Error in MatrixGenerics #10
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Hi @yojetsharma, unfortunately I'm unsure what causes this, since the error seems to be thrown by |
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Sure, thank you! Please let me know if there is anything else required
from my side.
On 2022-09-26 14:50, jonas wrote:
Hi @yojetsharma [1], unfortunately I'm unsure what causes this, since the error seems to be thrown by MatrixGenerics which is not a direct dependency of Pando. I will look into it and try to reproduce the error.
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If you like, you can try if installing older versions of |
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I see. I am using R=4.2.0 and Bioconductor version is 3.15. I am not
sure if I will be install older version in this new R.
What version is your R?
On 2022-09-26 15:08, jonas wrote:
If you like, you can try if installing older versions of MatrixGenerics or sparseMatrixStats might solve the issue. I have them at 1.6.0 currently and I'm not experiencing the issue
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My R is version 4.1.2 and so far I haven't tested Pando on newer versions, but usually package versions and R versions are not necessarily interlinked |
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Okay. How do I downgrade these packages? Since, I remember they were
already installed.
On 2022-09-26 19:18, jonas wrote:
My R is version 4.1.2 and so far I haven't tested Pando on newer versions, but usually package versions and R versions are not necessarily interlinked
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I ran it again with older versions of the packages that you earlier
mentioned but I am still getting the same error.
d149 <- infer_grn(d149)
Selecting candidate regulatory regions near genes
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) :
Failed to find a rowMaxs() method for lgCMatrix objects.
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK:
/ncbs_gs/nlsas_data/usershares/praghu/yojetsharma/.conda/envs/scenic/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=C LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sp_1.5-0 SeuratObject_4.1.2 Seurat_4.2.0 Pando_0.5.1
loaded via a namespace (and not attached):
[1] fastmatch_1.1-3 plyr_1.8.7
[3] igraph_1.3.5 lazyeval_0.2.2
[5] splines_4.1.2 BiocParallel_1.28.3
[7] listenv_0.8.0 scattermore_0.8
[9] GenomeInfoDb_1.30.1 ggplot2_3.3.6
[11] digest_0.6.29 htmltools_0.5.3
[13] viridis_0.6.2 fansi_1.0.3
[15] magrittr_2.0.3 tensor_1.5
[17] cluster_2.1.4 ROCR_1.0-11
[19] globals_0.16.1 Biostrings_2.62.0
[21] graphlayouts_0.8.1 matrixStats_0.62.0
[23] spatstat.sparse_2.1-1 colorspace_2.0-3
[25] ggrepel_0.9.1 dplyr_1.0.10
[27] crayon_1.5.1 RCurl_1.98-1.8
[29] jsonlite_1.8.0 progressr_0.11.0
[31] spatstat.data_2.2-0 survival_3.4-0
[33] zoo_1.8-11 glue_1.6.2
[35] polyclip_1.10-0 pals_1.7
[37] gtable_0.3.1 zlibbioc_1.40.0
[39] XVector_0.34.0 leiden_0.4.3
[41] DelayedArray_0.20.0 future.apply_1.9.1
[43] BiocGenerics_0.40.0 maps_3.4.0
[45] abind_1.4-5 scales_1.2.1
[47] DBI_1.1.3 Signac_1.8.0
[49] spatstat.random_2.2-0 miniUI_0.1.1.1
[51] Rcpp_1.0.9 viridisLite_0.4.1
[53] xtable_1.8-4 reticulate_1.26
[55] spatstat.core_2.4-4 mapproj_1.2.8
[57] stats4_4.1.2 htmlwidgets_1.5.4
[59] httr_1.4.4 RColorBrewer_1.1-3
[61] ellipsis_0.3.2 ica_1.0-3
[63] pkgconfig_2.0.3 farver_2.1.1
[65] uwot_0.1.14 deldir_1.0-6
[67] utf8_1.2.2 tidyselect_1.1.2
[69] rlang_1.0.6 reshape2_1.4.4
[71] later_1.3.0 munsell_0.5.0
[73] tools_4.1.2 cli_3.4.1
[75] generics_0.1.3 ggridges_0.5.4
[77] stringr_1.4.1 fastmap_1.1.0
[79] goftest_1.2-3 fitdistrplus_1.1-8
[81] tidygraph_1.2.2 purrr_0.3.4
[83] RANN_2.6.1 ggraph_2.0.6
[85] pbapply_1.5-0 future_1.28.0
[87] nlme_3.1-159 sparseMatrixStats_1.6.0
[89] mime_0.12 grr_0.9.5
[91] RcppRoll_0.3.0 compiler_4.1.2
[93] plotly_4.10.0 png_0.1-7
[95] spatstat.utils_2.3-1 tibble_3.1.8
[97] tweenr_2.0.2 stringi_1.7.8
[99] rgeos_0.5-9 lattice_0.20-45
[101] Matrix_1.5-1 vctrs_0.4.1
[103] pillar_1.8.1 lifecycle_1.0.2
[105] BiocManager_1.30.18 spatstat.geom_2.4-0
[107] lmtest_0.9-40 RcppAnnoy_0.0.19
[109] data.table_1.14.2 cowplot_1.1.1
[111] bitops_1.0-7 irlba_2.3.5
[113] Matrix.utils_0.9.8 httpuv_1.6.6
[115] patchwork_1.1.2 GenomicRanges_1.46.1
[117] R6_2.5.1 promises_1.2.0.1
[119] KernSmooth_2.23-20 gridExtra_2.3
[121] IRanges_2.28.0 parallelly_1.32.1
[123] codetools_0.2-18 dichromat_2.0-0.1
[125] MASS_7.3-58.1 assertthat_0.2.1
[127] withr_2.5.0 sctransform_0.3.5
[129] Rsamtools_2.10.0 S4Vectors_0.32.4
[131] GenomeInfoDbData_1.2.7 mgcv_1.8-40
[133] parallel_4.1.2 grid_4.1.2
[135] rpart_4.1.16 tidyr_1.2.1
[137] ggpointdensity_0.1.0 DelayedMatrixStats_1.16.0
[139] MatrixGenerics_1.6.0 Rtsne_0.16
[141] ggforce_0.3.4 shiny_1.7.2
On 2022-09-26 19:18, jonas wrote:
My R is version 4.1.2 and so far I haven't tested Pando on newer versions, but usually package versions and R versions are not necessarily interlinked
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On 2022-09-26 19:18, jonas wrote:
My R is version 4.1.2 and so far I haven't tested Pando on newer versions, but usually package versions and R versions are not necessarily interlinked
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I used remotes:: to install the Pando and not dev tools. Could that be
the issue?
Links:
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[1]
#10 (comment)
[2]
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I'm not sure if there is a functional difference the between and devtools function... We will test it on the new versions and let you know. Also it might be helpful if you could send the full error traceback by typing |
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I am also having this error - here is the traceback: |
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On 2022-09-27 18:54, jonas wrote:
I'm not sure if there is a functional difference the between and devtools function... We will test it on the new versions and let you know. Also it might be helpful if you could send the full error traceback by typing traceback() right after you get the error
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Now, I reinstalled everything (bioconductor and its packages) and
installed Pando using dev tools. MatrixGenerics and sparseMatrixStats
are at 1.6.0 as you suggested. But still the same error
D149 <- INFER_GRN(D149)
SELECTING CANDIDATE REGULATORY REGIONS NEAR GENES
ERROR IN MATRIXGENERICS:::.LOAD_NEXT_SUGGESTED_PACKAGE_TO_SEARCH(X) :
FAILED TO FIND A ROWMAXS() METHOD FOR LGCMATRIX OBJECTS.
traceback()
13: stop(short_errmsg)
12: MatrixGenerics:::.load_next_suggested_package_to_search(x)
11: rowMaxs(x = x)
10: rowMaxs(x = x)
9: eval(call, parent.frame())
8: eval(call, parent.frame())
7: callGeneric()
6: rowMaxs(peaks2motif)
5: rowMaxs(peaks2motif)
4: fit_grn_models.SeuratPlus(object = object, genes = genes,
network_name = network_name,
peak_to_gene_method = peak_to_gene_method, upstream = upstream,
downstream = downstream, extend = extend, only_tss = only_tss,
parallel = parallel, tf_cor = tf_cor, peak_cor = peak_cor,
aggregate_rna_col = aggregate_rna_col, aggregate_peaks_col =
aggregate_peaks_col,
method = method, alpha = alpha, family = family, interaction_term
= interaction_term,
adjust_method = adjust_method, scale = scale, verbose = verbose,
...)
3: fit_grn_models(object = object, genes = genes, network_name =
network_name,
peak_to_gene_method = peak_to_gene_method, upstream = upstream,
downstream = downstream, extend = extend, only_tss = only_tss,
parallel = parallel, tf_cor = tf_cor, peak_cor = peak_cor,
aggregate_rna_col = aggregate_rna_col, aggregate_peaks_col =
aggregate_peaks_col,
method = method, alpha = alpha, family = family, interaction_term
= interaction_term,
adjust_method = adjust_method, scale = scale, verbose = verbose,
...)
2: infer_grn.SeuratPlus(d149)
1: infer_grn(d149)
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK:
/ncbs_gs/nlsas_data/usershares/praghu/yojetsharma/.conda/envs/scenic/lib/libopenblasp-r0.3.21.so
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=C LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome_1.62.0
[3] rtracklayer_1.54.0 Biostrings_2.62.0
[5] XVector_0.34.0 GenomicRanges_1.46.1
[7] GenomeInfoDb_1.30.1 IRanges_2.28.0
[9] S4Vectors_0.32.4 BiocGenerics_0.40.0
[11] sp_1.5-0 SeuratObject_4.1.2
[13] Seurat_4.2.0 Pando_0.5.1
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.26
[3] tidyselect_1.1.2 htmlwidgets_1.5.4
[5] grid_4.1.2 BiocParallel_1.28.3
[7] Rtsne_0.16 devtools_2.4.4
[9] munsell_0.5.0 codetools_0.2-18
[11] ica_1.0-3 future_1.28.0
[13] miniUI_0.1.1.1 withr_2.5.0
[15] spatstat.random_2.2-0 colorspace_2.0-3
[17] progressr_0.11.0 Biobase_2.54.0
[19] ROCR_1.0-11 tensor_1.5
[21] listenv_0.8.0 MatrixGenerics_1.6.0
[23] GenomeInfoDbData_1.2.7 polyclip_1.10-0
[25] farver_2.1.1 Matrix.utils_0.9.8
[27] parallelly_1.32.1 vctrs_0.4.1
[29] generics_0.1.3 R6_2.5.1
[31] graphlayouts_0.8.1 pals_1.7
[33] DelayedArray_0.20.0 bitops_1.0-7
[35] spatstat.utils_2.3-1 cachem_1.0.6
[37] assertthat_0.2.1 promises_1.2.0.1
[39] BiocIO_1.4.0 scales_1.2.1
[41] ggraph_2.0.6 rgeos_0.5-9
[43] gtable_0.3.1 globals_0.16.1
[45] processx_3.7.0 goftest_1.2-3
[47] tidygraph_1.2.2 rlang_1.0.6
[49] RcppRoll_0.3.0 splines_4.1.2
[51] lazyeval_0.2.2 dichromat_2.0-0.1
[53] spatstat.geom_2.4-0 BiocManager_1.30.18
[55] yaml_2.3.5 reshape2_1.4.4
[57] abind_1.4-5 httpuv_1.6.6
[59] tools_4.1.2 usethis_2.1.6
[61] ggplot2_3.3.6 ellipsis_0.3.2
[63] spatstat.core_2.4-4 RColorBrewer_1.1-3
[65] sessioninfo_1.2.2 ggridges_0.5.4
[67] Rcpp_1.0.9 plyr_1.8.7
[69] sparseMatrixStats_1.6.0 zlibbioc_1.40.0
[71] purrr_0.3.4 RCurl_1.98-1.8
[73] ps_1.7.1 prettyunits_1.1.1
[75] rpart_4.1.16 deldir_1.0-6
[77] pbapply_1.5-0 viridis_0.6.2
[79] cowplot_1.1.1 urlchecker_1.0.1
[81] zoo_1.8-11 grr_0.9.5
[83] SummarizedExperiment_1.24.0 ggrepel_0.9.1
[85] cluster_2.1.4 fs_1.5.2
[87] magrittr_2.0.3 data.table_1.14.2
[89] scattermore_0.8 lmtest_0.9-40
[91] RANN_2.6.1 fitdistrplus_1.1-8
[93] Signac_1.8.0 matrixStats_0.62.0
[95] pkgload_1.3.0 patchwork_1.1.2
[97] mime_0.12 xtable_1.8-4
[99] XML_3.99-0.10 gridExtra_2.3
[101] compiler_4.1.2 tibble_3.1.8
[103] maps_3.4.0 KernSmooth_2.23-20
[105] crayon_1.5.1 ggpointdensity_0.1.0
[107] htmltools_0.5.3 mgcv_1.8-40
[109] later_1.3.0 tidyr_1.2.1
[111] DBI_1.1.3 tweenr_2.0.2
[113] MASS_7.3-58.1 Matrix_1.5-1
[115] cli_3.4.1 parallel_4.1.2
[117] igraph_1.3.5 pkgconfig_2.0.3
[119] GenomicAlignments_1.30.0 plotly_4.10.0
[121] spatstat.sparse_2.1-1 stringr_1.4.1
[123] callr_3.7.2 digest_0.6.29
[125] sctransform_0.3.5 RcppAnnoy_0.0.19
[127] spatstat.data_2.2-0 leiden_0.4.3
[129] fastmatch_1.1-3 uwot_0.1.14
[131] DelayedMatrixStats_1.16.0 restfulr_0.0.15
[133] curl_4.3.2 shiny_1.7.2
[135] Rsamtools_2.10.0 rjson_0.2.21
[137] lifecycle_1.0.2 nlme_3.1-159
[139] jsonlite_1.8.0 mapproj_1.2.8
[141] viridisLite_0.4.1 fansi_1.0.3
[143] pillar_1.8.1 lattice_0.20-45
[145] fastmap_1.1.0 httr_1.4.4
[147] pkgbuild_1.3.1 survival_3.4-0
[149] glue_1.6.2 remotes_2.4.2
[151] png_0.1-7 ggforce_0.3.4
[153] stringi_1.7.8 profvis_0.3.7
[155] memoise_2.0.1 dplyr_1.0.10
[157] irlba_2.3.5 future.apply_1.9.1
Links:
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[1]
#10 (comment)
[2]
https://github.com/notifications/unsubscribe-auth/AS6UNG7QOZHF3EDUZSS6JTLWALYSRANCNFSM6AAAAAAQT4E7EI
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Working on this, it looks like the problem is at line 255 of the function
Where basically there no longer seems to be a function (from some package that got updated i assume) to call a maximum value (aka true) on a logical matrix. I am far too stupid to figure it out but that does appear to be the problem. As a workaround, I just made the function only use the peaks that are in genes Anyways, I removed it and it seems to be running fine now, so we'll see.... |
I’m new to this so can you please provide the details of how you removed it? And how to make the function use only the peaks that are in genes peaks_at_gene and ignore the peaks_with_motif? |
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Great, thank you for the detailed descriptions and suggested fix. I assume @johnblair7 you are also running a more recent version of R and/or |
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Thanks Jonas, Here is my session info - Running R4.1.3 and MatrixGenerics 1.6. Also my fix doesn't seem to fully work as I ran the function overnight just now and it still didn't finish (trying to do 1605 genes? is that too many?) @yojetsharma I just "forked" pando into my own repository (basically means that i copied the whole code to my own profile) and then went into where the "infer_grn" scripts were (R/grn.R from the main folder) and just deleted/edited those two lines. Then I uninstalled the version of pando that I had and reinstalled my own version using devtools::install_github('johnblair7/pando2') and ran everything as I would in pando "normal". But seeing as how it didn't end up running all the way through (no error, just timed out), its probably better just to wait for @joschif to look into it and deal with it properly |
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Hi all, it seems like there are some issues with some of the matrix classes of newer Matrix versions. I have pushed a new commit to the |
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I now had some time to test a new version for 4.2 and pushed it to main. I believe this issue should be fixed, but please let me know how it works for you. |
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Thank you guys for making such a great tool and I am trying to use it in my research. However I am still running into the same issue as people were describing above. Here's the session info and error: Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] sparseMatrixStats_1.11.1 MatrixGenerics_1.10.0
[3] matrixStats_0.63.0 TFBSTools_1.36.0
[5] JASPAR2022_0.99.7 BiocFileCache_2.6.1
[7] dbplyr_2.3.2 future_1.32.0
[9] doParallel_1.0.17 iterators_1.0.14
[11] foreach_1.5.2 Signac_1.9.0
[13] lubridate_1.9.2 forcats_1.0.0
[15] stringr_1.5.0 dplyr_1.1.1
[17] purrr_1.0.1 readr_2.1.4
[19] tidyr_1.3.0 tibble_3.2.1
[21] ggplot2_3.4.2 tidyverse_2.0.0
[23] EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.22.0
[25] AnnotationFilter_1.22.0 GenomicFeatures_1.50.4
[27] AnnotationDbi_1.60.2 Biobase_2.58.0
[29] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.66.3
[31] rtracklayer_1.58.0 Biostrings_2.66.0
[33] XVector_0.38.0 GenomicRanges_1.50.2
[35] GenomeInfoDb_1.34.9 IRanges_2.32.0
[37] S4Vectors_0.36.2 BiocGenerics_0.44.0
[39] SeuratObject_4.1.3 Seurat_4.3.0
[41] Pando_1.0.3
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 pbdZMQ_0.3-9
[3] scattermore_0.8 R.methodsS3_1.8.2
[5] bit64_4.0.5 irlba_2.3.5.1
[7] DelayedArray_0.24.0 R.utils_2.12.2
[9] data.table_1.14.8 KEGGREST_1.38.0
[11] RCurl_1.98-1.12 generics_0.1.3
[13] cowplot_1.1.1 RSQLite_2.3.1
[15] RANN_2.6.1 ggpointdensity_0.1.0
[17] bit_4.0.5 tzdb_0.3.0
[19] spatstat.data_3.0-1 xml2_1.3.3
[21] httpuv_1.6.9 SummarizedExperiment_1.28.0
[23] DirichletMultinomial_1.40.0 viridis_0.6.2
[25] hms_1.1.3 evaluate_0.20
[27] promises_1.2.0.1 fansi_1.0.4
[29] restfulr_0.0.15 progress_1.2.2
[31] caTools_1.18.2 igraph_1.4.2
[33] DBI_1.1.3 htmlwidgets_1.6.2
[35] spatstat.geom_3.1-0 ellipsis_0.3.2
[37] annotate_1.76.0 biomaRt_2.54.1
[39] deldir_1.0-6 vctrs_0.6.1
[41] ROCR_1.0-11 abind_1.4-5
[43] cachem_1.0.7 withr_2.5.0
[45] ggforce_0.4.1 grr_0.9.5
[47] progressr_0.13.0 sctransform_0.3.5
[49] GenomicAlignments_1.34.1 prettyunits_1.1.1
[51] goftest_1.2-3 cluster_2.1.4
[53] IRdisplay_1.1 lazyeval_0.2.2
[55] seqLogo_1.64.0 crayon_1.5.2
[57] spatstat.explore_3.1-0 pkgconfig_2.0.3
[59] tweenr_2.0.2 nlme_3.1-162
[61] ProtGenerics_1.30.0 pals_1.7
[63] rlang_1.1.0 globals_0.16.2
[65] lifecycle_1.0.3 miniUI_0.1.1.1
[67] filelock_1.0.2 dichromat_2.0-0.1
[69] polyclip_1.10-4 lmtest_0.9-40
[71] Matrix_1.5-1 IRkernel_1.3.2
[73] zoo_1.8-12 base64enc_0.1-3
[75] ggridges_0.5.4 png_0.1-8
[77] viridisLite_0.4.1 rjson_0.2.21
[79] bitops_1.0-7 R.oo_1.25.0
[81] KernSmooth_2.23-20 blob_1.2.4
[83] parallelly_1.35.0 spatstat.random_3.1-4
[85] CNEr_1.34.0 scales_1.2.1
[87] memoise_2.0.1 magrittr_2.0.3
[89] plyr_1.8.8 ica_1.0-3
[91] zlibbioc_1.44.0 compiler_4.2.3
[93] BiocIO_1.8.0 RColorBrewer_1.1-3
[95] fitdistrplus_1.1-8 Rsamtools_2.14.0
[97] cli_3.6.1 listenv_0.9.0
[99] patchwork_1.1.2 pbapply_1.7-0
[101] MASS_7.3-58.3 tidyselect_1.2.0
[103] stringi_1.7.12 yaml_2.3.7
[105] ggrepel_0.9.3 grid_4.2.3
[107] fastmatch_1.1-3 tools_4.2.3
[109] timechange_0.2.0 future.apply_1.10.0
[111] uuid_1.1-0 TFMPvalue_0.0.9
[113] gridExtra_2.3 farver_2.1.1
[115] Rtsne_0.16 ggraph_2.1.0
[117] digest_0.6.31 shiny_1.7.4
[119] pracma_2.4.2 Rcpp_1.0.10
[121] later_1.3.0 RcppAnnoy_0.0.20
[123] httr_1.4.5 colorspace_2.1-0
[125] XML_3.99-0.14 tensor_1.5
[127] reticulate_1.28 splines_4.2.3
[129] uwot_0.1.14 RcppRoll_0.3.0
[131] spatstat.utils_3.0-2 graphlayouts_0.8.4
[133] sp_1.6-0 mapproj_1.2.11
[135] plotly_4.10.1 xtable_1.8-4
[137] jsonlite_1.8.4 poweRlaw_0.70.6
[139] tidygraph_1.2.3 R6_2.5.1
[141] pillar_1.9.0 htmltools_0.5.5
[143] mime_0.12 glue_1.6.2
[145] fastmap_1.1.1 BiocParallel_1.32.6
[147] codetools_0.2-19 maps_3.4.1
[149] utf8_1.2.3 lattice_0.20-45
[151] spatstat.sparse_3.0-1 curl_5.0.0
[153] leiden_0.4.3 gtools_3.9.4
[155] GO.db_3.16.0 survival_3.5-3
[157] repr_1.1.6 munsell_0.5.0
[159] GenomeInfoDbData_1.2.9 reshape2_1.4.4
[161] gtable_0.3.3 Error Messages: I have previously used R version 4.1.3 with sparseMatrixStats and MatrixGenerics 1.6.0 but that did not work either. Can anyone help me with this? Thank you all very much! |
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I ran the Joint RNA and ATAC multiomic tutorial till the Peak Calling and added MACS2 peak set to the Seurat Object (d149 in this case) and started running Pando from thereon. But later I get error in MatrixGenerics:::. I am not sure what I did wrong. Please help.
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