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Error: getRealizationBackend is defunct. #9

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Error: getRealizationBackend is defunct.#9
@maxim-h

Description

@maxim-h
maxim-h
opened on May 16, 2022

While trying the vanilla analysis from the vignette after the following call:

run_atac("ChrAccR_analysis", "bamFilenameFull", sampleAnnot, genome="hg38", sampleIdCol="sampleId", regionSets=regionSetList)

I get the error:

Error: 'getRealizationBackend' is defunct.
Use 'getAutoRealizationBackend' instead.
See help("Defunct")
Here are the logs preceding the error. 2022-05-16 15:27:28 2.4 STATUS STARTED ChrAccR analysis 2022-05-16 15:27:28 2.4 INFO Detected input type: bulk_bam 2022-05-16 15:27:28 2.4 STATUS STARTED Preparing DsATAC dataset from input files Loading required namespace: HDF5Array 2022-05-16 15:27:28 2.4 STATUS STARTED Creating DsATAC object 2022-05-16 15:27:28 2.4 INFO Including region set: tiling500bp 2022-05-16 15:27:36 3.2 INFO Including region set: cancerPeaks 2022-05-16 15:27:37 3.2 STATUS COMPLETED Creating DsATAC object 2022-05-16 15:27:37 3.2 STATUS STARTED Reading ATAC data 2022-05-16 15:27:37 3.2 STATUS STARTED Adding insertion data from files 2022-05-16 15:27:37 3.2 STATUS Importing sample : TCD8EM_S_1001_a (1 of 33) 2022-05-16 15:27:37 3.2 STATUS STARTED Reading insertion data for sample: TCD8EM_S_1001_a 2022-05-16 15:27:38 3.3 INFO detected paired-end data 2022-05-16 15:27:38 3.3 INFO 194449 fragments found 2022-05-16 15:27:38 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_S_1001_a 2022-05-16 15:27:38 3.3 STATUS Importing sample : TCD8EM_S_1002_a (2 of 33) 2022-05-16 15:27:39 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_S_1002_a 2022-05-16 15:27:39 3.3 INFO detected paired-end data 2022-05-16 15:27:39 3.3 INFO 126042 fragments found 2022-05-16 15:27:39 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_S_1002_a 2022-05-16 15:27:40 3.3 STATUS Importing sample : TCD8EM_S_1003_a (3 of 33) 2022-05-16 15:27:40 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_S_1003_a 2022-05-16 15:27:40 3.3 INFO detected paired-end data 2022-05-16 15:27:40 3.3 INFO 82194 fragments found 2022-05-16 15:27:40 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_S_1003_a 2022-05-16 15:27:40 3.3 STATUS Importing sample : TCD8EM_S_1004_a (4 of 33) 2022-05-16 15:27:40 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_S_1004_a 2022-05-16 15:27:41 3.3 INFO detected paired-end data 2022-05-16 15:27:41 3.3 INFO 127899 fragments found 2022-05-16 15:27:41 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_S_1004_a 2022-05-16 15:27:41 3.3 STATUS Importing sample : TCD8EM_U_1001_a (5 of 33) 2022-05-16 15:27:41 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_U_1001_a 2022-05-16 15:27:42 3.3 INFO detected paired-end data 2022-05-16 15:27:43 3.3 INFO 220122 fragments found 2022-05-16 15:27:43 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_U_1001_a 2022-05-16 15:27:43 3.3 STATUS Importing sample : TCD8EM_U_1002_a (6 of 33) 2022-05-16 15:27:43 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_U_1002_a 2022-05-16 15:27:43 3.3 INFO detected paired-end data 2022-05-16 15:27:44 3.3 INFO 112974 fragments found 2022-05-16 15:27:44 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_U_1002_a 2022-05-16 15:27:44 3.3 STATUS Importing sample : TCD8EM_U_1003_a (7 of 33) 2022-05-16 15:27:44 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_U_1003_a 2022-05-16 15:27:44 3.3 INFO detected paired-end data 2022-05-16 15:27:44 3.3 INFO 81910 fragments found 2022-05-16 15:27:44 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_U_1003_a 2022-05-16 15:27:45 3.3 STATUS Importing sample : TCD8EM_U_1004_a (8 of 33) 2022-05-16 15:27:45 3.3 STATUS STARTED Reading insertion data for sample: TCD8EM_U_1004_a 2022-05-16 15:27:45 3.3 INFO detected paired-end data 2022-05-16 15:27:46 3.3 INFO 140700 fragments found 2022-05-16 15:27:46 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8EM_U_1004_a 2022-05-16 15:27:46 3.3 STATUS Importing sample : TCD8naive_S_1001_a (9 of 33) 2022-05-16 15:27:46 3.3 STATUS STARTED Reading insertion data for sample: TCD8naive_S_1001_a 2022-05-16 15:27:46 3.3 INFO detected paired-end data 2022-05-16 15:27:47 3.3 INFO 147192 fragments found 2022-05-16 15:27:47 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8naive_S_1001_a 2022-05-16 15:27:47 3.3 STATUS Importing sample : TCD8naive_S_1002_a (10 of 33) 2022-05-16 15:27:47 3.3 STATUS STARTED Reading insertion data for sample: TCD8naive_S_1002_a 2022-05-16 15:27:48 3.3 INFO detected paired-end data 2022-05-16 15:27:48 3.3 INFO 162182 fragments found 2022-05-16 15:27:48 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8naive_S_1002_a 2022-05-16 15:27:48 3.3 STATUS Importing sample : TCD8naive_S_1003_a (11 of 33) 2022-05-16 15:27:48 3.3 STATUS STARTED Reading insertion data for sample: TCD8naive_S_1003_a 2022-05-16 15:27:49 3.3 INFO detected paired-end data 2022-05-16 15:27:49 3.3 INFO 90932 fragments found 2022-05-16 15:27:49 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8naive_S_1003_a 2022-05-16 15:27:49 3.3 STATUS Importing sample : TCD8naive_S_1004_a (12 of 33) 2022-05-16 15:27:49 3.3 STATUS STARTED Reading insertion data for sample: TCD8naive_S_1004_a 2022-05-16 15:27:49 3.3 INFO detected paired-end data 2022-05-16 15:27:50 3.3 INFO 111048 fragments found 2022-05-16 15:27:50 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8naive_S_1004_a 2022-05-16 15:27:50 3.3 STATUS Importing sample : TCD8naive_U_1001_a (13 of 33) 2022-05-16 15:27:50 3.3 STATUS STARTED Reading insertion data for sample: TCD8naive_U_1001_a 2022-05-16 15:27:50 3.3 INFO detected paired-end data 2022-05-16 15:27:50 3.3 INFO 112998 fragments found 2022-05-16 15:27:51 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8naive_U_1001_a 2022-05-16 15:27:51 3.3 STATUS Importing sample : TCD8naive_U_1002_a (14 of 33) 2022-05-16 15:27:51 3.3 STATUS STARTED Reading insertion data for sample: TCD8naive_U_1002_a 2022-05-16 15:27:52 3.2 INFO detected paired-end data 2022-05-16 15:27:52 3.2 INFO 186081 fragments found 2022-05-16 15:27:52 3.2 STATUS COMPLETED Reading insertion data for sample: TCD8naive_U_1002_a 2022-05-16 15:27:52 3.2 STATUS Importing sample : TCD8naive_U_1003_a (15 of 33) 2022-05-16 15:27:52 3.2 STATUS STARTED Reading insertion data for sample: TCD8naive_U_1003_a 2022-05-16 15:27:53 3.2 INFO detected paired-end data 2022-05-16 15:27:53 3.2 INFO 81234 fragments found 2022-05-16 15:27:53 3.2 STATUS COMPLETED Reading insertion data for sample: TCD8naive_U_1003_a 2022-05-16 15:27:53 3.2 STATUS Importing sample : TCD8naive_U_1004_a (16 of 33) 2022-05-16 15:27:53 3.2 STATUS STARTED Reading insertion data for sample: TCD8naive_U_1004_a 2022-05-16 15:27:54 3.3 INFO detected paired-end data 2022-05-16 15:27:54 3.3 INFO 261598 fragments found 2022-05-16 15:27:54 3.3 STATUS COMPLETED Reading insertion data for sample: TCD8naive_U_1004_a 2022-05-16 15:27:54 3.3 STATUS Importing sample : TeffMem_S_1001_a (17 of 33) 2022-05-16 15:27:54 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_S_1001_a 2022-05-16 15:27:55 3.3 INFO detected paired-end data 2022-05-16 15:27:55 3.3 INFO 110410 fragments found 2022-05-16 15:27:55 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_S_1001_a 2022-05-16 15:27:55 3.3 STATUS Importing sample : TeffMem_S_1002_a (18 of 33) 2022-05-16 15:27:55 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_S_1002_a 2022-05-16 15:27:56 3.3 INFO detected paired-end data 2022-05-16 15:27:56 3.3 INFO 119518 fragments found 2022-05-16 15:27:56 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_S_1002_a 2022-05-16 15:27:56 3.3 STATUS Importing sample : TeffMem_S_1003_a (19 of 33) 2022-05-16 15:27:56 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_S_1003_a 2022-05-16 15:27:57 3.3 INFO detected paired-end data 2022-05-16 15:27:57 3.3 INFO 61062 fragments found 2022-05-16 15:27:57 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_S_1003_a 2022-05-16 15:27:57 3.3 STATUS Importing sample : TeffMem_S_1004_a (20 of 33) 2022-05-16 15:27:57 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_S_1004_a 2022-05-16 15:27:58 3.3 INFO detected paired-end data 2022-05-16 15:27:58 3.3 INFO 146879 fragments found 2022-05-16 15:27:58 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_S_1004_a 2022-05-16 15:27:58 3.3 STATUS Importing sample : TeffMem_U_1001_a (21 of 33) 2022-05-16 15:27:58 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_U_1001_a 2022-05-16 15:27:59 3.3 INFO detected paired-end data 2022-05-16 15:27:59 3.3 INFO 111274 fragments found 2022-05-16 15:27:59 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_U_1001_a 2022-05-16 15:27:59 3.3 STATUS Importing sample : TeffMem_U_1002_a (22 of 33) 2022-05-16 15:27:59 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_U_1002_a 2022-05-16 15:28:00 3.3 INFO detected paired-end data 2022-05-16 15:28:00 3.3 INFO 161368 fragments found 2022-05-16 15:28:00 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_U_1002_a 2022-05-16 15:28:00 3.3 STATUS Importing sample : TeffMem_U_1003_a (23 of 33) 2022-05-16 15:28:00 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_U_1003_a 2022-05-16 15:28:01 3.3 INFO detected paired-end data 2022-05-16 15:28:01 3.3 INFO 74197 fragments found 2022-05-16 15:28:01 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_U_1003_a 2022-05-16 15:28:01 3.3 STATUS Importing sample : TeffMem_U_1004_a (24 of 33) 2022-05-16 15:28:01 3.3 STATUS STARTED Reading insertion data for sample: TeffMem_U_1004_a 2022-05-16 15:28:01 3.3 INFO detected paired-end data 2022-05-16 15:28:01 3.3 INFO 108418 fragments found 2022-05-16 15:28:02 3.3 STATUS COMPLETED Reading insertion data for sample: TeffMem_U_1004_a 2022-05-16 15:28:02 3.3 STATUS Importing sample : TeffNaive_S_1001_a (25 of 33) 2022-05-16 15:28:02 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_S_1001_a 2022-05-16 15:28:02 3.3 INFO detected paired-end data 2022-05-16 15:28:03 3.3 INFO 145525 fragments found 2022-05-16 15:28:03 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_S_1001_a 2022-05-16 15:28:03 3.3 STATUS Importing sample : TeffNaive_S_1002_a (26 of 33) 2022-05-16 15:28:03 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_S_1002_a 2022-05-16 15:28:03 3.3 INFO detected paired-end data 2022-05-16 15:28:04 3.3 INFO 109275 fragments found 2022-05-16 15:28:04 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_S_1002_a 2022-05-16 15:28:04 3.3 STATUS Importing sample : TeffNaive_S_1003_a (27 of 33) 2022-05-16 15:28:04 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_S_1003_a 2022-05-16 15:28:04 3.3 INFO detected paired-end data 2022-05-16 15:28:04 3.3 INFO 66745 fragments found 2022-05-16 15:28:04 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_S_1003_a 2022-05-16 15:28:04 3.3 STATUS Importing sample : TeffNaive_S_1004_a (28 of 33) 2022-05-16 15:28:04 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_S_1004_a 2022-05-16 15:28:05 3.3 INFO detected paired-end data 2022-05-16 15:28:05 3.3 INFO 181287 fragments found 2022-05-16 15:28:06 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_S_1004_a 2022-05-16 15:28:06 3.3 STATUS Importing sample : TeffNaive_S_1011_a (29 of 33) 2022-05-16 15:28:06 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_S_1011_a 2022-05-16 15:28:06 3.3 INFO detected paired-end data 2022-05-16 15:28:07 3.3 INFO 153259 fragments found 2022-05-16 15:28:07 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_S_1011_a 2022-05-16 15:28:07 3.3 STATUS Importing sample : TeffNaive_U_1001_a (30 of 33) 2022-05-16 15:28:07 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_U_1001_a 2022-05-16 15:28:07 3.3 INFO detected paired-end data 2022-05-16 15:28:08 3.3 INFO 111424 fragments found 2022-05-16 15:28:08 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_U_1001_a 2022-05-16 15:28:08 3.3 STATUS Importing sample : TeffNaive_U_1002_a (31 of 33) 2022-05-16 15:28:08 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_U_1002_a 2022-05-16 15:28:09 3.3 INFO detected paired-end data 2022-05-16 15:28:09 3.3 INFO 207690 fragments found 2022-05-16 15:28:09 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_U_1002_a 2022-05-16 15:28:09 3.3 STATUS Importing sample : TeffNaive_U_1003_a (32 of 33) 2022-05-16 15:28:09 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_U_1003_a 2022-05-16 15:28:10 3.3 INFO detected paired-end data 2022-05-16 15:28:10 3.3 INFO 77190 fragments found 2022-05-16 15:28:10 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_U_1003_a 2022-05-16 15:28:10 3.3 STATUS Importing sample : TeffNaive_U_1004_a (33 of 33) 2022-05-16 15:28:10 3.3 STATUS STARTED Reading insertion data for sample: TeffNaive_U_1004_a 2022-05-16 15:28:11 3.3 INFO detected paired-end data 2022-05-16 15:28:11 3.3 INFO 160976 fragments found 2022-05-16 15:28:11 3.3 STATUS COMPLETED Reading insertion data for sample: TeffNaive_U_1004_a 2022-05-16 15:28:11 3.3 STATUS COMPLETED Adding insertion data from files 2022-05-16 15:28:11 3.3 STATUS STARTED Agregating region count data
And here is my sessionInfo R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux

Matrix products: default
BLAS: /usr/lib/libblas.so.3.10.1
LAPACK: /usr/lib/liblapack.so.3.10.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome_1.64.0 rtracklayer_1.56.0
[4] Biostrings_2.64.0 XVector_0.36.0 GenomicRanges_1.48.0
[7] GenomeInfoDb_1.32.1 IRanges_2.30.0 S4Vectors_0.34.0
[10] BiocGenerics_0.42.0 ggplot2_3.3.6 ChrAccR_0.9.17

loaded via a namespace (and not attached):
[1] lattice_0.20-45 Rsamtools_2.12.0 assertthat_0.2.1
[4] digest_0.6.29 utf8_1.2.2 R6_2.5.1
[7] evaluate_0.15 pillar_1.7.0 zlibbioc_1.42.0
[10] rlang_1.0.2 rstudioapi_0.13 data.table_1.14.2
[13] Matrix_1.4-1 rmarkdown_2.14 BiocParallel_1.30.0
[16] muLogR_0.2 pheatmap_1.0.12 RCurl_1.98-1.6
[19] munsell_0.5.0 HDF5Array_1.24.0 DelayedArray_0.22.0
[22] compiler_4.2.0 xfun_0.31 pkgconfig_2.0.3
[25] htmltools_0.5.2 tidyselect_1.1.2 SummarizedExperiment_1.26.1
[28] tibble_3.1.7 GenomeInfoDbData_1.2.8 matrixStats_0.62.0
[31] ChrAccRex_0.2 XML_3.99-0.9 fansi_1.0.3
[34] crayon_1.5.1 dplyr_1.0.9 withr_2.5.0
[37] rhdf5filters_1.8.0 GenomicAlignments_1.32.0 muRtools_0.9.5
[40] bitops_1.0-7 grid_4.2.0 jsonlite_1.8.0
[43] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[46] magrittr_2.0.3 scales_1.2.0 cli_3.3.0
[49] renv_0.15.4 ellipsis_0.3.2 generics_0.1.2
[52] vctrs_0.4.1 Rhdf5lib_1.18.0 rjson_0.2.21
[55] restfulr_0.0.13 RColorBrewer_1.1-3 tools_4.2.0
[58] Biobase_2.56.0 glue_1.6.2 purrr_0.3.4
[61] MatrixGenerics_1.8.0 parallel_4.2.0 fastmap_1.1.0
[64] yaml_2.3.5 rhdf5_2.40.0 colorspace_2.0-3
[67] BiocManager_1.30.17 knitr_1.39 BiocIO_1.6.0

Looks like some dependency broke the api.

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