fmcsR 1.26.0
Thomas Girke
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/fmcsR |
| Branch: RELEASE_3_9 |
| Last Commit: 0162d97 |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fmcsR_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/fmcsR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fmcsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmcsR’ version ‘1.26.0’
* 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 ... OK
* 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 = "2019", key = "_2019"): 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fmcsR-package 2.207 0.116 13.342
fmcsBatch 0.092 0.034 11.143
* 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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/fmcsR.Rcheck/00check.log’
for details.