rcorces
commented
3 years ago what version of MACS2 are you running?
Closed zhaoliyang0429 closed 3 years ago
rcorces
commented
3 years ago what version of MACS2 are you running?
zhaoliyang0429
commented
3 years ago macs2 version 2.1.1.20160309
rcorces
commented
3 years ago Can you try updating your macs2 version?
zhaoliyang0429
commented
3 years ago I have updated my macs2 version to macs2 2.2.7.1, but it went the same error. What can I do?
rcorces
commented
3 years ago can you upload the log file of your most recent attempt?
indicated by ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet...
zhaoliyang0429
commented
3 years ago rcorces
commented
3 years ago Sorry - I dont know what is causing your problem. I dont see anything abnormal in the log file (nor any errors for that matter). The tutorial has been heavily validated and the fact that you are experiencing issues with running the tutorial indicates to me that either something is off with your configuration or that there is some user input that is wrong. I doubt that this is causing this problem but we have not validated ArchR with R v4.* and you are using v4.0.3. You could try using R v3.6.3 for example. Sorry to not be of more help. Maybe @jgranja24 has some ideas.
zhaoliyang0429
commented
3 years ago Many thanks. I am running it on R 3.6 now
RinconFer
commented
3 years ago Many thanks. I am running it on R 3.6 now
Did this work? I am facing the same issue with R4 and I would like to know if that fixed the problem before going through the process of installing R3.6 and reinstall all the packages I am using right now.
Thank you!
rcorces
commented
3 years ago This is not a problem with R v4 (we've tested on Rv4 now) but may be environment specific. It could be a problem with how you have MACS2 installed (for example, problems with conda and R or something).
RinconFer
commented
3 years ago Could it be related with python version? I am running python 3.8 and installed Macs2 with "pip install MACS2". If I try to install it through conda with "conda install -c bioconda macs2" it says that Macs2 is only available for python[versions ='>=3.5, <3.6.0a0']
Edit: I uninstall MACS2 and reinstall it and upgrade numpy from 1.19.2 to 1.20.2 and now seems to work. Thank you!!
strawberry789
commented
3 years ago I have a similar issue.
My command is: projT1ci <- addReproduciblePeakSet( ArchRProj = projT1c, groupBy = "Clusters2", pathToMacs2 = pathToMacs2 )
And I get this error: Error in (function (bedFile = NULL, pathToMacs2 = "macs2", genomeSize = 2.7e+09, : !is.null(genomeSize) is not TRUE
Here is my log file ArchR-addReproduciblePeakSet-3a187333d9b2-Date-2021-04-28_Time-18-58-53.log
Thank you.
rcorces
commented
3 years ago @strawberry789 - what genome are you using? What does this show:
getGenome(projT1c)
kvshams
commented
3 years ago Could it be related with python version? I am running python 3.8 and installed Macs2 with "pip install MACS2". If I try to install it through conda with "conda install -c bioconda macs2" it says that Macs2 is only available for python[versions ='>=3.5, <3.6.0a0']
Edit: I uninstall MACS2 and reinstall it and upgrade numpy from 1.19.2 to 1.20.2 and now seems to work. Thank you!!
Worked by just doing a macs force reinstallation pip install --upgrade --force-reinstall MACS2
strawberry789
commented
3 years ago getGenome(projT1c)
The result is: "BSgenome.Dmelanogaster.UCSC.dm6"
strawberry789
commented
3 years ago Could it be related with python version? I am running python 3.8 and installed Macs2 with "pip install MACS2". If I try to install it through conda with "conda install -c bioconda macs2" it says that Macs2 is only available for python[versions ='>=3.5, <3.6.0a0'] Edit: I uninstall MACS2 and reinstall it and upgrade numpy from 1.19.2 to 1.20.2 and now seems to work. Thank you!!
Worked by just doing a macs force reinstallation
pip install --upgrade --force-reinstall MACS2
I tried the force reinstallation, but it didn't work. Also, numpy is only upgraded to 1.19.5, not 1.20.2
strawberry789
commented
3 years ago Seems I cannot run Macs2, while I can run Tiles.
rcorces
commented
3 years ago @strawberry789 - you are using a non-standard (non-human/mouse) genome. Your error says that genomeSize is NULL. You must provide the genome size as an argument to addReproduciblePeakSet(). I have made this more explicit and added a check for this via https://github.com/GreenleafLab/ArchR/commit/7ff7e4d2306d06304d0a1a73bd6bb2a718a3a724
strawberry789
commented
3 years ago addReproduciblePeakSet
It now works! Thanks!
billzt
commented
3 years ago I also have the same problem. Numpy v1.19.5 didn't work while v1.21.1 worked.
GouQiao
commented
1 year ago I was running tutorial hematopoiesis dataset following the tutorial, in the step projHeme4 <- addReproduciblePeakSet( ArchRProj = projHeme4, groupBy = "Clusters2", pathToMacs2 = "/home/zhaoliyang/anaconda3/envs/ATACSeq/bin/macs2" ) it came up an error. ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-a325acb7b94-Date-2020-11-10_Time-17-01-14.log If there is an issue, please report to github with logFile! 2020-11-10 17:01:14 : Peak Calling Parameters!, 0.003 mins elapsed. Group nCells nCellsUsed nReplicates nMin CD4.N CD4.N 296 296 2 40 Erythroid Erythroid 564 540 2 40 Mono Mono 1009 540 2 40 NK NK 68 62 2 40 pDC pDC 208 208 2 40 PreB PreB 136 136 2 40 Progenitor Progenitor 906 540 2 40 nMax maxPeaks CD4.N 256 148000 Erythroid 500 150000 Mono 500 150000 NK 40 31000 pDC 168 104000 PreB 96 68000 Progenitor 500 150000 2020-11-10 17:01:14 : Batching Peak Calls!, 0.004 mins elapsed. 2020-11-10 17:01:14 : Batch Execution w/ safelapply!, 0 mins elapsed. Error in (function (..., threads = 1, preschedule = FALSE) : Error Found Iteration 1 : [1] "Error in data.table::fread(summitsFile, select = c(1, 2, 3, 5)) : \n File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep1-1_summits.bed' does not exist or is non-readable. getwd()=='/media/sf_sharefolder/ArchR'\n" <simpleError in data.table::fread(summitsFile, select = c(1, 2, 3, 5)): File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep1-1_summits.bed' does not exist or is non-readable. getwd()=='/media/sf_sharefolder/ArchR'> Error Found Iteration 2 : [1] "Error in data.table::fread(summitsFile, select = c(1, 2, 3, 5)) : \n File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep2-2_summits.bed' does not exist or is non-readable. getwd()=='/media/sf_sharefolder/ArchR'\n" <simpleError in data.table::fread(summitsFile, select = c(1, 2, 3, 5)): File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep2-2_summits.bed' does not exi In addition: Warning message: In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 14 function calls resulted in an error
it seemed that "summits.bed" does not exist, I can't find them in the path, only "insertions.bed".
traceback() 6: stop(errorMsg) 5: (function (..., threads = 1, preschedule = FALSE) { if (tolower(.Platform$OS.type) == "windows") { threads <- 1 } if (threads > 1) { o <- mclapply(..., mc.cores = threads, mc.preschedule = preschedule) errorMsg <- list() for (i in seqalong(o)) { if (inherits(o[[i]], "try-error")) { capOut <- utils::capture.output(o[[i]]) capOut <- capOut[!grepl("attr(\,|try-error", capOut)] capOut <- head(capOut, 10) capOut <- unlist(lapply(capOut, function(x) substr(x, 1, 250))) capOut <- paste0("\t", capOut) errorMsg[[length(errorMsg) + 1]] <- paste0(c(paste0("Error Found Iteration ", i, " : "), capOut), "\n") } } if (length(errorMsg) != 0) { errorMsg <- unlist(errorMsg) errorMsg <- head(errorMsg, 50) errorMsg[1] <- paste0("\n", errorMsg[1]) stop(errorMsg) } } else { o <- lapply(...) } o })(X = 1:14, FUN = function (i = NULL, coverageFiles = NULL, outFiles = NULL, peakParams = NULL, bedDir = NULL, excludeChr = NULL, subThreads = 1, tstart = NULL, logFile = NULL) { .logDiffTime(sprintf("Group %s of %s, Calling Peaks with MACS2!", i, length(coverageFiles)), tstart, verbose = TRUE, logFile = logFile) bedFile <- file.path(bedDir, paste0(make.names(basename(names(coverageFiles)[i])), "-", i, ".insertions.bed")) o <- .writeCoverageToBed(coverageFiles[i], bedFile, excludeChr = excludeChr, logFile = logFile) peakParams$bedFile <- bedFile peakParams$logFile <- logFile summits <- do.call(.callSummitsMACS2, peakParams) rmf <- file.remove(bedFile) saveRDS(summits, outFiles[i]) outFiles[i] }, coverageFiles = c(CD4.N..Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/CD4.N..Rep1.insertions.coverage.h5", CD4.N._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/CD4.N..Rep2.insertions.coverage.h5", Erythroid._.Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/Erythroid..Rep1.insertions.coverage.h5", Erythroid._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/Erythroid..Rep2.insertions.coverage.h5", Mono._.Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/Mono..Rep1.insertions.coverage.h5", Mono._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/Mono..Rep2.insertions.coverage.h5", NK._.Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/NK..Rep1.insertions.coverage.h5", NK._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/NK..Rep2.insertions.coverage.h5", pDC._.Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/pDC..Rep1.insertions.coverage.h5", pDC._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/pDC..Rep2.insertions.coverage.h5", PreB._.Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/PreB..Rep1.insertions.coverage.h5", PreB._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/PreB..Rep2.insertions.coverage.h5", Progenitor._.Rep1 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/Progenitor..Rep1.insertions.coverage.h5", Progenitor._.Rep2 = "/media/sfsharefolder/ArchR/HemeTutorial/GroupCoverages/Clusters2/Progenitor..Rep2.insertions.coverage.h5" ), outFiles = c("/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/CD4.N..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/CD4.N..Rep2-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/Erythroid..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/Erythroid..Rep2-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/Mono..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/Mono..Rep2-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/NK..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/NK..Rep2-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/pDC..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/pDC..Rep2-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/PreB..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/PreB..Rep2-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/Progenitor..Rep1-summits.rds", "/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/ReplicateCalls/Progenitor..Rep2-summits.rds" ), bedDir = "/media/sf_sharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds", excludeChr = c("chrM", "chrY"), peakParams = list(pathToMacs2 = "/home/zhaoliyang/anaconda3/envs/ATACSeq/bin/macs2", genomeSize = 2.7e+09, shift = -75, extsize = 150, cutOff = 0.1, method = "q", additionalParams = "--nomodel --nolambda"), threads = 2L, logFile = "ArchRLogs/ArchR-addReproduciblePeakSet-a32797e1504-Date-2020-11-11_Time-14-50-18.log", tstart = structure(1605077418.72268, class = c("POSIXct", "POSIXt")), subThreads = 1) 4: do.call(.safelapply, args) 3: .batchlapply(args) 2: unlist(.batchlapply(args)) 1: addReproduciblePeakSet(ArchRProj = projHeme4, groupBy = "Clusters2", pathToMacs2 = "/home/zhaoliyang/anaconda3/envs/ATACSeq/bin/macs2")
Session Info
sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.56.0 rtracklayer_1.48.0 [4] Biostrings_2.56.0 XVector_0.28.0 gridExtra_2.3 [7] Seurat_3.2.2 gtable_0.3.0 ggrepel_0.8.2 [10] rhandsontable_0.3.7 shiny_1.5.0 ArchR_1.0.0 [13] magrittr_1.5 rhdf5_2.32.4 Matrix_1.2-18 [16] data.table_1.13.2 SummarizedExperiment_1.18.2 DelayedArray_0.14.1 [19] matrixStats_0.57.0 Biobase_2.48.0 GenomicRanges_1.40.0 [22] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1 [25] BiocGenerics_0.34.0 ggplot2_3.3.2
loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_1.4-1 deldir_0.1-29 ellipsis_0.3.1 [5] ggridges_0.5.2 spatstat.data_1.4-3 rstudioapi_0.11 hexbin_1.28.1 [9] leiden_0.3.4 listenv_0.8.0 farver_2.0.3 RSpectra_0.16-0 [13] codetools_0.2-16 splines_4.0.3 shinythemes_1.1.2 polyclip_1.10-0 [17] jsonlite_1.7.1 Rsamtools_2.4.0 Cairo_1.5-12.2 ica_1.0-2 [21] cluster_2.1.0 png_0.1-7 uwot_0.1.8 sctransform_0.3.1 [25] compiler_4.0.3 httr_1.4.2 fastmap_1.0.1 lazyeval_0.2.2 [29] later_1.1.0.1 htmltools_0.5.0 tools_4.0.3 rsvd_1.0.3 [33] igraph_1.2.6 glue_1.4.2 GenomeInfoDbData_1.2.3 reshape2_1.4.4 [37] RANN_2.6.1 dplyr_1.0.2 spatstat_1.64-1 Rcpp_1.0.5 [41] vctrs_0.3.4 nlme_3.1-150 lmtest_0.9-38 stringr_1.4.0 [45] globals_0.13.1 mime_0.9 miniUI_0.1.1.1 lifecycle_0.2.0 [49] irlba_2.3.3 gtools_3.8.2 goftest_1.2-2 XML_3.99-0.5 [53] future_1.19.1 zlibbioc_1.34.0 MASS_7.3-53 zoo_1.8-8 [57] scales_1.1.1 spatstat.utils_1.17-0 promises_1.1.1 RColorBrewer_1.1-2 [61] yaml_2.2.1 reticulate_1.18 pbapply_1.4-3 rpart_4.1-15 [65] stringi_1.5.3 BiocParallel_1.22.0 rlang_0.4.8 pkgconfig_2.0.3 [69] bitops_1.0-6 lattice_0.20-41 tensor_1.5 ROCR_1.0-11 [73] purrr_0.3.4 Rhdf5lib_1.10.1 GenomicAlignments_1.24.0 patchwork_1.0.1 [77] htmlwidgets_1.5.2 labeling_0.4.2 cowplot_1.1.0 tidyselect_1.1.0 [81] RcppAnnoy_0.0.16 plyr_1.8.6 R6_2.5.0 generics_0.1.0 [85] mgcv_1.8-33 pillar_1.4.6 withr_2.3.0 fitdistrplus_1.1-1 [89] abind_1.4-5 survival_3.2-7 RCurl_1.98-1.2 tibble_3.0.4 [93] future.apply_1.6.0 crayon_1.3.4 KernSmooth_2.23-18 plotly_4.9.2.1 [97] nabor_0.5.0 digest_0.6.27 xtable_1.8-4 tidyr_1.1.2 [101] httpuv_1.5.4 munsell_0.5.0 viridisLite_0.3.0
Could you tell me how to solve the problem? Many thanks.
Hi, I met the same error. Did you solve it?
yaohuayang-uva
commented
8 months ago A data point for solving the problem "summits.bed' does not exist or is non-readable." when using addReproduciblePeakSet(). To me, it seems like an issue related to MACS2 version. I use R 4.3.2, Python 3.8.6, ArchR 1.0.1. I met this error when using MACS2 v2.2.9.1 (latest version), and can not fix it by using any versions of numpy suggested by previous posts. Finnaly fix it by using MACS2 version 2.2.6 (Dec 2019 release).
JiaxinLi-lipluszn
commented
7 months ago A data point for solving the problem "summits.bed' does not exist or is non-readable." when using addReproduciblePeakSet(). To me, it seems like an issue related to MACS2 version. I use R 4.3.2, Python 3.8.6, ArchR 1.0.1. I met this error when using MACS2 v2.2.9.1 (latest version), and can not fix it by using any versions of numpy suggested by previous posts. Finnaly fix it by using MACS2 version 2.2.6 (Dec 2019 release).
Did you also downgraded your python to 3.6.x?
yaohuayang-uva
commented
7 months ago A data point for solving the problem "summits.bed' does not exist or is non-readable." when using addReproduciblePeakSet(). To me, it seems like an issue related to MACS2 version. I use R 4.3.2, Python 3.8.6, ArchR 1.0.1. I met this error when using MACS2 v2.2.9.1 (latest version), and can not fix it by using any versions of numpy suggested by previous posts. Finnaly fix it by using MACS2 version 2.2.6 (Dec 2019 release).
Did you also downgraded your python to 3.6.x?
No. I used Python 3.8.6.
I was running tutorial hematopoiesis dataset following the tutorial, in the step projHeme4 <- addReproduciblePeakSet( ArchRProj = projHeme4, groupBy = "Clusters2", pathToMacs2 = "/home/zhaoliyang/anaconda3/envs/ATACSeq/bin/macs2" ) it came up an error. ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-a325acb7b94-Date-2020-11-10_Time-17-01-14.log If there is an issue, please report to github with logFile! 2020-11-10 17:01:14 : Peak Calling Parameters!, 0.003 mins elapsed. Group nCells nCellsUsed nReplicates nMin CD4.N CD4.N 296 296 2 40 Erythroid Erythroid 564 540 2 40 Mono Mono 1009 540 2 40 NK NK 68 62 2 40 pDC pDC 208 208 2 40 PreB PreB 136 136 2 40 Progenitor Progenitor 906 540 2 40 nMax maxPeaks CD4.N 256 148000 Erythroid 500 150000 Mono 500 150000 NK 40 31000 pDC 168 104000 PreB 96 68000 Progenitor 500 150000 2020-11-10 17:01:14 : Batching Peak Calls!, 0.004 mins elapsed. 2020-11-10 17:01:14 : Batch Execution w/ safelapply!, 0 mins elapsed. Error in (function (..., threads = 1, preschedule = FALSE) : Error Found Iteration 1 : [1] "Error in data.table::fread(summitsFile, select = c(1, 2, 3, 5)) : \n File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep1-1_summits.bed' does not exist or is non-readable. getwd()=='/media/sf_sharefolder/ArchR'\n" <simpleError in data.table::fread(summitsFile, select = c(1, 2, 3, 5)): File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep1-1_summits.bed' does not exist or is non-readable. getwd()=='/media/sf_sharefolder/ArchR'> Error Found Iteration 2 : [1] "Error in data.table::fread(summitsFile, select = c(1, 2, 3, 5)) : \n File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep2-2_summits.bed' does not exist or is non-readable. getwd()=='/media/sf_sharefolder/ArchR'\n" <simpleError in data.table::fread(summitsFile, select = c(1, 2, 3, 5)): File '/media/sfsharefolder/ArchR/HemeTutorial/PeakCalls/InsertionBeds/CD4.N..Rep2-2_summits.bed' does not exi In addition: Warning message: In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 14 function calls resulted in an error
it seemed that "summits.bed" does not exist, I can't find them in the path, only "insertions.bed".
Session Info
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.56.0 rtracklayer_1.48.0
[4] Biostrings_2.56.0 XVector_0.28.0 gridExtra_2.3
[7] Seurat_3.2.2 gtable_0.3.0 ggrepel_0.8.2
[10] rhandsontable_0.3.7 shiny_1.5.0 ArchR_1.0.0
[13] magrittr_1.5 rhdf5_2.32.4 Matrix_1.2-18
[16] data.table_1.13.2 SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[19] matrixStats_0.57.0 Biobase_2.48.0 GenomicRanges_1.40.0
[22] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[25] BiocGenerics_0.34.0 ggplot2_3.3.2
loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_1.4-1 deldir_0.1-29 ellipsis_0.3.1
[5] ggridges_0.5.2 spatstat.data_1.4-3 rstudioapi_0.11 hexbin_1.28.1
[9] leiden_0.3.4 listenv_0.8.0 farver_2.0.3 RSpectra_0.16-0
[13] codetools_0.2-16 splines_4.0.3 shinythemes_1.1.2 polyclip_1.10-0
[17] jsonlite_1.7.1 Rsamtools_2.4.0 Cairo_1.5-12.2 ica_1.0-2
[21] cluster_2.1.0 png_0.1-7 uwot_0.1.8 sctransform_0.3.1
[25] compiler_4.0.3 httr_1.4.2 fastmap_1.0.1 lazyeval_0.2.2
[29] later_1.1.0.1 htmltools_0.5.0 tools_4.0.3 rsvd_1.0.3
[33] igraph_1.2.6 glue_1.4.2 GenomeInfoDbData_1.2.3 reshape2_1.4.4
[37] RANN_2.6.1 dplyr_1.0.2 spatstat_1.64-1 Rcpp_1.0.5
[41] vctrs_0.3.4 nlme_3.1-150 lmtest_0.9-38 stringr_1.4.0
[45] globals_0.13.1 mime_0.9 miniUI_0.1.1.1 lifecycle_0.2.0
[49] irlba_2.3.3 gtools_3.8.2 goftest_1.2-2 XML_3.99-0.5
[53] future_1.19.1 zlibbioc_1.34.0 MASS_7.3-53 zoo_1.8-8
[57] scales_1.1.1 spatstat.utils_1.17-0 promises_1.1.1 RColorBrewer_1.1-2
[61] yaml_2.2.1 reticulate_1.18 pbapply_1.4-3 rpart_4.1-15
[65] stringi_1.5.3 BiocParallel_1.22.0 rlang_0.4.8 pkgconfig_2.0.3
[69] bitops_1.0-6 lattice_0.20-41 tensor_1.5 ROCR_1.0-11
[73] purrr_0.3.4 Rhdf5lib_1.10.1 GenomicAlignments_1.24.0 patchwork_1.0.1
[77] htmlwidgets_1.5.2 labeling_0.4.2 cowplot_1.1.0 tidyselect_1.1.0
[81] RcppAnnoy_0.0.16 plyr_1.8.6 R6_2.5.0 generics_0.1.0
[85] mgcv_1.8-33 pillar_1.4.6 withr_2.3.0 fitdistrplus_1.1-1
[89] abind_1.4-5 survival_3.2-7 RCurl_1.98-1.2 tibble_3.0.4
[93] future.apply_1.6.0 crayon_1.3.4 KernSmooth_2.23-18 plotly_4.9.2.1
[97] nabor_0.5.0 digest_0.6.27 xtable_1.8-4 tidyr_1.1.2
[101] httpuv_1.5.4 munsell_0.5.0 viridisLite_0.3.0
Could you tell me how to solve the problem? Many thanks.