ArchR
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20 hours ago •
GreenleafLab
GreenleafLab
AddDoubletScore - TileMatrix/chr5/rowSums does not exist
I am having some issues with AddDoubletScore(), I have used before on these samples however I am now getting this error message indicating there is an issue with the HDF5 file, which I have never had before and have processed them no problem.
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2024-10-23 13:59:52.868972 : ERROR Found in addIterativeLSI for Cis_4weeksOFF (5 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores-435b5c4d2e0-Date-2024-10-23_Time-13-30-55.887278.log
<simpleError in h5read(ArrowFiles[y], paste0(useMatrix, "/", seqnames[x], "/rowSums")): Object 'TileMatrix/chr5/rowSums' does not exist in this HDF5 file.>
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Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above
Session information is as follows:
─ Session info ─────────────────────────────────────────────────────────────
setting value
version R version 4.3.3 (2024-02-29)
os macOS 15.0.1
system x86_64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/London
date 2024-10-23
rstudio 2024.09.0+375 Cranberry Hibiscus (desktop)
pandoc NA
─ Packages ─────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [1] CRAN (R 4.3.3)
AnnotationDbi * 1.64.1 2023-11-03 [1] Bioconductor
AnnotationFilter * 1.26.0 2023-10-24 [1] Bioconductor
ArchR * 1.0.2 2024-10-23 [1] Github (GreenleafLab/ArchR@6a0ec0c)
Biobase * 2.62.0 2023-10-24 [1] Bioconductor
BiocFileCache 2.10.2 2024-03-27 [1] Bioconductor 3.18 (R 4.3.3)
BiocGenerics * 0.48.1 2023-11-01 [1] Bioconductor
BiocIO * 1.12.0 2023-10-24 [1] Bioconductor
BiocManager * 1.30.23 2024-05-04 [1] CRAN (R 4.3.2)
BiocParallel 1.36.0 2023-10-24 [1] Bioconductor
biomaRt 2.58.2 2024-01-30 [1] Bioconductor 3.18 (R 4.3.2)
Biostrings * 2.70.3 2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
bit 4.5.0 2024-09-20 [1] CRAN (R 4.3.3)
bit64 4.5.2 2024-09-22 [1] CRAN (R 4.3.3)
bitops 1.0-9 2024-10-03 [1] CRAN (R 4.3.3)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
BSgenome * 1.70.2 2024-02-08 [1] Bioconductor 3.18 (R 4.3.2)
BSgenome.Hsapiens.UCSC.hg38 * 1.4.5 2024-05-01 [1] Bioconductor
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.3.3)
Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.3.0)
callr 3.7.6 2024-03-25 [1] CRAN (R 4.3.2)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.3.3)
cluster 2.1.6 2023-12-01 [2] CRAN (R 4.3.3)
codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.3)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.3.3)
cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.3.2)
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.3.3)
curl 5.2.3 2024-09-20 [1] CRAN (R 4.3.3)
data.table * 1.16.2 2024-10-10 [1] CRAN (R 4.3.3)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.3.3)
dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.3.2)
DelayedArray 0.28.0 2023-10-24 [1] Bioconductor
deldir 2.0-4 2024-02-28 [1] CRAN (R 4.3.2)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.0)
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.37 2024-08-19 [1] CRAN (R 4.3.3)
doParallel * 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.3.0)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
EnsDb.Hsapiens.v86 * 2.99.0 2024-05-14 [1] Bioconductor
ensembldb * 2.26.1 2024-04-15 [1] Bioconductor 3.18 (R 4.3.3)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.0)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.3.3)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.3.3)
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.3.0)
fitdistrplus 1.2-1 2024-07-12 [1] CRAN (R 4.3.3)
foreach * 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
fs 1.6.4 2024-04-25 [1] CRAN (R 4.3.2)
future 1.34.0 2024-07-29 [1] CRAN (R 4.3.3)
future.apply 1.11.2 2024-03-28 [1] CRAN (R 4.3.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.38.8 2024-03-15 [1] Bioconductor 3.18 (R 4.3.3)
GenomeInfoDbData 1.2.11 2024-05-01 [1] Bioconductor
GenomicAlignments 1.38.2 2024-01-16 [1] Bioconductor 3.18 (R 4.3.2)
GenomicFeatures * 1.54.4 2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
GenomicRanges * 1.54.1 2023-10-29 [1] Bioconductor
ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.3.3)
ggrepel 0.9.6 2024-09-07 [1] CRAN (R 4.3.3)
ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.3.2)
globals 0.16.3 2024-03-08 [1] CRAN (R 4.3.2)
glue 1.8.0 2024-09-30 [1] CRAN (R 4.3.3)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.0)
gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable * 0.3.5 2024-04-22 [1] CRAN (R 4.3.2)
gtools * 3.9.5 2023-11-20 [1] CRAN (R 4.3.0)
harmony 1.2.0 2024-05-01 [1] Github (immunogenomics/harmony@f054b03)
hdf5r * 1.3.11 2024-07-07 [1] CRAN (R 4.3.3)
hexbin * 1.28.4 2024-09-04 [1] CRAN (R 4.3.3)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.2)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.0)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.2)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.3.0)
igraph 2.0.3 2024-03-13 [1] CRAN (R 4.3.2)
IRanges * 2.36.0 2023-10-24 [1] Bioconductor
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.3)
iterators * 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
jsonlite 1.8.9 2024-09-20 [1] CRAN (R 4.3.3)
KEGGREST 1.42.0 2023-10-24 [1] Bioconductor
KernSmooth 2.23-22 2023-07-10 [2] CRAN (R 4.3.3)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.0)
lattice 0.22-5 2023-10-24 [2] CRAN (R 4.3.3)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.3.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.0)
listenv 0.9.1 2024-01-29 [1] CRAN (R 4.3.2)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.3.0)
magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
MASS 7.3-60.0.1 2024-01-13 [2] CRAN (R 4.3.3)
Matrix * 1.6-5 2024-01-11 [1] CRAN (R 4.3.3)
MatrixGenerics * 1.14.0 2023-10-24 [1] Bioconductor
matrixStats * 1.4.1 2024-09-08 [1] CRAN (R 4.3.3)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
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)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.2)
nabor * 0.5.0 2018-07-11 [1] CRAN (R 4.3.0)
nlme 3.1-164 2023-11-27 [2] CRAN (R 4.3.3)
parallelly 1.38.0 2024-07-27 [1] CRAN (R 4.3.3)
patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.3.0)
pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.3.3)
plotly 4.10.4 2024-01-13 [1] CRAN (R 4.3.0)
plyr * 1.8.9 2023-10-02 [1] CRAN (R 4.3.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
polyclip 1.10-7 2024-07-23 [1] CRAN (R 4.3.3)
presto 1.0.0 2024-05-01 [1] Github (immunogenomics/presto@7636b3d)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.0)
processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.2)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.3.0)
progressr 0.14.0 2023-08-10 [1] CRAN (R 4.3.0)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.3.2)
ProtGenerics 1.34.0 2023-10-24 [1] Bioconductor
ps 1.7.7 2024-07-02 [1] CRAN (R 4.3.3)
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)
RANN 2.6.1 2019-01-08 [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 * 1.0.13 2024-07-17 [1] CRAN (R 4.3.3)
RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.3.2)
RCurl 1.98-1.16 2024-07-11 [1] CRAN (R 4.3.3)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.2)
renv 1.0.7 2024-04-11 [1] CRAN (R 4.3.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
reticulate 1.37.0 2024-05-21 [1] CRAN (R 4.3.3)
rhandsontable 0.3.8 2021-05-27 [1] CRAN (R 4.3.0)
rhdf5 * 2.46.1 2023-11-29 [1] Bioconductor
rhdf5filters 1.14.1 2023-11-06 [1] Bioconductor
Rhdf5lib 1.24.2 2024-02-07 [1] Bioconductor 3.18 (R 4.3.2)
rjson 0.2.23 2024-09-16 [1] CRAN (R 4.3.3)
rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.3)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.3.0)
Rsamtools 2.18.0 2023-10-24 [1] Bioconductor
RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.3.3)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.2)
rtracklayer * 1.62.0 2023-10-24 [1] Bioconductor
Rtsne 0.17 2023-12-07 [1] CRAN (R 4.3.0)
S4Arrays 1.2.1 2024-03-06 [1] Bioconductor 3.18 (R 4.3.3)
S4Vectors * 0.40.2 2023-11-23 [1] Bioconductor
scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.0)
scattermore 1.2 2023-06-12 [1] CRAN (R 4.3.0)
sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
Seurat * 4.3.0 2022-11-18 [1] CRAN (R 4.3.3)
SeuratObject * 5.0.2 2024-05-08 [1] CRAN (R 4.3.2)
shiny 1.9.1 2024-08-01 [1] CRAN (R 4.3.3)
shinythemes 1.2.0 2021-01-25 [1] CRAN (R 4.3.0)
sp 2.1-4 2024-04-30 [1] CRAN (R 4.3.2)
spam 2.10-0 2023-10-23 [1] CRAN (R 4.3.0)
SparseArray 1.2.4 2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
spatstat.data 3.1-2 2024-06-21 [1] CRAN (R 4.3.3)
spatstat.explore 3.3-1 2024-07-15 [1] CRAN (R 4.3.3)
spatstat.geom 3.3-2 2024-07-15 [1] CRAN (R 4.3.3)
spatstat.random 3.3-1 2024-07-15 [1] CRAN (R 4.3.3)
spatstat.sparse 3.1-0 2024-06-21 [1] CRAN (R 4.3.3)
spatstat.univar 3.0-0 2024-06-28 [1] CRAN (R 4.3.3)
spatstat.utils 3.1-0 2024-08-17 [1] CRAN (R 4.3.3)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.3.2)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.3.0)
SummarizedExperiment * 1.32.0 2023-10-24 [1] Bioconductor
survival 3.5-8 2024-02-14 [2] CRAN (R 4.3.3)
tensor 1.5 2012-05-05 [1] CRAN (R 4.3.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.3.2)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.2)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis * 3.0.0 2024-07-29 [1] CRAN (R 4.3.3)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.0)
uwot 0.2.2 2024-04-21 [1] CRAN (R 4.3.2)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.0)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
withr 3.0.1 2024-07-31 [1] CRAN (R 4.3.3)
XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.3.3)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector * 0.42.0 2023-10-24 [1] Bioconductor
yaml 2.3.10 2024-07-26 [1] CRAN (R 4.3.3)
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zoo 1.8-12 2023-04-13 [1] CRAN (R 4.3.0)
[1] /Users/shamer/Library/R/x86_64/4.3/library
[2] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
Hi @shamer3! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
