Further fix to vignette generation

DESCRIPTION

@@ -41,6 +41,6 @@ Imports:
 Suggests:
   knitr,
   rmarkdown
-VignetteBuilder: rmarkdown
+VignetteBuilder: knitr
 RoxygenNote: 7.2.3
 LazyData: true

NEWS.md

@@ -5,13 +5,10 @@
 
 # ogrdbstats 0.5.1
 
-* Fixed a problem which prevented haplotyping plots from being produced.
-* Fixed various issues with report formatting
-
-* Added support for recent versions of IgDiscover, which now uses a AIRR format for filtered.tsv
-* Added automatic sequence gapping for the AIRR format column sequence_alignment, should it not be gapped (this was required for IgDIscover support)
-* Fixed the creation of output files where the input file included more than one period in its name
+* Added support for recent versions of IgDiscover, which now uses AIRR format for filtered.tsv.
+* The AIRR format sequence column may now be supplied ungapped, in which case ogrdbstats will gap the sequences before use.
+* Output files will be named correctly even if the input file includes more than one period in its name.
 
 # ogrdbstats 0.5.2
 
-* Fixed an error in the CRAN package checks:  `grobs` must be a single grob or a list of grobs, not a list.
+* Changed the Vignette builder from knitr to rmarkdown to avoid an error during package creation.

vignettes/using_ogrdbstats.Rmd

@@ -289,7 +289,7 @@ rd = suppressMessages(
 barplot_grobs = make_barplot_grobs(rd$input_sequences, rd$genotype_db, rd$inferred_seqs, 
                                    rd$genotype, 'V', rd$calculated_NC)
 base_grobs = make_novel_base_grobs(rd$inferred_seqs, rd$input_sequences, 'V', FALSE)
-gridExtra::grid.arrange(grobs=list(barplot_grobs[3][[1]], base_grobs$end[1][[1]], 
+gridExtra::grid.arrange(grobs=list(barplot_grobs[2][[1]], base_grobs$end[1][[1]], 
                                    base_grobs$conc[1][[1]]),ncol=1)