hugheylab/pmparser

lintr found issues with code

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  1. tests/testthat/test_get_pubmed_files.R line 33: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/tests/testthat/test_get_pubmed_files.R#L33) 
    fileInfo[, md5_match := as.numeric(md5_match)]

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
tests/testthat/test_get_pubmed_files.R,33,Variable and function name style should be camelCase.,"fileInfo[, md5_match := as.numeric(md5_match)]"

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_parsing_tables.R line 94: Variable and function name style should be camelCase.
r r[[tableName]][, xml_filename := ac]
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 20: Variable and function name style should be camelCase.
r dNow[, sub_dir := subDir]}
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 61: Variable and function name style should be camelCase.
r d[, md5_match := md5_computed == md5_provided]
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_pubmed_files.R line 80: Variable and function name style should be camelCase.
r fileInfo[, md5_download := NA_integer_]
R/get_pubmed_files.R line 82: Variable and function name style should be camelCase.
r fileInfo[, md5_download := xml_download]}
R/get_pubmed_files.R line 91: Variable and function name style should be camelCase.
r fileInfo[is.na(md5_download), md5_download := r]
R/get_pubmed_files.R line 107: Variable and function name style should be camelCase.
r fileInfo[!(md5_match), xml_download := r]
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 62: Variable and function name style should be camelCase.
r dFile[, sample_base := gsub('\\.xml.*$', '', sampleBase)][]}
R/get_test_standard.R line 92: Variable and function name style should be camelCase.
r parsed$pmid_status = parsed$pmid_status[[2L]]
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 149: Variable and function name style should be camelCase.
r .N = id_type = NULL
R/parse_element.R line 168: Variable and function name style should be camelCase.
r pub_date = y = m = d = NULL
R/parse_element.R line 187: Variable and function name style should be camelCase.
r x4[, pub_date := as.Date(sprintf('%s-%s-%s', y, m, d))]
R/parse_element.R line 201: Variable and function name style should be camelCase.
r .N = pub_date = y = m = d = NULL
R/parse_element.R line 214: Variable and function name style should be camelCase.
r x4[, pub_date := as.Date(sprintf('%s-%s-%s', y, m, d))]
R/parse_element.R line 224: 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 225: Variable and function name style should be camelCase.
r pub_month_tmp2 = pub_date = date_idx = NULL
R/parse_element.R line 242: Variable and function name style should be camelCase.
r x2[is.na(pub_year), date_idx := regexpr('[0-9]{4}', medline_date)]
R/parse_element.R line 244: Variable and function name style should be camelCase.
r pub_year := as.integer(substr(medline_date, date_idx, date_idx + 3L))]
R/parse_element.R line 245: Variable and function name style should be camelCase.
r x2[, date_idx := NULL]
R/parse_element.R line 253: Variable and function name style should be camelCase.
r x2[, pub_month_tmp1 := tolower(pub_month)]
R/parse_element.R line 256: Variable and function name style should be camelCase.
r x3[, pub_day_tmp := pub_day]
R/parse_element.R line 257: Variable and function name style should be camelCase.
r x3[is.na(pub_day_tmp), pub_day_tmp := '01']
R/parse_element.R line 259: Variable and function name style should be camelCase.
r pub_date := as.Date(
R/parse_element.R line 271: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 289: Variable and function name style should be camelCase.
r indexing_method = .N = descriptor_pos = pmid = NULL
R/parse_element.R line 311: Variable and function name style should be camelCase.
r x3[, descriptor_pos := 1:.N, by = pmid]
R/parse_element.R line 313: Variable and function name style should be camelCase.
r x3[, descriptor_pos := ai]}
R/parse_element.R line 346: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 373: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 403: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 424: Variable and function name style should be camelCase.
r .N = accession_number = NULL
R/parse_element.R line 441: Variable and function name style should be camelCase.
r x5[, accession_number := unlist(lapply(x3, xml_text))]
R/parse_element.R line 450: Variable and function name style should be camelCase.
r .N = NULL
R/parse_element.R line 468: Variable and function name style should be camelCase.
r .N = abstract_pos = copyright = pmid = NULL
R/parse_element.R line 484: Variable and function name style should be camelCase.
r x5[, abstract_pos := 1:.N, by = pmid]
R/parse_element.R line 486: Variable and function name style should be camelCase.
r x5[, abstract_pos := as.integer()]}
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_person.R line 34: Variable and function name style should be camelCase.
r dPerson[, equal_contrib := xml_attr(x2, 'EqualContrib')]
R/parse_person.R line 35: Variable and function name style should be camelCase.
r dPerson[, collective_name :=
R/parse_person.R line 39: Variable and function name style should be camelCase.
r dPerson[, person_pos := 1:.N, by = pmid]
R/parse_person.R line 41: Variable and function name style should be camelCase.
r dPerson[, person_pos := ai]}
R/parse_person.R line 50: Variable and function name style should be camelCase.
r dAffil[, affiliation_pos := seq_len(.N), by = cols]
R/parse_person.R line 69: Variable and function name style should be camelCase.
r dAffil[, affil_idx := 1:.N]
R/parse_person.R line 74: Variable and function name style should be camelCase.
r dAffil[, affil_idx := NULL]
R/parse_person.R line 75: Variable and function name style should be camelCase.
r dAffilId[, affil_idx := NULL]
R/parse_person.R line 98: Variable and function name style should be camelCase.
r dPerson[, person_idx := 1:.N]
R/parse_person.R line 102: Variable and function name style should be camelCase.
r dPerson[, person_idx := NULL]
R/parse_person.R line 103: Variable and function name style should be camelCase.
r dAllId[, person_idx := NULL]
R/parse_person.R line 108: Variable and function name style should be camelCase.
r x10[is.na(n_affil_ids), n_affil_ids := 0]
R/parse_person.R line 109: Variable and function name style should be camelCase.
r x10[, n_person_ids := n_total_ids - n_affil_ids]
R/parse_person.R line 114: Variable and function name style should be camelCase.
r dAllId[, id_pos := seq_len(.N), by = cols]
R/parse_person.R line 116: Variable and function name style should be camelCase.
r dPersonId[, id_pos := NULL]
R/parse_pubmed_xml.R line 11: Variable and function name style should be camelCase.
r status = xml_filename = parseFunc = NULL
R/parse_pubmed_xml.R line 34: Variable and function name style should be camelCase.
r if (isEmpty(tableSuffix)) dPmid[, xml_filename := NULL]
R/parse_pubmed_xml.R line 60: 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 128: Variable and function name style should be camelCase.
r paste_ = function(...) {
tests/testthat/test_get_pubmed_files.R line 31: Variable and function name style should be camelCase.
r fileInfo[, md5_match := as.numeric(md5_match)]