[Bioc-devel] CITATION file issue

[Nitesh Turaga]

This has been fixed. 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

"I don’t expect you to respond to my email outside your work hours"



> On Aug 4, 2022, at 11:14 AM, Kevin Horan <khoran using cs.ucr.edu> wrote:
> 
> 
> 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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