[Bioc-devel] CITATION file issue

[Kevin Horan]

On ChemmineR 3.48.0 (release) and 3.49.1 (devel), I was getting a 
CITATION error on the landing page like:

Citation (from within R, enter|citation("ChemmineR")|):

Important note to the maintainer of the ChemmineR package: An error 
occured while trying to generate the citation from the CITATION file. 
This typically occurs when the file contains R code that relies on the 
package to be installed e.g. it contains calls to things 
like|packageVersion()|or|packageDate()|instead of 
using|meta$Version|or|meta$Date|. SeeR documentation 
<https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files>for 
more information.

In the Check result I could see the following WARNING:

* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
   Failed with error:  ‘there is no package called ‘bibtex’’
   Error in (function (bibtype, textVersion = NULL, header = NULL, footer = NULL,     key = NULL, ..., other = list(), mheader = NULL, mfooter = NULL) {    BibTeX_names <- names(BibLaTeX_entry_field_db)    args <- c(list(...), other)    if (!length(args))         return(structure(list(), class = "bibentry"))    if (any(vapply(names(args), .is_not_nonempty_text, FALSE)))         stop("all fields have to be named")    args <- c(list(bibtype = bibtype, textVersion = textVersion,         header = header, footer = footer, key = key), list(...))    args <- lapply(args, .listify)    other <- lapply(other, .listify)    max_length <- max(vapply(c(args, other), length, 0L))    args_length <- vapply(args, length, 0L)    if (!all(args_length_ok <- args_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, %s: %s",             "the following need to be recycled", paste(names(args)[!args_length_ok],                 collapse = ", ")), domain = NA)    args <- lapply(args, function(x) rep(x, length.out = max_length))    other_length <- vapply(other, length, 0L)    if (!all(other_length_ok <- other_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, %s: %s",             "the following need to be recycled", paste(names(other)[!other_length_ok],                 collapse = ", ")), domain = NA)    other <- lapply(other, function(x) rep(x, length.out = max_length))    bibentry1 <- function(bibtype, textVersion, header = NULL,         footer = NULL, key = NULL, ..., other = list()) {        bibtype <- as.character(bibtype)        stopifnot(length(bibtype) == 1L)        pos <- match(tolower(bibtype), tolower(BibTeX_names))        if (is.na(pos))             stop(gettextf("%s has to be one of %s", sQuote("bibtype"),                 paste(BibTeX_names, collapse = ", ")), domain = NA)        bibtype <- BibTeX_names[pos]        rval <- c(list(...), other)        rval <- rval[!vapply(rval, .is_not_nonempty_text, FALSE)]        fields <- tolower(names(rval))        names(rval) <- fields        attr(rval, "bibtype") <- bibtype        .BibEntryCheckBibEntry1(rval)        pos <- fields %in% .BibEntryNameList        if (any(pos)) {            for (i in which(pos)) if (!inherits(rval[[i]], "person"))                 rval[[i]] <- ArrangeAuthors(rval[[i]])        }        pos <- fields %in% c("dateobj") | pos        if (any(!pos)) {            for (i in which(!pos)) rval[[i]] <- as.character(rval[[i]])        }        attr(rval, "key") <- if (is.null(key))             NULL        else as.character(key)        if (is.null(rval[["dateobj"]])) {            tdate <- try(ProcessDates(rval), TRUE)            if (!inherits(tdate, "try-error"))                 attr(rval, "dateobj") <- tdate        }        else {            attr(rval, "dateobj") <- rval[["dateobj"]]            rval[["dateobj"]] <- NULL        }        if (!is.null(textVersion))             attr(rval, "textVersion") <- as.character(textVersion)        if (!.is_not_nonempty_text(header))             attr(rval, "header") <- paste(header, collapse = "\n")        if (!.is_not_nonempty_text(footer))             attr(rval, "footer") <- paste(footer, collapse = "\n")        return(rval)    }    rval <- lapply(seq_along(args$bibtype), function(i) do.call("bibentry1",         c(lapply(args, "[[", i), list(other = lapply(other, "[[",             i)))))    if (!.is_not_nonempty_text(mheader))         attr(rval, "mheader") <- paste(mheader, collapse = "\n")    if (!.is_not_nonempty_text(mfooter))         attr(rval, "mfooter") <- paste(mfooter, collapse = "\n")    class(rval) <- c("BibEntry", "bibentry")    rval})(year = "2022", key = "_2022"): argument "bibtype" is missing, with no default


As noted, the "bibtex" package was missing. I added it to the suggested 
package list in the DESCRIPTION file, deployed as version 3.49.2, and 
the warning has now gone away:

* checking package subdirectories ... OK

However, the citation error on the landing page for 3.49.2 
<https://www.bioconductor.org/packages/devel/bioc/html/ChemmineR.html> 
still remains. Is that just not getting updated somehow, or is there 
still some error occurring? If there is an error, how can I see what it is?

Thanks.

Kevin




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