Error in .valid.Vector.length(x) : could not find function ".valid.Vector.length"

[annrosebright]

Attach your log [file] ArchR-addMotifAnnotations-1ae2429e816fd-Date-2020-11-30_Time-21-18-52.log

Describe the bug

Whatever command I run as part of archr analysis I am getting the following error. It was running all fine a few days back but now I get this error. Seems like some package version issue, but not able to figure out what.

e12_e16_int3a <- addMotifAnnotations(ArchRProj = e12_e16_int3a, motifSet = "cisbp", name = "Motif") ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-1ae2429e816fd-Date-2020-11-30_Time-21-18-52.log If there is an issue, please report to github with logFile! 2020-11-30 21:18:52 : Gettting Motif Set, Species : Mus musculus, 0.015 mins elapsed. Using version 2 motifs! 2020-11-30 21:18:54 : Finding Motif Positions with motifmatchr!, 0.048 mins elapsed. Error in .valid.Vector.length(x) : could not find function ".valid.Vector.length"

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] BSgenome.Mmusculus.UCSC.mm10_1.4.0 BSgenome_1.56.0
[3] rtracklayer_1.46.0 Biostrings_2.56.0
[5] XVector_0.28.0 chromVARmotifs_0.2.0
[7] JASPAR2020_0.99.10 motifmatchr_1.8.0
[9] TFBSTools_1.28.0 ArchR_1.0.1
[11] magrittr_2.0.1 rhdf5_2.30.1
[13] Matrix_1.2-18 data.table_1.13.2
[15] SummarizedExperiment_1.16.1 DelayedArray_0.12.3
[17] BiocParallel_1.20.1 matrixStats_0.57.0
[19] Biobase_2.46.0 GenomicRanges_1.40.0
[21] GenomeInfoDb_1.24.2 IRanges_2.22.2
[23] S4Vectors_0.26.1 BiocGenerics_0.32.0
[25] ggplot2_3.3.2

loaded via a namespace (and not attached): [1] rappdirs_0.3.1 R.methodsS3_1.8.1
[3] tidyr_1.1.2 bit64_4.0.5
[5] irlba_2.3.3 R.utils_2.10.1
[7] rpart_4.1-15 KEGGREST_1.26.1
[9] RCurl_1.98-1.2 generics_0.1.0
[11] GenomicFeatures_1.40.1 cowplot_1.1.0
[13] RSQLite_2.2.1 RANN_2.6.1
[15] europepmc_0.4 future_1.20.1
[17] bit_4.0.4 enrichplot_1.6.1
[19] spatstat.data_1.5-2 xml2_1.3.2
[21] httpuv_1.5.4 assertthat_0.2.1
[23] DirichletMultinomial_1.28.0 viridis_0.5.1
[25] hms_0.5.3 promises_1.1.1
[27] progress_1.2.2 caTools_1.18.0
[29] dbplyr_2.0.0 igraph_1.2.6
[31] DBI_1.1.0 htmlwidgets_1.5.2
[33] purrr_0.3.4 ellipsis_0.3.1
[35] rGREAT_1.18.0 dplyr_1.0.2
[37] backports_1.2.0 annotate_1.64.0
[39] biomaRt_2.42.1 deldir_0.2-3
[41] vctrs_0.3.5 Cairo_1.5-12.2
[43] ROCR_1.0-11 abind_1.4-5
[45] withr_2.3.0 ggforce_0.3.2
[47] triebeard_0.3.0 presto_1.0.0
[49] checkmate_2.0.0 sctransform_0.3.1
[51] GenomicAlignments_1.24.0 prettyunits_1.1.1
[53] goftest_1.2-2 cluster_2.1.0
[55] DOSE_3.12.0 lazyeval_0.2.2
[57] seqLogo_1.52.0 crayon_1.3.4
[59] pkgconfig_2.0.3 tweenr_1.0.1
[61] nlme_3.1-148 rlang_0.4.9
[63] globals_0.14.0 lifecycle_0.2.0
[65] miniUI_0.1.1.1 BiocFileCache_1.10.2
[67] rsvd_1.0.3 polyclip_1.10-0
[69] lmtest_0.9-38 graph_1.64.0
[71] urltools_1.7.3 Rhdf5lib_1.8.0
[73] boot_1.3-25 zoo_1.8-8
[75] ggridges_0.5.2 GlobalOptions_0.1.2
[77] png_0.1-7 viridisLite_0.3.0
[79] rjson_0.2.20 bitops_1.0-6
[81] R.oo_1.24.0 KernSmooth_2.23-17
[83] blob_1.2.1 shape_1.4.5
[85] stringr_1.4.0 qvalue_2.18.0
[87] parallelly_1.21.0 readr_1.4.0
[89] gridGraphics_0.5-0 CNEr_1.22.0
[91] reactome.db_1.70.0 scales_1.1.1
[93] memoise_1.1.0 graphite_1.32.0
[95] plyr_1.8.6 ica_1.0-2
[97] gplots_3.1.0 zlibbioc_1.32.0
[99] compiler_3.6.0 RColorBrewer_1.1-2
[101] plotrix_3.7-8 clue_0.3-57
[103] fitdistrplus_1.1-1 Rsamtools_2.2.3
[105] listenv_0.8.0 patchwork_1.1.0
[107] pbapply_1.4-3 MASS_7.3-51.6
[109] mgcv_1.8-31 tidyselect_1.1.0
[111] stringi_1.5.3 GOSemSim_2.12.1
[113] askpass_1.1 ggrepel_0.8.2
[115] grid_3.6.0 fastmatch_1.1-0
[117] tools_3.6.0 future.apply_1.6.0
[119] circlize_0.4.11 rstudioapi_0.13
[121] TFMPvalue_0.0.8 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [123] gridExtra_2.3 farver_2.0.3
[125] Rtsne_0.15 ggraph_2.0.4
[127] digest_0.6.27 rvcheck_0.1.8
[129] BiocManager_1.30.10 shiny_1.5.0
[131] pracma_2.2.9 Rcpp_1.0.5
[133] later_1.1.0.1 harmony_1.0
[135] RcppAnnoy_0.0.16 httr_1.4.2
[137] AnnotationDbi_1.50.3 rhandsontable_0.3.7
[139] ComplexHeatmap_2.2.0 colorspace_2.0-0
[141] XML_3.99-0.3 tensor_1.5
[143] reticulate_1.18 splines_3.6.0
[145] uwot_0.1.8 spatstat.utils_1.17-0
[147] graphlayouts_0.7.1 shinythemes_1.1.2
[149] ggplotify_0.0.5 plotly_4.9.2.1
[151] xtable_1.8-4 jsonlite_1.7.1
[153] poweRlaw_0.70.6 spatstat_1.64-1
[155] tidygraph_1.2.0 R6_2.5.0
[157] pillar_1.4.7 htmltools_0.5.0
[159] mime_0.9 glue_1.4.2
[161] fastmap_1.0.1 codetools_0.2-16
[163] ChIPseeker_1.22.1 fgsea_1.12.0
[165] lattice_0.20-41 tibble_3.0.4
[167] curl_4.3 leiden_0.3.5
[169] gtools_3.8.2 ReactomePA_1.30.0
[171] GO.db_3.10.0 openssl_1.4.3
[173] survival_3.2-7 munsell_0.5.0
[175] DO.db_2.9 GetoptLong_1.0.4
[177] GenomeInfoDbData_1.2.2 reshape2_1.4.4
[179] gtable_0.3.0 Seurat_3.2.2

[rcorces]

looks like it might be a problem with the S4vectors package. Try installing an older version - I'm on 0.24.4

[rcorces]

though on second thought, your version is definitely not the latest. What happens when you do S4Vectors:::.valid.Vector.length()

[annrosebright]

S4Vectors:::.valid.Vector.length()

This is the output :

S4Vectors:::.valid.Vector.length() Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object '.valid.Vector.length' not found

[rcorces]

I think that is the problem. I'm not sure why though. For whatever reason, your S4Vectors install doesnt have that function.

[rcorces]

Sorry - submitted the comment too early. When I run this:

S4Vectors:::.valid.Vector.length(c(1,2,3))

I get NULL. Presumably you get something telling you that the function doesnt exist.

You can try downgrading your S4Vectors package. you might be able to do so by running this from terminal:

wget https://bioconductor.org/packages/3.10/bioc/src/contrib/S4Vectors_0.24.4.tar.gz
R CMD INSTALL S4Vectors_0.24.4.tar.gz

[nikostrasan]

Hello. I am actually facing the same issue since last week. I downgraded the S4Vectors package to 0.24.4 but now facing issues with GenomicRanges (see below).

library(ArchR) Loading required package: SummarizedExperiment Loading required package: GenomicRanges Error: package ‘S4Vectors’ 0.24.4 was found, but >= 0.25.14 is required by ‘GenomicRanges’

May I ask which version of GenomicRanges are you using? It would be great if you could share your sessionInfo() status. Thanks

[rcorces]

Unfortunately, it has been difficult to keep up with package versions. You will need to downgrade your GenomicRanges installation as well. We are working on ways to make this better. You can see the package versions that we used to run the tutorial at the end of the manual: https://www.archrproject.com/bookdown/session-information.html

[nikostrasan]

It makes sense. Thank you very much.

[annrosebright]

Thank you, the problem got solved when I downgraded the necessary packages.