Tutorial crashes at addMutTime()

[jeff-mandell]

Hi, your example code leads to an error:

library(MutationTimeR)
data(MutationTimeR)
mt = mutationTime(vcf, bb, clusters = clusters, n.boot = 10)

addMutTime(vcf, mt$V)

The message is:

Error in .combine_DFrame_rows(x, objects, strict.colnames = TRUE, use.names = use.names, :
the objects to combine must be DFrame objects or derivatives
In addition: Warning messages:
1: Not a validObject(): no slot of name "elementType" for this object of class "GRanges"
2: Not a validObject(): no slot of name "elementType" for this object of class "GRanges"

The following worked as a workaround:

# Re-implementMutationTimeR::addMutTime
i = info(header(vcf))
tmp = as.data.frame(i)
tmp$Number = as.character(tmp$Number)
i = DataFrame(tmp)
info(header(vcf)) <- rbind(i, MutationTimeR:::mtHeader()) # calling internal function
info(vcf) <- cbind(info(vcf), mt$V)

This doesn't resolve the various warnings for elementType/GRanges throughout package functions, probably due to changes in the GRanges package.

I'm running Bioconductor 3.18. Here's session info:

─ Session info ────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.1 (2023-06-16)
os macOS Sonoma 14.0
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-12-01
rstudio 2023.09.1+494 Desert Sunflower (desktop)
pandoc NA

─ Packages ────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
AnnotationDbi 1.62.2 2023-07-02 [1] Bioconductor
Biobase * 2.60.0 2023-05-08 [1] Bioconductor
BiocFileCache 2.8.0 2023-05-08 [1] Bioconductor
BiocGenerics * 0.46.0 2023-06-04 [1] Bioconductor
BiocIO 1.10.0 2023-05-08 [1] Bioconductor
BiocParallel 1.34.2 2023-05-28 [1] Bioconductor
biomaRt 2.56.1 2023-06-11 [1] Bioconductor
Biostrings * 2.68.1 2023-05-21 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
BSgenome 1.68.0 2023-05-08 [1] Bioconductor
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
curl 5.1.0 2023-10-02 [1] CRAN (R 4.3.1)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
dbplyr 2.3.4 2023-09-26 [1] CRAN (R 4.3.1)
DelayedArray 0.26.7 2023-07-30 [1] Bioconductor
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0)
dplyr 1.1.3 2023-09-03 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.36.4 2023-10-02 [1] Bioconductor
GenomeInfoDbData 1.2.10 2023-10-05 [1] Bioconductor
GenomicAlignments 1.36.0 2023-05-08 [1] Bioconductor
GenomicFeatures 1.52.2 2023-08-27 [1] Bioconductor
GenomicRanges * 1.52.0 2023-05-08 [1] Bioconductor
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.6 2023-08-10 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
IRanges * 2.34.1 2023-07-02 [1] Bioconductor
KEGGREST 1.40.1 2023-09-29 [1] Bioconductor
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.1)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
Matrix 1.5-4.1 2023-05-18 [1] CRAN (R 4.3.1)
MatrixGenerics * 1.12.3 2023-07-30 [1] Bioconductor
matrixStats * 1.0.0 2023-06-02 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mg14 0.0.6 2023-12-01 [1] Github (mg14/mg14@ee1aecb)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
MutationTimeR * 1.00.2 2023-12-01 [1] Github (e4e266a)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.2 2023-06-26 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.3.3 2023-09-22 [1] CRAN (R 4.3.1)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1)
processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.3.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0)
RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
Rsamtools * 2.16.0 2023-06-04 [1] Bioconductor
RSQLite 2.3.1 2023-04-03 [1] CRAN (R 4.3.0)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
rtracklayer 1.60.1 2023-08-20 [1] Bioconductor
S4Arrays 1.2.0 2023-10-26 [1] Bioconductor
S4Vectors * 0.38.2 2023-09-24 [1] Bioconductor
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shiny 1.7.5 2023-08-12 [1] CRAN (R 4.3.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
SummarizedExperiment * 1.30.2 2023-06-11 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis 2.2.2 2023-07-06 [1] CRAN (R 4.3.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
VariantAnnotation * 1.46.0 2023-06-04 [1] Bioconductor
vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.0)
VGAM 1.1-9 2023-09-19 [1] CRAN (R 4.3.1)
XML 3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
xml2 1.3.5 2023-07-06 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector * 0.40.0 2023-05-08 [1] Bioconductor
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
zlibbioc 1.46.0 2023-05-08 [1] Bioconductor

[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

[jeff-mandell]

Hi @mg14, just drawing attention to this bug that crashes the tutorial workflow.