BioC 3.5: CHECK report for bioassayR on toluca2

Package: bioassayR

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.13.2.tar.gz

StartedAt: 2017-04-23 00:55:10 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 00:56:55 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 105.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bioassayR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.13.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioassayR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioassayR’ version ‘1.13.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bioassayR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  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(sapply(names(args), .is_not_nonempty_text)))         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(sapply(c(args, other), length))    args_length <- sapply(args, length)    if (!all(args_length_ok <- args_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, the following need to be recycled: %s",             paste(names(args)[!args_length_ok], collapse = ", ")),             domain = NA)    args <- lapply(args, function(x) rep(x, length.out = max_length))    other_length <- sapply(other, length)    if (!all(other_length_ok <- other_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, the following need to be recycled: %s",             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[!sapply(rval, .is_not_nonempty_text)]        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 = "2017", key = "_2017"): argument "bibtype" is missing, with no default
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck/00check.log’
for details.

* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioassayR)

name	user	system	elapsed
BioAssayDB-class	0.002	0.000	0.001
activeAgainst	0.027	0.001	0.028
activeTargets	0.033	0.001	0.034
addBioassayIndex	0.013	0.003	0.017
addDataSource	0.041	0.006	0.047
allCids	0.007	0.001	0.009
allTargets	0.007	0.001	0.008
assaySetTargets	0.101	0.007	0.109
bioactivityFingerprint	0.265	0.002	0.266
bioassay-class	0.020	0.003	0.023
bioassaySet-class	0.001	0.001	0.001
connectBioassayDB	0.012	0.002	0.014
crossReactivityProbability	0.402	0.003	0.405
disconnectBioassayDB	0.010	0.002	0.012
dropBioassay	0.188	0.006	0.197
dropBioassayIndex	0.019	0.007	0.027
getAssay	0.024	0.001	0.025
getAssays	0.061	0.001	0.062
getBioassaySetByCids	0.233	0.002	0.234
inactiveTargets	0.011	0.001	0.011
loadBioassay	0.267	0.006	0.276
loadIdMapping	0.008	0.002	0.011
newBioassayDB	0.009	0.002	0.010
parsePubChemBioassay	0.018	0.000	0.018
perTargetMatrix	0.225	0.003	0.226
queryBioassayDB	0.024	0.009	0.033
samplebioassay	0.003	0.001	0.004
scaleBioassaySet	0.029	0.001	0.030
screenedAtLeast	0.010	0.001	0.011
selectiveAgainst	0.127	0.002	0.129
targetSelectivity	0.152	0.001	0.153
translateTargetId	0.011	0.002	0.014
trinarySimilarity	0.197	0.001	0.197