lintr found issues with code

Question

lintr found issues with code

Closed this issue 2 years ago · 0 comments

R/get_citation.R line 5: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_citation.R#L5)
```
published_date = name = NULL   
```
R/get_parsing_tables.R line 2: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_parsing_tables.R#L2)
```
xml_filename = NULL   
```
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   
```
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   
```
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 =   
```
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   
```
R/get_test_standard.R line 19: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_test_standard.R#L19)
```
.N = pmid = N = . = step = NULL   
```
R/get_test_standard.R line 51: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_test_standard.R#L51)
```
sub_dir = .N = sample_base = NULL   
```
R/get_test_standard.R line 99: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_test_standard.R#L99)
```
sub_dir = NULL   
```
R/get_test_standard.R line 106: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/get_test_standard.R#L106)
```
sub_dir = xml_download = xml_filename = md5_filename = NULL   
```
R/modify_pubmed_db.R line 41: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/modify_pubmed_db.R#L41)
```
processed = .N = md5_match = xml_filename = . = step = NULL   
```
R/parse_element.R line 155: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L155)
```
.N = id_type = NULL   
```
R/parse_element.R line 174: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L174)
```
pub_date = y = m = d = title = NULL   
```
R/parse_element.R line 209: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L209)
```
.N = pub_date = y = m = d = NULL   
```
R/parse_element.R line 232: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L232)
```
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. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L233)
```
pub_month_tmp2 = pub_date = date_idx = NULL   
```
R/parse_element.R line 279: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L279)
```
.N = NULL   
```
R/parse_element.R line 297: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L297)
```
indexing_method = .N = descriptor_pos = pmid = NULL   
```
R/parse_element.R line 354: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L354)
```
.N = NULL   
```
R/parse_element.R line 381: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L381)
```
.N = NULL   
```
R/parse_element.R line 411: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L411)
```
.N = NULL   
```
R/parse_element.R line 432: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L432)
```
.N = accession_number = NULL   
```
R/parse_element.R line 458: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L458)
```
.N = NULL   
```
R/parse_element.R line 476: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L476)
```
.N = abstract_pos = copyright = pmid = NULL   
```
R/parse_element.R line 507: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_element.R#L507)
```
.N = pmid = NULL   
```
R/parse_person.R line 4: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_person.R#L4)
```
. = pmid = .N = equal_contrib = collective_name = person_pos  =   
```
R/parse_person.R line 5: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_person.R#L5)
```
affiliation_pos = affiliation = affil_idx = person_idx = n_affil_ids =   
```
R/parse_person.R line 6: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_person.R#L6)
```
n_person_ids = n_total_ids = id_pos = NULL   
```
R/parse_pubmed_xml.R line 12: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_pubmed_xml.R#L12)
```
status = xml_filename = parseFunc = NULL   
```
R/parse_pubmed_xml.R line 61: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/parse_pubmed_xml.R#L61)
```
xml_filename = filenameNow = NULL   
```
R/utilities.R line 2: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/utilities.R#L2)
```
status = xml_filename = NULL   
```
R/utilities.R line 9: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/utilities.R#L9)
```
. = xml_filename = NULL   
```
R/utilities.R line 77: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/utilities.R#L77)
```
. = xml_filename = step = NULL   
```
R/utilities.R line 129: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/master/R/utilities.R#L129)
```
paste_ = function(...) {   
```

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_citation.R,5,Variable and function name style should be camelCase.,published_date = name = NULL
R/get_parsing_tables.R,2,Variable and function name style should be camelCase.,xml_filename = NULL
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
R/get_test_standard.R,19,Variable and function name style should be camelCase.,.N = pmid = N = . = step = NULL
R/get_test_standard.R,51,Variable and function name style should be camelCase.,sub_dir = .N = sample_base = NULL
R/get_test_standard.R,99,Variable and function name style should be camelCase.,sub_dir = NULL
R/get_test_standard.R,106,Variable and function name style should be camelCase.,sub_dir = xml_download = xml_filename = md5_filename = NULL
R/modify_pubmed_db.R,41,Variable and function name style should be camelCase.,processed = .N = md5_match = xml_filename = . = step = NULL
R/parse_element.R,155,Variable and function name style should be camelCase.,.N = id_type = NULL
R/parse_element.R,174,Variable and function name style should be camelCase.,pub_date = y = m = d = title = NULL
R/parse_element.R,209,Variable and function name style should be camelCase.,.N = pub_date = y = m = d = NULL
R/parse_element.R,232,Variable and function name style should be camelCase.,medline_date = pub_month_tmp1 = pub_month = pub_day_tmp = pub_day = pub_year =
R/parse_element.R,233,Variable and function name style should be camelCase.,pub_month_tmp2 = pub_date = date_idx = NULL
R/parse_element.R,279,Variable and function name style should be camelCase.,.N = NULL
R/parse_element.R,297,Variable and function name style should be camelCase.,indexing_method = .N = descriptor_pos = pmid = NULL
R/parse_element.R,354,Variable and function name style should be camelCase.,.N = NULL
R/parse_element.R,381,Variable and function name style should be camelCase.,.N = NULL
R/parse_element.R,411,Variable and function name style should be camelCase.,.N = NULL
R/parse_element.R,432,Variable and function name style should be camelCase.,.N = accession_number = NULL
R/parse_element.R,458,Variable and function name style should be camelCase.,.N = NULL
R/parse_element.R,476,Variable and function name style should be camelCase.,.N = abstract_pos = copyright = pmid = NULL
R/parse_element.R,507,Variable and function name style should be camelCase.,.N = pmid = NULL
R/parse_person.R,4,Variable and function name style should be camelCase.,. = pmid = .N = equal_contrib = collective_name = person_pos  =
R/parse_person.R,5,Variable and function name style should be camelCase.,affiliation_pos = affiliation = affil_idx = person_idx = n_affil_ids =
R/parse_person.R,6,Variable and function name style should be camelCase.,n_person_ids = n_total_ids = id_pos = NULL
R/parse_pubmed_xml.R,12,Variable and function name style should be camelCase.,status = xml_filename = parseFunc = NULL
R/parse_pubmed_xml.R,61,Variable and function name style should be camelCase.,xml_filename = filenameNow = NULL
R/utilities.R,2,Variable and function name style should be camelCase.,status = xml_filename = NULL
R/utilities.R,9,Variable and function name style should be camelCase.,. = xml_filename = NULL
R/utilities.R,77,Variable and function name style should be camelCase.,. = xml_filename = step = NULL
R/utilities.R,129,Variable and function name style should be camelCase.,paste_ = function(...) {