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Prevent more 'subscript out of bounds' by using the first citation
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@lcolladotor
lcolladotor committed Dec 12, 2024
1 parent 531c2a7 commit 95b6b15
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32 changes: 16 additions & 16 deletions vignettes/derfinder-quickstart.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ library("RefManageR")
## Write bibliography information
bib <- c(
derfinder = citation("derfinder")[1],
BiocStyle = citation("BiocStyle"),
BiocStyle = citation("BiocStyle")[1],
knitr = citation("knitr")[3],
rmarkdown = citation("rmarkdown")[1],
brainspan = RefManageR::BibEntry(
Expand All @@ -82,36 +82,36 @@ bib <- c(
),
originalder = citation("derfinder")[2],
R = citation(),
IRanges = citation("IRanges"),
sessioninfo = citation("sessioninfo"),
testthat = citation("testthat"),
IRanges = citation("IRanges")[1],
sessioninfo = citation("sessioninfo")[1],
testthat = citation("testthat")[1],
GenomeInfoDb = RefManageR::BibEntry(
bibtype = "manual",
key = "GenomeInfoDb",
author = "Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès",
title = "GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers",
year = 2017, doi = "10.18129/B9.bioc.GenomeInfoDb"
),
GenomicRanges = citation("GenomicRanges"),
ggplot2 = citation("ggplot2"),
GenomicRanges = citation("GenomicRanges")[1],
ggplot2 = citation("ggplot2")[1],
bumphunter = citation("bumphunter")[1],
TxDb.Hsapiens.UCSC.hg19.knownGene = citation("TxDb.Hsapiens.UCSC.hg19.knownGene"),
TxDb.Hsapiens.UCSC.hg19.knownGene = citation("TxDb.Hsapiens.UCSC.hg19.knownGene")[1],
AnnotationDbi = RefManageR::BibEntry(
bibtype = "manual",
key = "AnnotationDbi",
author = "Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li",
title = "AnnotationDbi: Annotation Database Interface",
year = 2017, doi = "10.18129/B9.bioc.AnnotationDbi"
),
BiocParallel = citation("BiocParallel"),
BiocParallel = citation("BiocParallel")[1],
derfinderHelper = citation("derfinderHelper")[1],
GenomicAlignments = citation("GenomicAlignments"),
GenomicFeatures = citation("GenomicFeatures"),
GenomicFiles = citation("GenomicFiles"),
Hmisc = citation("Hmisc"),
qvalue = citation("qvalue"),
Rsamtools = citation("Rsamtools"),
rtracklayer = citation("rtracklayer"),
GenomicAlignments = citation("GenomicAlignments")[1],
GenomicFeatures = citation("GenomicFeatures")[1],
GenomicFiles = citation("GenomicFiles")[1],
Hmisc = citation("Hmisc")[1],
qvalue = citation("qvalue")[1],
Rsamtools = citation("Rsamtools")[1],
rtracklayer = citation("rtracklayer")[1],
S4Vectors = RefManageR::BibEntry(
bibtype = "manual", key = "S4Vectors",
author = "Hervé Pagès and Michael Lawrence and Patrick Aboyoun",
Expand All @@ -125,7 +125,7 @@ bib <- c(
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"),
derfinderData = citation("derfinderData")[1],
RefManageR = citation("RefManageR")[1]
)
```
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32 changes: 16 additions & 16 deletions vignettes/derfinder-users-guide.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ library("RefManageR")
## Write bibliography information
bib <- c(
derfinder = citation("derfinder")[1],
BiocStyle = citation("BiocStyle"),
BiocStyle = citation("BiocStyle")[1],
knitr = citation("knitr")[3],
rmarkdown = citation("rmarkdown")[1],
brainspan = RefManageR::BibEntry(
Expand All @@ -48,36 +48,36 @@ bib <- c(
),
originalder = citation("derfinder")[2],
R = citation(),
IRanges = citation("IRanges"),
sessioninfo = citation("sessioninfo"),
testthat = citation("testthat"),
IRanges = citation("IRanges")[1],
sessioninfo = citation("sessioninfo")[1],
testthat = citation("testthat")[1],
GenomeInfoDb = RefManageR::BibEntry(
bibtype = "manual",
key = "GenomeInfoDb",
author = "Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès",
title = "GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers",
year = 2017, doi = "10.18129/B9.bioc.GenomeInfoDb"
),
GenomicRanges = citation("GenomicRanges"),
ggplot2 = citation("ggplot2"),
GenomicRanges = citation("GenomicRanges")[1],
ggplot2 = citation("ggplot2")[1],
bumphunter = citation("bumphunter")[1],
TxDb.Hsapiens.UCSC.hg19.knownGene = citation("TxDb.Hsapiens.UCSC.hg19.knownGene"),
TxDb.Hsapiens.UCSC.hg19.knownGene = citation("TxDb.Hsapiens.UCSC.hg19.knownGene")[1],
AnnotationDbi = RefManageR::BibEntry(
bibtype = "manual",
key = "AnnotationDbi",
author = "Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li",
title = "AnnotationDbi: Annotation Database Interface",
year = 2017, doi = "10.18129/B9.bioc.AnnotationDbi"
),
BiocParallel = citation("BiocParallel"),
BiocParallel = citation("BiocParallel")[1],
derfinderHelper = citation("derfinderHelper")[1],
GenomicAlignments = citation("GenomicAlignments"),
GenomicFeatures = citation("GenomicFeatures"),
GenomicFiles = citation("GenomicFiles"),
Hmisc = citation("Hmisc"),
qvalue = citation("qvalue"),
Rsamtools = citation("Rsamtools"),
rtracklayer = citation("rtracklayer"),
GenomicAlignments = citation("GenomicAlignments")[1],
GenomicFeatures = citation("GenomicFeatures")[1],
GenomicFiles = citation("GenomicFiles")[1],
Hmisc = citation("Hmisc")[1],
qvalue = citation("qvalue")[1],
Rsamtools = citation("Rsamtools")[1],
rtracklayer = citation("rtracklayer")[1],
S4Vectors = RefManageR::BibEntry(
bibtype = "manual", key = "S4Vectors",
author = "Hervé Pagès and Michael Lawrence and Patrick Aboyoun",
Expand All @@ -91,7 +91,7 @@ bib <- c(
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"),
derfinderData = citation("derfinderData")[1],
RefManageR = citation("RefManageR")[1]
)
```
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