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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings fmcsR_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/fmcsR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fmcsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmcsR’ version ‘1.46.0’
* 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 ‘fmcsR’ can be installed ... WARNING
Found the following significant warnings:
  MCSCompound.cpp:87:74: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct FMCS::MCSCompound::Atom’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  MCSCompound.cpp:123:68: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct FMCS::MCSCompound::Atom’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/fmcsR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘ChemmineR’
A package should be listed in only one of these fields.
* 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(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 = "2024", key = "_2024"): argument "bibtype" is missing, with no default
* checking code 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 ... NOTE
'library' or 'require' call to ‘ChemmineR’ which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘RUnit’ ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fmcs: no visible global function definition for ‘as’
fmcs: no visible global function definition for ‘new’
fmcsBatch: no visible global function definition for ‘as’
fmcsBatch : score: no visible global function definition for ‘as’
plotMCS: no visible global function definition for ‘par’
coerce,list-MCS: no visible global function definition for ‘new’
Undefined global functions or variables:
  as new par
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
fmcsR-package 1.357  0.020   9.681
fmcsBatch     0.046  0.014   8.234
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/fmcsR.Rcheck/00check.log’
for details.