[error] addDoubletScores function: "addIterativeLSI" - tutorial data

[jinhys]

Describe the bug
Hi. According to the log file, I keep getting an error which is found in addIterativeLSI for one of Arrow files generated using the tutorial dataset when I run the addDoubletScores function. As requested, I included the details of this error below.
Thanks in advance for your help!

Attach your log file
ArchR-addDoubletScores-2c496e3354b1-Date-2023-12-22_Time-14-41-33.log

To Reproduce
I used the tutorial dataset using this command as mentioned on the ArchR tutorial web page included below. According to the attached log file, I get an error on the first sample (i.e., scATAC_BMMC_R1).

• tutorial dataset used:
  getTutorialData("Hematopoiesis")

• tutorial web page:
  https://www.archrproject.com/articles/Articles/tutorial.html#getting-set-up-1

Expected behavior
These are the expectations:

• Get the inference results on the potential doublets (using the addDoubletScores function)
• Based on the step above, run the following steps such as the addIterativeLSI function, etc.

[rcorces]

Hi @jinhys! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.

__In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[hira-anis]

Hey. I have the same error showing up. Please note that i have run ArchR on the same dataset previously and it had worked. Here is the error and the sessioninfo along with output of the logfile. I get the error when i try to run DoubletScores.
Please note, i have tried installing RSpectre, tried using 1 thread and nothing has worked so far. Please help me..

The error :

---

2024-02-22 17:07:55 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log

<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>

---

---

2024-02-22 17:07:55 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log

<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>

---

---

2024-02-22 17:07:55 : ERROR Found in addIterativeLSI for Sample1 (1 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log

<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>

---

Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above

Here is the sessioninfo()

─ Session info ───────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.3 (2023-03-15)
os macOS Big Sur 11.0.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-02-22
rstudio 2023.03.0+386 Cherry Blossom (desktop)
pandoc 2.11.3.2 @ /usr/local/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
ArchR * 1.0.3 2023-11-08 [1] Github (65968a4)
Biobase * 2.58.0 2022-11-01 [1] Bioconductor
BiocGenerics * 0.44.0 2022-11-01 [1] Bioconductor
BiocIO 1.8.0 2022-11-01 [1] Bioconductor
BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.2.0)
BiocParallel 1.32.6 2023-03-17 [1] Bioconductor
Biostrings * 2.66.0 2022-11-01 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
BSgenome * 1.66.3 2023-02-16 [1] Bioconductor
BSgenome.Hsapiens.UCSC.hg38 * 1.4.5 2023-07-11 [1] Bioconductor
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.2.0)
Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.2.3)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.2.3)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.3)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
data.table * 1.15.0 2024-01-30 [1] CRAN (R 4.2.3)
DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
digest 0.6.34 2024-01-11 [1] CRAN (R 4.2.3)
dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.2.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.2.3)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
GenomeInfoDb * 1.34.9 2023-02-02 [1] Bioconductor
GenomeInfoDbData 1.2.9 2023-03-26 [1] Bioconductor
GenomicAlignments 1.34.1 2023-03-09 [1] Bioconductor
GenomicRanges * 1.50.2 2022-12-16 [1] Bioconductor
ggplot2 * 3.4.4 2023-10-12 [1] CRAN (R 4.2.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.2.3)
gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.2.0)
gtable * 0.3.4 2023-08-21 [1] CRAN (R 4.2.0)
gtools * 3.9.5 2023-11-20 [1] CRAN (R 4.2.3)
htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.2.3)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.2.3)
httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.2.3)
IRanges * 2.32.0 2022-11-01 [1] Bioconductor
irlba * 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.2.3)
lattice 0.22-5 2023-10-24 [1] CRAN (R 4.2.3)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.2.3)
magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
Matrix * 1.6-4 2023-11-30 [1] CRAN (R 4.2.0)
MatrixGenerics * 1.10.0 2022-11-01 [1] Bioconductor
matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0)
pkgbuild 1.4.3 2023-12-10 [1] CRAN (R 4.2.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.2.3)
plyr * 1.8.9 2023-10-02 [1] CRAN (R 4.2.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.2.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.2.0)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp * 1.0.12 2024-01-09 [1] CRAN (R 4.2.3)
RcppArmadillo * 0.12.6.6.1 2023-12-04 [1] CRAN (R 4.2.0)
RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.2.3)
remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.2.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0)
rhdf5 * 2.42.1 2023-04-07 [1] Bioconductor
rhdf5filters 1.10.1 2023-03-24 [1] Bioconductor
Rhdf5lib 1.20.0 2022-11-01 [1] Bioconductor
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.2.3)
Rsamtools * 2.14.0 2022-11-01 [1] Bioconductor
RSpectra * 0.16-1 2022-04-24 [1] CRAN (R 4.2.0)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.2.0)
rtracklayer * 1.58.0 2022-11-01 [1] Bioconductor
S4Vectors * 0.36.2 2023-02-26 [1] Bioconductor
scales 1.3.0 2023-11-28 [1] CRAN (R 4.2.3)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shiny 1.8.0 2023-11-17 [1] CRAN (R 4.2.3)
sparseMatrixStats * 1.10.0 2022-11-01 [1] Bioconductor
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.2.3)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.2.3)
SummarizedExperiment * 1.28.0 2022-11-01 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
usethis * 2.2.2 2023-07-06 [1] CRAN (R 4.2.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.2.3)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.2.3)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.2.3)
XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.2.3)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
XVector * 0.38.0 2022-11-01 [1] Bioconductor
yaml 2.3.8 2023-12-11 [1] CRAN (R 4.2.3)
zlibbioc 1.44.0 2022-11-01 [1] Bioconductor

[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library

──────────────────────────────────────────────────────────────────────────────────────

And here is the output of the logfile

       ___      .______        ______  __    __  .______      
      /   \     |   _  \      /      ||  |  |  | |   _  \     
     /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
    /  /_\  \   |      /     |  |     |   __   | |      /     
   /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
  /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|

Logging With ArchR!

Start Time : 2024-02-22 17:07:46

------- ArchR Info

ArchRThreads = 1
ArchRGenome = Hg38

------- System Info

Computer OS = unix

------- Session Info

R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods
[9] base

other attached packages:
[1] Rsamtools_2.14.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[3] BSgenome_1.66.3 rtracklayer_1.58.0
[5] Biostrings_2.66.0 XVector_0.38.0
[7] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[9] Biobase_2.58.0 RcppArmadillo_0.12.6.6.1
[11] Rcpp_1.0.12 GenomicRanges_1.50.2
[13] GenomeInfoDb_1.34.9 IRanges_2.32.0
[15] S4Vectors_0.36.2 BiocGenerics_0.44.0
[17] sparseMatrixStats_1.10.0 MatrixGenerics_1.10.0
[19] matrixStats_1.2.0 data.table_1.15.0
[21] stringr_1.5.1 plyr_1.8.9
[23] magrittr_2.0.3 ggplot2_3.4.4
[25] gtable_0.3.4 gtools_3.9.5
[27] gridExtra_2.3 devtools_2.4.5
[29] usethis_2.2.2 ArchR_1.0.3
[31] RSpectra_0.16-1 irlba_2.3.5.1
[33] Matrix_1.6-4

loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.6.3 tools_4.2.3
[4] profvis_0.3.8 utf8_1.2.4 R6_2.5.1
[7] colorspace_2.1-0 rhdf5filters_1.10.1 urlchecker_1.0.1
[10] withr_3.0.0 tidyselect_1.2.0 compiler_4.2.3
[13] cli_3.6.2 Cairo_1.6-2 DelayedArray_0.24.0
[16] scales_1.3.0 digest_0.6.34 pkgconfig_2.0.3
[19] htmltools_0.5.7 sessioninfo_1.2.2 fastmap_1.1.1
[22] htmlwidgets_1.6.4 rlang_1.1.3 rstudioapi_0.15.0
[25] shiny_1.8.0 BiocIO_1.8.0 generics_0.1.3
[28] BiocParallel_1.32.6 dplyr_1.1.4 RCurl_1.98-1.14
[31] GenomeInfoDbData_1.2.9 munsell_0.5.0 Rhdf5lib_1.20.0
[34] fansi_1.0.6 lifecycle_1.0.4 yaml_2.3.8
[37] stringi_1.8.3 zlibbioc_1.44.0 pkgbuild_1.4.3
[40] parallel_4.2.3 promises_1.2.1 crayon_1.5.2
[43] miniUI_0.1.1.1 lattice_0.22-5 pillar_1.9.0
[46] rjson_0.2.21 codetools_0.2-19 pkgload_1.3.4
[49] XML_3.99-0.16.1 glue_1.7.0 remotes_2.4.2.1
[52] BiocManager_1.30.22 vctrs_0.6.5 httpuv_1.6.14
[55] purrr_1.0.2 cachem_1.0.8 mime_0.12
[58] xtable_1.8-4 restfulr_0.0.15 later_1.3.2
[61] tibble_3.2.1 GenomicAlignments_1.34.1 memoise_2.0.1
[64] ellipsis_0.3.2

------- Log Info

2024-02-22 17:07:46 : addDoubletScores Input-Parameters, Class = list

addDoubletScores Input-Parameters$input: length = 5
[1] "Sample1.arrow" "Sample2.arrow" "Sample3.arrow"
[4] "Sample4.arrow" "Sample5.arrow"

addDoubletScores Input-Parameters$useMatrix: length = 1
[1] "TileMatrix"

addDoubletScores Input-Parameters$k: length = 1
[1] 10

addDoubletScores Input-Parameters$nTrials: length = 1
[1] 5

addDoubletScores Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6

addDoubletScores Input-Parameters$LSIMethod: length = 1
[1] 1

addDoubletScores Input-Parameters$scaleDims: length = 1
[1] FALSE

addDoubletScores Input-Parameters$corCutOff: length = 1
[1] 0.75

addDoubletScores Input-Parameters$knnMethod: length = 1
[1] "UMAP"

addDoubletScores Input-Parameters$outDir: length = 1
[1] "QualityControl"

addDoubletScores Input-Parameters$threads: length = 1
[1] 1

addDoubletScores Input-Parameters$force: length = 1
[1] FALSE

addDoubletScores Input-Parameters$parallelParam: length = 0
NULL

addDoubletScores Input-Parameters$verbose: length = 1
[1] TRUE

addDoubletScores Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"

2024-02-22 17:07:46 : Batch Execution w/ safelapply!, 0 mins elapsed.
2024-02-22 17:07:46 : Sample1(1 of 5) : Computing Doublet Statistics, 0 mins elapsed.
2024-02-22 17:07:46 : Running IterativeLSI, 0.004 mins elapsed.

2024-02-22 17:07:46 : IterativeLSI Input-Parameters, Class = list

IterativeLSI Input-Parameters$ArchRProj: length = 1

IterativeLSI Input-Parameters$useMatrix: length = 1
[1] "TileMatrix"

IterativeLSI Input-Parameters$name: length = 1
[1] "IterativeLSI"

IterativeLSI Input-Parameters$iterations: length = 1
[1] 2

IterativeLSI Input-Parameters$firstSelection: length = 1
[1] "top"

IterativeLSI Input-Parameters$depthCol: length = 1
[1] "nFrags"

IterativeLSI Input-Parameters$varFeatures: length = 1
[1] 25000

IterativeLSI Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6

IterativeLSI Input-Parameters$LSIMethod: length = 1
[1] 1

IterativeLSI Input-Parameters$scaleDims: length = 1
[1] FALSE

IterativeLSI Input-Parameters$corCutOff: length = 1
[1] 0.75

IterativeLSI Input-Parameters$binarize: length = 1
[1] TRUE

IterativeLSI Input-Parameters$outlierQuantiles: length = 0
NULL

IterativeLSI Input-Parameters$filterBias: length = 1
[1] FALSE

IterativeLSI Input-Parameters$sampleCellsPre: length = 1
[1] 10000

IterativeLSI Input-Parameters$projectCellsPre: length = 1
[1] FALSE

IterativeLSI Input-Parameters$sampleCellsFinal: length = 0
NULL

IterativeLSI Input-Parameters$selectionMethod: length = 1
[1] "var"

IterativeLSI Input-Parameters$scaleTo: length = 1
[1] 10000

IterativeLSI Input-Parameters$totalFeatures: length = 1
[1] 5e+05

IterativeLSI Input-Parameters$filterQuantile: length = 1
[1] 0.995

IterativeLSI Input-Parameters$excludeChr: length = 0
NULL

IterativeLSI Input-Parameters$keep0lsi: length = 1
[1] FALSE

IterativeLSI Input-Parameters$saveIterations: length = 1
[1] FALSE

IterativeLSI Input-Parameters$nPlot: length = 1
[1] 10000

IterativeLSI Input-Parameters$outDir: length = 1
[1] "/Users/hiraanis/Desktop/PhD/Hira-multiome/ArchR_analysis/tmp/tmp-2ee34c5ab8c5-Date-2024-02-22_Time-17-07-46"

IterativeLSI Input-Parameters$threads: length = 1
[1] 1

IterativeLSI Input-Parameters$seed: length = 1
[1] 1

IterativeLSI Input-Parameters$verbose: length = 1
[1] FALSE

IterativeLSI Input-Parameters$force: length = 1
[1] TRUE

IterativeLSI Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"

2024-02-22 17:07:46 : Computing Total Across All Features, 0 mins elapsed.
2024-02-22 17:07:47 : Computing Top Features, 0.023 mins elapsed.
###########
2024-02-22 17:07:48 : Running LSI (1 of 2) on Top Features, 0.038 mins elapsed.
###########
2024-02-22 17:07:48 : Creating Partial Matrix, 0.038 mins elapsed.
2024-02-22 17:07:54 : Computing LSI, 0.13 mins elapsed.

2024-02-22 17:07:54 : LSI Parameters, Class = list

LSI Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

LSI Parameters$mat: nRows = 25000, nCols = 1788
LSI Parameters$mat: NonZeroEntries = 10513861, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1
[1,] 1 1
[2,] 1 1
[3,] . 1
[4,] 1 1
[5,] 1 1
Sample1#CCCAGTTTCTTGATGA-1 Sample1#CCGCAAATCGATTATG-1
[1,] 1 .
[2,] 1 .
[3,] . 1
[4,] 1 1
[5,] 1 1
Sample1#CCAAGTTAGCCACATG-1
[1,] 1
[2,] 1
[3,] .
[4,] .
[5,] 1

LSI Parameters$LSIMethod: length = 1
[1] 1

LSI Parameters$scaleTo: length = 1
[1] 10000

LSI Parameters$nDimensions: length = 1
[1] 30

LSI Parameters$binarize: length = 1
[1] TRUE

LSI Parameters$outlierQuantiles: length = 0
NULL

LSI Parameters$keep0lsi: length = 1
[1] FALSE

LSI Parameters$seed: length = 1
[1] 1

LSI Parameters$verbose: length = 1
[1] FALSE

LSI Parameters$tstart: length = 1
[1] "2024-02-22 17:07:46 EST"

LSI Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"

2024-02-22 17:07:54 : Running LSI, Input Matrix = 0.126 GB, 0.132 mins elapsed.
2024-02-22 17:07:54 : Binarizing Matrix, 0.132 mins elapsed.
2024-02-22 17:07:54 : Computing Term Frequency, 0.133 mins elapsed.
2024-02-22 17:07:54 : Removing 0 Sum Rows, 0.133 mins elapsed.
2024-02-22 17:07:54 : Computing Inverse Document Frequency, 0.135 mins elapsed.
2024-02-22 17:07:54 : Computing TF-IDF Matrix, 0.135 mins elapsed.
2024-02-22 17:07:55 : Computing SVD using irlba, 0.145 mins elapsed.

---

2024-02-22 17:07:55 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log

<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>

2024-02-22 17:07:55 : errorList, Class = list

errorList$mat: nRows = 25000, nCols = 1788
errorList$mat: NonZeroEntries = 10513861, EntryRange = [ 6.05921387773296e-05 , 0.019743480836276 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1
[1,] 1.003779e-04 9.683009e-05
[2,] 8.973452e-05 8.656289e-05
[3,] . 9.005340e-05
[4,] 7.383138e-05 7.122185e-05
[5,] 9.618878e-05 9.278904e-05
Sample1#CCCAGTTTCTTGATGA-1 Sample1#CCGCAAATCGATTATG-1
[1,] 1.026353e-04 .
[2,] 9.175255e-05 .
[3,] . 9.387405e-05
[4,] 7.549177e-05 7.424354e-05
[5,] 9.835197e-05 9.672575e-05
Sample1#CCAAGTTAGCCACATG-1
[1,] 9.992355e-05
[2,] 8.932835e-05
[3,] .
[4,] .
[5,] 9.575340e-05

errorList$colSm: length = 1
[1] "Error with colSm!"

errorList$idf: length = 1
[1] "Error with idf!"

errorList$V: length = 1
[1] "Error with V!"

errorList$matSVD: length = 1
[1] "Error with matSVD!"

errorList$out: length = 1
[1] "Error with out!"

---

---

2024-02-22 17:07:55 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log

<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>

2024-02-22 17:07:55 : errorList, Class = list

errorList$: length = 1

1 function (name)
2 .Internal(args(name))

errorList$ArrowFiles: length = 1
[1] "Sample1.arrow"

errorList$useMatrix: length = 1
[1] "TileMatrix"

errorList$cellNames: length = 1788
[1] "Sample1#GTCTTGCTCATGGTTA-1" "Sample1#GACCTTTGTGTCCTGC-1"
[3] "Sample1#CCCAGTTTCTTGATGA-1" "Sample1#CCGCAAATCGATTATG-1"
[5] "Sample1#CCAAGTTAGCCACATG-1" "Sample1#AACCTAATCTTGTCCA-1"

errorList$cellDepth: length = 1788
Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1
4.982931 4.980317
Sample1#CCCAGTTTCTTGATGA-1Sample1#CCGCAAATCGATTATG-1
4.965225 4.961654
Sample1#CCAAGTTAGCCACATG-1 Sample1#AACCTAATCTTGTCCA-1
4.961169 4.958750

errorList$sampleNames: length = 1788
[1] "Sample1" "Sample1" "Sample1" "Sample1" "Sample1"
[6] "Sample1"

errorList$dimsToUse: length = 30
[1] 1 2 3 4 5 6

errorList$binarize: length = 1
[1] TRUE

errorList$outlierQuantiles: length = 0
NULL

errorList$keep0lsi: length = 1
[1] FALSE

errorList$LSIMethod: length = 1
[1] 1

errorList$scaleTo: length = 1
[1] 10000

errorList$sampleCells: length = 0
NULL

errorList$projectAll: length = 0
logical(0)

errorList$threads: length = 1
[1] 1

errorList$seed: length = 1
[1] 1

errorList$useIndex: length = 1
[1] FALSE

errorList$tstart: length = 1
[1] "2024-02-22 17:07:46 EST"

errorList$verbose: length = 1
[1] FALSE

errorList$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"

errorList$outLSI: length = 1
[1] "Error with outLSI!"

errorList$matSVD: length = 1
[1] "Error with matSVD!"

---

---

2024-02-22 17:07:55 : ERROR Found in addIterativeLSI for Sample1 (1 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log

<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>

2024-02-22 17:07:55 : errorList, Class = list

errorList$ArrowFile: length = 1
[1] "Sample1.arrow"

---

[hira-anis]

I have a feeling that this is related to Matrix/irlba and i did try downgrading them but i wasn't able to. I have a MAC for reference.

[xmliu01]

I have the same error and I don't know how to fix it.