote.dedup : dedup_checks_4: no visible binding for global variable
  '.'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'drop_na'
endnote.dedup : dedup_checks_4: no visible global function definition
  for 'distinct'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'select'
endnote.dedup : dedup_checks_3: no visible global function definition
  for '%>%'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'mutate'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'across'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'everything'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'filter_all'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'any_vars'
endnote.dedup : dedup_checks_3: no visible binding for global variable
  '.'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'drop_na'
endnote.dedup : dedup_checks_3: no visible global function definition
  for 'distinct'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'select'
endnote.dedup : dedup_checks_2: no visible global function definition
  for '%>%'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'mutate'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'across'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'everything'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'filter_all'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'any_vars'
endnote.dedup : dedup_checks_2: no visible binding for global variable
  '.'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'drop_na'
endnote.dedup : dedup_checks_2: no visible global function definition
  for 'distinct'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'select'
endnote.dedup : dedup_checks_1: no visible global function definition
  for '%>%'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'mutate'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'across'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'everything'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'filter_all'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'any_vars'
endnote.dedup : dedup_checks_1: no visible binding for global variable
  '.'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'drop_na'
endnote.dedup : dedup_checks_1: no visible global function definition
  for 'distinct'
export_ris.dedup: no visible global function definition for
  'write_bibliography'
export_summary.dedup: no visible global function definition for
  'write.csv'
import.dedup : <anonymous>: no visible global function definition for
  'read_bibliography'
import.dedup: no visible global function definition for '%>%'
import.dedup: no visible global function definition for 'mutate'
import.dedup: no visible global function definition for 'row_number'
import.dedup: no visible global function definition for 'mutate_all'
import.dedup: no visible global function definition for 'separate'
import.dedup: no visible binding for global variable 'pages'
summary.dedup: no visible global function definition for '%>%'
summary.dedup: no visible global function definition for 'group_by'
summary.dedup: no visible binding for global variable 'Database'
summary.dedup: no visible global function definition for 'tally'
Undefined global functions or variables:
  %>% . Database across any_vars distinct drop_na everything filter_all
  group_by mutate mutate_all pages read_bibliography row_number select
  separate tally write.csv write_bibliography
Consider adding
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 examples ... ERROR
Running examples in 'Deduplicator1-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chaipat.dedup
> ### Title: chaipat.dedup: A Bibliographic deduplication function
> ### Aliases: chaipat.dedup
> 
> ### ** Examples
> 
> deduplicated_dataset <- chaipat.dedup();
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.4.4     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ purrr::%||%()   masks base::%||%()
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Error in `distinct()`:
ℹ In argument: `T2[, 2:ncol(T2)]`.
Caused by error in `[.data.frame`:
! undefined columns selected
Backtrace:
     ▆
  1. ├─Deduplicator1::chaipat.dedup()
  2. │ └─Deduplicator1 (local) dedup_checks_1(final_datasetx, "id", "doi")
  3. │   └─T2 %>% distinct(T2[, 2:ncol(T2)], .keep_all = TRUE, )
  4. ├─dplyr::distinct(., T2[, 2:ncol(T2)], .keep_all = TRUE, )
  5. ├─dplyr:::distinct.data.frame(., T2[, 2:ncol(T2)], .keep_all = TRUE, )
  6. │ └─dplyr::distinct_prepare(...)
  7. │   └─dplyr:::add_computed_columns(.data, vars, error_call = error_call)
  8. │     └─dplyr:::mutate_cols(...)
  9. │       ├─base::withCallingHandlers(...)
 10. │       └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 11. │         └─mask$eval_all_mutate(quo)
 12. │           └─dplyr (local) eval()
 13. ├─T2[, 2:ncol(T2)]
 14. ├─base::`[.data.frame`(T2, , 2:ncol(T2))
 15. │ └─base::stop("undefined columns selected")
 16. └─base::.handleSimpleError(...)
 17.   └─dplyr (local) h(simpleError(msg, call))
 18.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 2 NOTEs