From fb5564fbeb020ca1c21359e922d4b9e013151dc7 Mon Sep 17 00:00:00 2001 From: Marty Pradere Date: Fri, 12 Jun 2026 15:23:29 -0600 Subject: [PATCH] Fall back to unaligned pedigree plot when kinship2 alignment fails kinship2's QP-based alignment (align=TRUE) can fail with "constraints are inconsistent, no solution!" on deep or looped pedigrees, which aborts the entire Pedigree report. Wrap the plot call in tryCatch so that this specific alignment failure is caught and retried with align=FALSE, letting the report render rather than error out. Any other error is re-raised unchanged. --- .../reports/schemas/study/Pedigree/Pedigree.r | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r index 24259fdfa..684a7d708 100644 --- a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r +++ b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r @@ -300,7 +300,19 @@ if ((nrow(labkey.data) == 0) | (all(is.na(labkey.data$dam)) & all(is.na(labkey.d png(filename="${imgout:png_pedigree}", width = plotWidth, height=plotHeight); par(xpd=TRUE); - plot(ptemp, align=T, width=15, symbolsize=symSize, cex=cexSize, col=fixedPed$colors, mar=c(4.1,3.5,4.1,3.8)) + # kinship2's QP-based alignment (align=TRUE) can fail with "constraints are inconsistent, + # no solution!" on deep/looped pedigrees. Fall back to the unaligned layout in that case so + # the report still renders rather than aborting. + tryCatch( + plot(ptemp, align=TRUE, width=15, symbolsize=symSize, cex=cexSize, col=fixedPed$colors, mar=c(4.1,3.5,4.1,3.8)), + error = function(e) { + # Only the QP alignment failure is recoverable by dropping alignment; re-raise anything else. + if (!grepl("constraints are inconsistent", conditionMessage(e), fixed = TRUE)) + stop(e) + message("Pedigree alignment failed (", conditionMessage(e), "); retrying with align=FALSE.") + plot(ptemp, align=FALSE, width=15, symbolsize=symSize, cex=cexSize, col=fixedPed$colors, mar=c(4.1,3.5,4.1,3.8)) + } + ) mtext("Unknown animals are marked with xxs ## or xxd ## where ## is a randomly generated unique number. This identifier is used only in this plot and is re-generated each time the plot is rendered.", side = 1, font = 3, cex = 0.95) leg.txt <- c("Male", "Female", "Deceased")