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October 2, 2017 22:47
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| library('knitcitations') | |
| check_bib <- function() { | |
| xx <- sapply(bib, function(x) { | |
| tryCatch(citep(x), error = function(e) { | |
| message(paste('found an error attempting to cite', names(x))) | |
| print(e) | |
| }) | |
| }) | |
| } | |
| ## derfinderHelper | |
| bib <- c(knitcitations = citation('knitcitations'), | |
| derfinderHelper = citation('derfinderHelper')[1], | |
| BiocStyle = citation('BiocStyle'), | |
| knitr = citation('knitr')[3], | |
| rmarkdown = citation('rmarkdown'), | |
| BiocParallel = citation('BiocParallel'), | |
| R = citation(), | |
| IRanges = citation('IRanges'), | |
| Matrix = citation('Matrix'), | |
| S4Vectors = citation('S4Vectors'), | |
| devtools = citation('devtools'), | |
| testthat = citation('testthat')) | |
| check_bib() | |
| ## derfinderPlot | |
| bib <- c(knitcitations = citation('knitcitations'), | |
| derfinderPlot = citation('derfinderPlot')[1], | |
| BiocStyle = citation('BiocStyle'), | |
| knitr = citation('knitr')[3], | |
| rmarkdown = citation('rmarkdown'), | |
| derfinder = citation('derfinder')[1], | |
| ggbio = citation('ggbio'), | |
| brainspan = RefManageR::BibEntry(bibtype = 'Unpublished', | |
| key = 'brainspan', | |
| title = 'Atlas of the Developing Human Brain [Internet]. Funded by ARRA Awards 1RC2MH089921-01, 1RC2MH090047-01, and 1RC2MH089929-01.', | |
| author = 'BrainSpan', year = 2011, url = 'http://www.brainspan.org/'), | |
| R = citation(), | |
| IRanges = citation('IRanges'), | |
| devtools = citation('devtools'), | |
| testthat = citation('testthat'), | |
| GenomeInfoDb = citation('GenomeInfoDb'), | |
| GenomicRanges = citation('GenomicRanges'), | |
| ggplot2 = citation('ggplot2'), | |
| plyr = citation('plyr'), | |
| RColorBrewer = citation('RColorBrewer'), | |
| reshape2 = citation('reshape2'), | |
| scales = citation('scales'), | |
| biovizBase = citation('biovizBase'), | |
| bumphunter = citation('bumphunter')[1], | |
| TxDb.Hsapiens.UCSC.hg19.knownGene = citation('TxDb.Hsapiens.UCSC.hg19.knownGene'), | |
| bumphunterPaper = RefManageR::BibEntry(bibtype = 'article', | |
| key = 'bumphunterPaper', | |
| title = 'Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies', | |
| author = 'Jaffe, Andrew E and Murakami, Peter and Lee, Hwajin and Leek, Jeffrey T and Fallin, M Daniele and Feinberg, Andrew P and Irizarry, Rafael A', | |
| year = 2012, journal = 'International Journal of Epidemiology'), | |
| derfinderData = citation('derfinderData') | |
| ) | |
| check_bib() | |
| ## derfinder quickstart | |
| bib <- c(knitcitations = citation('knitcitations'), | |
| derfinder = citation('derfinder')[1], | |
| BiocStyle = citation('BiocStyle'), | |
| knitrBootstrap = citation('knitrBootstrap'), | |
| knitr = citation('knitr')[3], | |
| rmarkdown = citation('rmarkdown'), | |
| brainspan = RefManageR::BibEntry(bibtype = 'Unpublished', | |
| key = 'brainspan', | |
| title = 'Atlas of the Developing Human Brain [Internet]. Funded by ARRA Awards 1RC2MH089921-01, 1RC2MH090047-01, and 1RC2MH089929-01.', | |
| author = 'BrainSpan', year = 2011, url = 'http://www.brainspan.org/'), | |
| originalder = citation('derfinder')[2], | |
| R = citation(), | |
| IRanges = citation('IRanges'), | |
| devtools = citation('devtools'), | |
| testthat = citation('testthat'), | |
| GenomeInfoDb = citation('GenomeInfoDb'), | |
| GenomicRanges = citation('GenomicRanges'), | |
| ggplot2 = citation('ggplot2'), | |
| biovizBase = citation('biovizBase'), | |
| bumphunter = citation('bumphunter')[1], | |
| TxDb.Hsapiens.UCSC.hg19.knownGene = citation('TxDb.Hsapiens.UCSC.hg19.knownGene'), | |
| AnnotationDbi = citation('AnnotationDbi'), | |
| BiocParallel = citation('BiocParallel'), | |
| derfinderHelper = citation('derfinderHelper'), | |
| GenomicAlignments = citation('GenomicAlignments'), | |
| GenomicFeatures = citation('GenomicFeatures'), | |
| GenomicFiles = citation('GenomicFiles'), | |
| Hmisc = citation('Hmisc'), | |
| qvalue = citation('qvalue'), | |
| Rsamtools = citation('Rsamtools'), | |
| rtracklayer = citation('rtracklayer'), | |
| S4Vectors = citation('S4Vectors'), | |
| bumphunterPaper = RefManageR::BibEntry(bibtype = 'article', | |
| key = 'bumphunterPaper', | |
| title = 'Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies', | |
| author = 'Jaffe, Andrew E and Murakami, Peter and Lee, Hwajin and Leek, Jeffrey T and Fallin, M Daniele and Feinberg, Andrew P and Irizarry, Rafael A', | |
| year = 2012, journal = 'International Journal of Epidemiology'), | |
| derfinderData = citation('derfinderData') | |
| ) | |
| check_bib() | |
| ## derfinder users guide | |
| bib <- c(knitcitations = citation('knitcitations'), | |
| derfinder = citation('derfinder')[1], | |
| BiocStyle = citation('BiocStyle'), | |
| knitrBootstrap = citation('knitrBootstrap'), | |
| knitr = citation('knitr')[3], | |
| rmarkdown = citation('rmarkdown'), | |
| brainspan = RefManageR::BibEntry(bibtype = 'Unpublished', | |
| key = 'brainspan', | |
| title = 'Atlas of the Developing Human Brain [Internet]. Funded by ARRA Awards 1RC2MH089921-01, 1RC2MH090047-01, and 1RC2MH089929-01.', | |
| author = 'BrainSpan', year = 2011, url = 'http://www.brainspan.org/'), | |
| originalder = citation('derfinder')[2], | |
| R = citation(), | |
| IRanges = citation('IRanges'), | |
| devtools = citation('devtools'), | |
| testthat = citation('testthat'), | |
| GenomeInfoDb = citation('GenomeInfoDb'), | |
| GenomicRanges = citation('GenomicRanges'), | |
| ggplot2 = citation('ggplot2'), | |
| biovizBase = citation('biovizBase'), | |
| bumphunter = citation('bumphunter')[1], | |
| TxDb.Hsapiens.UCSC.hg19.knownGene = citation('TxDb.Hsapiens.UCSC.hg19.knownGene'), | |
| AnnotationDbi = citation('AnnotationDbi'), | |
| BiocParallel = citation('BiocParallel'), | |
| derfinderHelper = citation('derfinderHelper'), | |
| GenomicAlignments = citation('GenomicAlignments'), | |
| GenomicFeatures = citation('GenomicFeatures'), | |
| GenomicFiles = citation('GenomicFiles'), | |
| Hmisc = citation('Hmisc'), | |
| qvalue = citation('qvalue'), | |
| Rsamtools = citation('Rsamtools'), | |
| rtracklayer = citation('rtracklayer'), | |
| S4Vectors = citation('S4Vectors'), | |
| bumphunterPaper = RefManageR::BibEntry(bibtype = 'article', | |
| key = 'bumphunterPaper', | |
| title = 'Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies', | |
| author = 'Jaffe, Andrew E and Murakami, Peter and Lee, Hwajin and Leek, Jeffrey T and Fallin, M Daniele and Feinberg, Andrew P and Irizarry, Rafael A', | |
| year = 2012, journal = 'International Journal of Epidemiology'), | |
| derfinderData = citation('derfinderData') | |
| ) | |
| check_bib() | |
| ## regionReport | |
| bib <- c(knitcitations = citation('knitcitations'), | |
| derfinder = citation('derfinder')[1], | |
| regionReport = citation('regionReport')[1], | |
| knitrBootstrap = citation('knitrBootstrap'), | |
| BiocStyle = citation('BiocStyle'), | |
| ggbio = citation('ggbio'), | |
| ggplot2 = citation('ggplot2'), | |
| knitr = citation('knitr')[3], | |
| rmarkdown = citation('rmarkdown'), | |
| DT = citation('DT'), | |
| R = citation(), | |
| IRanges = citation('IRanges'), | |
| devtools = citation('devtools'), | |
| GenomeInfoDb = citation('GenomeInfoDb'), | |
| GenomicRanges = citation('GenomicRanges'), | |
| biovizBase = citation('biovizBase'), | |
| TxDb.Hsapiens.UCSC.hg19.knownGene = citation('TxDb.Hsapiens.UCSC.hg19.knownGene'), | |
| derfinderPlot = citation('derfinderPlot')[1], | |
| grid = citation('grid'), | |
| gridExtra = citation('gridExtra'), | |
| mgcv = citation('mgcv'), | |
| RColorBrewer = citation('RColorBrewer'), | |
| whikser = citation('whisker'), | |
| bumphunter = citation('bumphunter')[1], | |
| pheatmap = citation('pheatmap'), | |
| DESeq2 = citation('DESeq2'), | |
| edgeR1 = citation('edgeR')[1], | |
| edgeR2 = citation('edgeR')[2], | |
| edgeR5 = citation('edgeR')[5], | |
| edgeR6 = RefManageR::BibEntry('inbook', key = 'edgeR6', | |
| author = 'Chen, Yunshun and Lun, Aaron T. L. and Smyth, Gordon K.', | |
| title = 'Differential expression analysis of complex RNA-seq experiments using edgeR', | |
| booktitle = 'Statistical Analysis of Next Generation Sequencing Data', | |
| year = 2014, | |
| editor = 'Datta, Somnath and Nettleton, Dan', publisher = 'Springer', | |
| location = 'New York', pages = '51-74'), | |
| DEFormats = citation('DEFormats') | |
| ) | |
| check_bib() | |
| ## recount | |
| bib <- c( | |
| AnnotationDbi = citation('AnnotationDbi'), | |
| BiocParallel = citation('BiocParallel'), | |
| BiocStyle = citation('BiocStyle'), | |
| derfinder = citation('derfinder')[1], | |
| DESeq2 = citation('DESeq2'), | |
| devtools = citation('devtools'), | |
| downloader = citation('downloader'), | |
| EnsDb.Hsapiens.v79 = citation('EnsDb.Hsapiens.v79'), | |
| GEOquery = citation('GEOquery'), | |
| GenomeInfoDb = citation('GenomeInfoDb'), | |
| GenomicFeatures = citation('GenomicFeatures'), | |
| GenomicRanges = citation('GenomicRanges'), | |
| IRanges = citation('IRanges'), | |
| knitcitations = citation('knitcitations'), | |
| knitr = citation('knitr')[3], | |
| org.Hs.eg.db = citation('org.Hs.eg.db'), | |
| R = citation(), | |
| RCurl = citation('RCurl'), | |
| recount = citation('recount'), | |
| regionReport = citation('regionReport'), | |
| rentrez = citation('rentrez'), | |
| rmarkdown = citation('rmarkdown'), | |
| rtracklayer = citation('rtracklayer'), | |
| S4Vectors = citation('S4Vectors'), | |
| SummarizedExperiment = citation('SummarizedExperiment'), | |
| testthat = citation('testthat') | |
| ) | |
| check_bib() | |
| ## Reproduce all issues | |
| citep(bib[['GenomeInfoDb']]) | |
| citep(bib[['AnnotationDbi']]) | |
| citep(bib[['S4Vectors']]) | |
| citep(bib[['SummarizedExperiment']]) | |
| traceback() | |
| # > citep(bib[['GenomeInfoDb']]) | |
| # Error in nchar(aut) : invalid multibyte string, element 1 | |
| # > citep(bib[['AnnotationDbi']]) | |
| # Error in nchar(aut) : invalid multibyte string, element 1 | |
| # > citep(bib[['S4Vectors']]) | |
| # Error in nchar(aut) : invalid multibyte string, element 1 | |
| # > citep(bib[['SummarizedExperiment']]) | |
| # Error in nchar(aut) : invalid multibyte string, element 1 | |
| # > traceback() | |
| # 12: nchar(aut) | |
| # 11: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) | |
| # 10: suppressWarnings({ | |
| # ind <- nchar(aut) == 0L & !x$bibtype %in% c("XData", "Set") | |
| # aut[ind] <- x$title[ind] | |
| # x$.duplicated <- duplicated(aut) | |
| # }) | |
| # 9: sort.BibEntry(bib, sorting = "none", .bibstyle = bibstyle, return.labs = TRUE) | |
| # 8: sort(bib, sorting = "none", .bibstyle = bibstyle, return.labs = TRUE) | |
| # 7: eval(substitute(expr), data, enclos = parent.frame()) | |
| # 6: eval(substitute(expr), data, enclos = parent.frame()) | |
| # 5: with.default(BibOptions(), { | |
| # style <- .BibEntry_match_format_style(style) | |
| # papers <- suppressMessages(do.call(`[.BibEntry`, list(x = bib, | |
| # ...))) | |
| # keys <- unlist(papers$key) | |
| # if (!length(papers)) | |
| # return("") | |
| # if (cite.style == "pandoc") { | |
| # MakePandocCitation(papers, keys, textual, bibpunct, before, | |
| # after) | |
| # } | |
| # else { | |
| # numeric <- "numeric" %in% cite.style | |
| # alphabetic <- "alphabetic" %in% cite.style | |
| # if (cite.style != .cites$sty) | |
| # ClearLabs(cite.style) | |
| # n <- length(papers) | |
| # cited <- names(.cites$indices) | |
| # first <- !(keys %in% cited) | |
| # if (cite.style != "numeric") { | |
| # if (any(!names(bib) %in% names(.cites$labs))) { | |
| # bibstyle <- switch(cite.style, authortitle = "authoryear", | |
| # cite.style) | |
| # bib <- sort(bib, sorting = "none", .bibstyle = bibstyle, | |
| # return.labs = TRUE) | |
| # newinds <- bib$.index | |
| # .labs <- newinds[keys] | |
| # .cites$labs <- c(.cites$labs, newinds) | |
| # } | |
| # else { | |
| # .labs <- .cites$labs[keys] | |
| # } | |
| # } | |
| # else { | |
| # first.ind <- if (!length(.cites$labs)) | |
| # seq_along(papers) | |
| # else which(first | !keys %in% names(.cites$labs)) | |
| # if (length(first.ind)) { | |
| # shorthands <- unlist(papers$shorthand) | |
| # max.ind <- suppressWarnings(sum(!is.na(as.numeric(.cites$labs)))) | |
| # newinds <- seq.int(max.ind + 1L, length.out = length(first.ind)) | |
| # names(newinds) <- keys[first.ind] | |
| # if (length(shorthands)) | |
| # newinds[names(shorthands)] <- shorthands | |
| # .cites$labs <- c(.cites$labs, newinds) | |
| # } | |
| # .labs <- .cites$labs[keys] | |
| # } | |
| # AddCite(keys, !identical(hyperlink, FALSE)) | |
| # year <- match(keys, names(.cites$indices)) | |
| # if (alphabetic || numeric) { | |
| # year <- structure(.labs, names = NULL) | |
| # } | |
| # else { | |
| # year <- structure(unlist(lapply(papers$dateobj, MakeAuthorYear()$DateFormatter)), | |
| # names = NULL) | |
| # if (any(.labs %in% letters)) | |
| # year <- paste0(year, .labs) | |
| # } | |
| # if (textual || (!numeric && !alphabetic)) { | |
| # auth <- character(n) | |
| # authorLists <- lapply(papers, authorList) | |
| # lastAuthors <- NULL | |
| # for (i in seq_len(n)) { | |
| # authors <- authorLists[[i]] | |
| # if (length(authors) > max.names && !(first[i] && | |
| # longnamesfirst)) { | |
| # authors <- authors[seq_len(max.names)] | |
| # authors[length(authors)] <- paste0(authors[length(authors)], | |
| # ", et al.") | |
| # } | |
| # else { | |
| # if (length(authors) > 1L) | |
| # authors[length(authors)] <- paste("and", | |
| # authors[length(authors)]) | |
| # } | |
| # if (length(authors) > 2L) | |
| # auth[i] <- paste(authors, collapse = ", ") | |
| # else auth[i] <- paste(authors, collapse = " ") | |
| # } | |
| # } | |
| # make.hyper <- !identical(hyperlink, FALSE) | |
| # if (textual) { | |
| # if (numeric || alphabetic) { | |
| # result <- paste0(bibpunct[3L], before, year, | |
| # after, bibpunct[4L]) | |
| # } | |
| # else { | |
| # result <- paste0(bibpunct[1L], before, year, | |
| # after, bibpunct[2L]) | |
| # } | |
| # if (super && numeric && (!style %in% c("markdown", | |
| # "html") || !make.hyper)) | |
| # result <- paste0(auth, "^{", result, "}") | |
| # else if (!super || !numeric) | |
| # result <- paste0(auth, " ", result) | |
| # } | |
| # else if (numeric || alphabetic) { | |
| # result <- year | |
| # } | |
| # else { | |
| # result <- paste0(auth, bibpunct[6L], " ", year) | |
| # } | |
| # result <- if (make.hyper) | |
| # MakeCiteHyperlink(result, papers, hyperlink, keys, | |
| # auth, style, first, numeric, alphabetic, super, | |
| # textual, bibpunct, before, after) | |
| # else AddCitationPunct(result, bibpunct, before, after, | |
| # textual, numeric, alphabetic, super) | |
| # result | |
| # } | |
| # }) | |
| # 4: with(BibOptions(), { | |
| # style <- .BibEntry_match_format_style(style) | |
| # papers <- suppressMessages(do.call(`[.BibEntry`, list(x = bib, | |
| # ...))) | |
| # keys <- unlist(papers$key) | |
| # if (!length(papers)) | |
| # return("") | |
| # if (cite.style == "pandoc") { | |
| # MakePandocCitation(papers, keys, textual, bibpunct, before, | |
| # after) | |
| # } | |
| # else { | |
| # numeric <- "numeric" %in% cite.style | |
| # alphabetic <- "alphabetic" %in% cite.style | |
| # if (cite.style != .cites$sty) | |
| # ClearLabs(cite.style) | |
| # n <- length(papers) | |
| # cited <- names(.cites$indices) | |
| # first <- !(keys %in% cited) | |
| # if (cite.style != "numeric") { | |
| # if (any(!names(bib) %in% names(.cites$labs))) { | |
| # bibstyle <- switch(cite.style, authortitle = "authoryear", | |
| # cite.style) | |
| # bib <- sort(bib, sorting = "none", .bibstyle = bibstyle, | |
| # return.labs = TRUE) | |
| # newinds <- bib$.index | |
| # .labs <- newinds[keys] | |
| # .cites$labs <- c(.cites$labs, newinds) | |
| # } | |
| # else { | |
| # .labs <- .cites$labs[keys] | |
| # } | |
| # } | |
| # else { | |
| # first.ind <- if (!length(.cites$labs)) | |
| # seq_along(papers) | |
| # else which(first | !keys %in% names(.cites$labs)) | |
| # if (length(first.ind)) { | |
| # shorthands <- unlist(papers$shorthand) | |
| # max.ind <- suppressWarnings(sum(!is.na(as.numeric(.cites$labs)))) | |
| # newinds <- seq.int(max.ind + 1L, length.out = length(first.ind)) | |
| # names(newinds) <- keys[first.ind] | |
| # if (length(shorthands)) | |
| # newinds[names(shorthands)] <- shorthands | |
| # .cites$labs <- c(.cites$labs, newinds) | |
| # } | |
| # .labs <- .cites$labs[keys] | |
| # } | |
| # AddCite(keys, !identical(hyperlink, FALSE)) | |
| # year <- match(keys, names(.cites$indices)) | |
| # if (alphabetic || numeric) { | |
| # year <- structure(.labs, names = NULL) | |
| # } | |
| # else { | |
| # year <- structure(unlist(lapply(papers$dateobj, MakeAuthorYear()$DateFormatter)), | |
| # names = NULL) | |
| # if (any(.labs %in% letters)) | |
| # year <- paste0(year, .labs) | |
| # } | |
| # if (textual || (!numeric && !alphabetic)) { | |
| # auth <- character(n) | |
| # authorLists <- lapply(papers, authorList) | |
| # lastAuthors <- NULL | |
| # for (i in seq_len(n)) { | |
| # authors <- authorLists[[i]] | |
| # if (length(authors) > max.names && !(first[i] && | |
| # longnamesfirst)) { | |
| # authors <- authors[seq_len(max.names)] | |
| # authors[length(authors)] <- paste0(authors[length(authors)], | |
| # ", et al.") | |
| # } | |
| # else { | |
| # if (length(authors) > 1L) | |
| # authors[length(authors)] <- paste("and", | |
| # authors[length(authors)]) | |
| # } | |
| # if (length(authors) > 2L) | |
| # auth[i] <- paste(authors, collapse = ", ") | |
| # else auth[i] <- paste(authors, collapse = " ") | |
| # } | |
| # } | |
| # make.hyper <- !identical(hyperlink, FALSE) | |
| # if (textual) { | |
| # if (numeric || alphabetic) { | |
| # result <- paste0(bibpunct[3L], before, year, | |
| # after, bibpunct[4L]) | |
| # } | |
| # else { | |
| # result <- paste0(bibpunct[1L], before, year, | |
| # after, bibpunct[2L]) | |
| # } | |
| # if (super && numeric && (!style %in% c("markdown", | |
| # "html") || !make.hyper)) | |
| # result <- paste0(auth, "^{", result, "}") | |
| # else if (!super || !numeric) | |
| # result <- paste0(auth, " ", result) | |
| # } | |
| # else if (numeric || alphabetic) { | |
| # result <- year | |
| # } | |
| # else { | |
| # result <- paste0(auth, bibpunct[6L], " ", year) | |
| # } | |
| # result <- if (make.hyper) | |
| # MakeCiteHyperlink(result, papers, hyperlink, keys, | |
| # auth, style, first, numeric, alphabetic, super, | |
| # textual, bibpunct, before, after) | |
| # else AddCitationPunct(result, bibpunct, before, after, | |
| # textual, numeric, alphabetic, super) | |
| # result | |
| # } | |
| # }) | |
| # 3: Cite(bib, ..., textual = FALSE, before = before, after = after, | |
| # .opts = .opts) | |
| # 2: Citep(bib, ...) | |
| # 1: citep(bib[["SummarizedExperiment"]]) | |
| ## Reproducibility information | |
| sessionInfo() | |
| # R version 3.4.2 (2017-09-28) | |
| # Platform: x86_64-w64-mingw32/x64 (64-bit) | |
| # Running under: Windows 10 x64 (build 15063) | |
| # Matrix products: default | |
| # locale: | |
| # [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 | |
| # [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C | |
| # [5] LC_TIME=English_United States.1252 | |
| # attached base packages: | |
| # [1] stats graphics grDevices utils datasets methods base | |
| # other attached packages: | |
| # [1] knitcitations_1.0.8 | |
| # loaded via a namespace (and not attached): | |
| # [1] httr_1.3.1 compiler_3.4.2 plyr_1.8.4 R6_2.2.2 magrittr_1.5 | |
| # [6] tools_3.4.2 Rcpp_0.12.13 lubridate_1.6.0 xml2_1.1.1 RefManageR_0.14.20 | |
| # [11] stringi_1.1.5 digest_0.6.12 jsonlite_1.5 stringr_1.2.0 bibtex_0.4.2 |
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