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tgjohnst
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@tgjohnst-14344
Last seen 7.1 years ago
My team recently updated our Rstudio server (which involved updating R 3.3.2 to 3.4.1 and building the newest version of all packages including DiffBind - previously 2.2.12, now 2.6.0) and since the update, we have been receiving errors when attempting to run the dba.count() function. Following is the output when running the command on a dba object that was imported using the same process that worked in the previous version. I googled around but can't figure out the origin of the error and was wondering if anyone has any insight into what might be causing it?
> replicate_peaks_lenient_counts <- dba.count(replicate_peaks_lenient, minOverlap=1) Error: Error processing one or more read files. Check warnings(). In addition: There were 25 warnings (use warnings() to see them) > warnings() Warning messages: 1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) : all scheduled cores encountered errors in user code 2: "croi_count_reads" not resolved from current namespace (DiffBind) 3: "croi_count_reads" not resolved from current namespace (DiffBind) 4: "croi_count_reads" not resolved from current namespace (DiffBind) 5: "croi_count_reads" not resolved from current namespace (DiffBind) 6: "croi_count_reads" not resolved from current namespace (DiffBind) 7: "croi_count_reads" not resolved from current namespace (DiffBind) 8: "croi_count_reads" not resolved from current namespace (DiffBind) 9: "croi_count_reads" not resolved from current namespace (DiffBind) 10: "croi_count_reads" not resolved from current namespace (DiffBind) 11: "croi_count_reads" not resolved from current namespace (DiffBind) 12: "croi_count_reads" not resolved from current namespace (DiffBind) 13: "croi_count_reads" not resolved from current namespace (DiffBind) 14: "croi_count_reads" not resolved from current namespace (DiffBind) 15: "croi_count_reads" not resolved from current namespace (DiffBind) 16: "croi_count_reads" not resolved from current namespace (DiffBind) 17: "croi_count_reads" not resolved from current namespace (DiffBind) 18: "croi_count_reads" not resolved from current namespace (DiffBind) 19: "croi_count_reads" not resolved from current namespace (DiffBind) 20: "croi_count_reads" not resolved from current namespace (DiffBind) 21: "croi_count_reads" not resolved from current namespace (DiffBind) 22: "croi_count_reads" not resolved from current namespace (DiffBind) 23: "croi_count_reads" not resolved from current namespace (DiffBind) 24: "croi_count_reads" not resolved from current namespace (DiffBind) 25: "croi_count_reads" not resolved from current namespace (DiffBind)
And below is my sessionInfo():
> sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] 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] DiffBind_2.6.0 SummarizedExperiment_1.8.0 DelayedArray_0.4.1 matrixStats_0.52.2 Biobase_2.38.0 [6] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 [11] BiocInstaller_1.28.0 loaded via a namespace (and not attached): [1] Category_2.44.0 bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2 progress_1.1.2 [6] Rgraphviz_2.22.0 tools_3.4.1 backports_1.1.1 R6_2.2.2 KernSmooth_2.23-15 [11] DBI_0.7 lazyeval_0.2.1 colorspace_1.3-2 prettyunits_1.0.2 RMySQL_0.10.13 [16] bit_1.1-12 compiler_3.4.1 sendmailR_1.2-1 graph_1.56.0 rtracklayer_1.38.0 [21] caTools_1.17.1 scales_0.5.0 checkmate_1.8.5 BatchJobs_1.6 genefilter_1.60.0 [26] RBGL_1.54.0 stringr_1.2.0 digest_0.6.12 Rsamtools_1.30.0 AnnotationForge_1.20.0 [31] XVector_0.18.0 base64enc_0.1-3 pkgconfig_2.0.1 limma_3.34.0 rlang_0.1.4 [36] RSQLite_2.0 BBmisc_1.11 bindr_0.1 GOstats_2.44.0 hwriter_1.3.2 [41] BiocParallel_1.12.0 gtools_3.5.0 dplyr_0.7.4 RCurl_1.95-4.8 magrittr_1.5 [46] GO.db_3.4.2 GenomeInfoDbData_0.99.1 Matrix_1.2-11 Rcpp_0.12.13 munsell_0.4.3 [51] yaml_2.1.14 stringi_1.1.5 edgeR_3.20.1 zlibbioc_1.24.0 gplots_3.0.1 [56] fail_1.3 plyr_1.8.4 grid_3.4.1 blob_1.1.0 ggrepel_0.7.0 [61] gdata_2.18.0 lattice_0.20-35 Biostrings_2.46.0 splines_3.4.1 GenomicFeatures_1.30.0 [66] annotate_1.56.0 locfit_1.5-9.1 rjson_0.2.15 systemPipeR_1.12.0 biomaRt_2.34.0 [71] glue_1.2.0 XML_3.98-1.9 ShortRead_1.36.0 latticeExtra_0.6-28 gtable_0.2.0 [76] amap_0.8-14 assertthat_0.2.0 ggplot2_2.2.1 xtable_1.8-2 survival_2.41-3 [81] tibble_1.3.4 pheatmap_1.0.8 GenomicAlignments_1.14.0 AnnotationDbi_1.40.0 memoise_1.1.0 [86] bindrcpp_0.2 brew_1.0-6 GSEABase_1.40.0
Hi,
Yes, it's broken. I'll check in a fix ASAP. The rules for registering native routines were tightened up a bit, and the one used by dba.count wasn't (isn't) registered properly. I'l. post as soon as I check in the fix. Sorry about that.