hugheylab/pmparser

lintr found issues with code

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  1. R/get_pubmed_files.R line 16: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_pubmed_files.R#L16) 
    sub_dir = subDir = . = xml_filename = NULL
  2. R/get_pubmed_files.R line 59: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_pubmed_files.R#L59) 
    md5_match = md5_computed = md5_provided = NULL
  3. R/get_pubmed_files.R line 70: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_pubmed_files.R#L70) 
    md5_download = xml_download = f = sub_dir = xml_filename = md5_filename =
  4. R/get_pubmed_files.R line 71: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_pubmed_files.R#L71) 
    md5_match = NULL

To have lintr ignore any of these issues, add the appropriate lines of those shown below to lint_ignore.csv at the top-level of the repository:

filename,line_number,message,line
R/get_pubmed_files.R,16,Variable and function name style should be camelCase.,sub_dir = subDir = . = xml_filename = NULL
R/get_pubmed_files.R,59,Variable and function name style should be camelCase.,md5_match = md5_computed = md5_provided = NULL
R/get_pubmed_files.R,70,Variable and function name style should be camelCase.,md5_download = xml_download = f = sub_dir = xml_filename = md5_filename =
R/get_pubmed_files.R,71,Variable and function name style should be camelCase.,md5_match = NULL

Warning, lint_ignore.csv contains lines not found in the current code:
R/get_citation.R line 5: Variable and function name style should be camelCase.
r published_date = name = NULL
R/get_parsing_tables.R line 2: Variable and function name style should be camelCase.
r xml_filename = NULL
R/get_pubmed_files.R line 15: Variable and function name style should be camelCase.
r sub_dir = subDir = . = xml_filename = NULL
R/get_pubmed_files.R line 58: Variable and function name style should be camelCase.
r md5_match = md5_computed = md5_provided = NULL
R/get_pubmed_files.R line 69: Variable and function name style should be camelCase.
r md5_download = xml_download = f = sub_dir = xml_filename = md5_filename =
R/get_pubmed_files.R line 70: Variable and function name style should be camelCase.
r md5_match = NULL
R/get_test_standard.R line 19: Variable and function name style should be camelCase.
r .N = pmid = N = . = step = NULL
R/get_test_standard.R line 51: Variable and function name style should be camelCase.
r sub_dir = .N = sample_base = NULL
R/get_test_standard.R line 99: Variable and function name style should be camelCase.
r sub_dir = NULL
R/get_test_standard.R line 106: Variable and function name style should be camelCase.
r sub_dir = xml_download = xml_filename = md5_filename = NULL
R/modify_pubmed_db.R line 41: Variable and function name style should be camelCase.
r processed = .N = md5_match = xml_filename = . = step = NULL
R/parse_element.R line 155: Variable and function name style should be camelCase.
r .N = id_type = NULL
R/parse_element.R line 174: Variable and function name style should be camelCase.
r pub_date = y = m = d = title = NULL
R/parse_element.R line 209: Variable and function name style should be camelCase.
r .N = pub_date = y = m = d = NULL
R/parse_element.R line 232: Variable and function name style should be camelCase.
r medline_date = pub_month_tmp1 = pub_month = pub_day_tmp = pub_day = pub_year =
R/parse_element.R line 233: Variable and function name style should be camelCase.
r pub_month_tmp2 = pub_date = date_idx = NULL
R/parse_element.R line 279: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 297: Variable and function name style should be camelCase.
r indexing_method = .N = descriptor_pos = pmid = NULL
R/parse_element.R line 354: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 381: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 411: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 432: Variable and function name style should be camelCase.
r .N = accession_number = NULL
R/parse_element.R line 458: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 476: Variable and function name style should be camelCase.
r .N = abstract_pos = copyright = pmid = NULL
R/parse_element.R line 507: Variable and function name style should be camelCase.
r .N = pmid = NULL
R/parse_person.R line 4: Variable and function name style should be camelCase.
r . = pmid = .N = equal_contrib = collective_name = person_pos =
R/parse_person.R line 5: Variable and function name style should be camelCase.
r affiliation_pos = affiliation = affil_idx = person_idx = n_affil_ids =
R/parse_person.R line 6: Variable and function name style should be camelCase.
r n_person_ids = n_total_ids = id_pos = NULL
R/parse_pubmed_xml.R line 12: Variable and function name style should be camelCase.
r status = xml_filename = parseFunc = NULL
R/parse_pubmed_xml.R line 61: Variable and function name style should be camelCase.
r xml_filename = filenameNow = NULL
R/utilities.R line 2: Variable and function name style should be camelCase.
r status = xml_filename = NULL
R/utilities.R line 9: Variable and function name style should be camelCase.
r . = xml_filename = NULL
R/utilities.R line 77: Variable and function name style should be camelCase.
r . = xml_filename = step = NULL
R/utilities.R line 129: Variable and function name style should be camelCase.
r paste_ = function(...) {