I got a new Laptop to analyse OMICS data (MacBook Pro with Apple M1 Max Chip) and I tried to analyse RNA Seq Data with Outrider. I installed Rossette 2, gfortran and openblas, because the parallelisation with MulticoreParam() failed at the beginning. Now the parallelization works, but I get this strange error:

a = 5

b = min(ncol(ods), nrow(ods)) / 3 # N/3

Nsteps = min(20, ncol(ods)/3, nrow(ods)/3) # Do either 20 steps or N

pars_q <- round(exp(seq(log(a),log(b),length.out = Nsteps))) %>% unique

ods <- findEncodingDim(ods, lnorm = T, BPPARAM = MulticoreParam(as.integer(8)), params = pars_q)

Tue Nov 8 13:43:17 2022: SizeFactor estimation ...

Tue Nov 8 13:43:17 2022: Controlling for confounders ...

Tue Nov 8 13:43:18 2022: Using the autoencoder implementation for controlling.

[1] "Tue Nov 8 13:43:26 2022: Initial PCA loss: 8.33004023797846"

[1] "Tue Nov 8 13:44:47 2022: Iteration: 1 loss: 6.74682189972167"

[1] "Tue Nov 8 14:01:36 2022: Iteration: 2 loss: 6.72701244516823"

[1] "Tue Nov 8 14:50:26 2022: Iteration: 3 loss: 6.72234802906423"

[1] "Tue Nov 8 14:51:05 2022: Iteration: 4 loss: 6.72036914942374"

[1] "Tue Nov 8 14:51:40 2022: Iteration: 5 loss: 6.71919362326822"

[1] "Tue Nov 8 14:52:15 2022: Iteration: 6 loss: 6.71838850026935"

[1] "Tue Nov 8 14:52:49 2022: Iteration: 7 loss: 6.71779557227038"

[1] "Tue Nov 8 15:17:21 2022: Iteration: 8 loss: 6.71733460748282"

[1] "Tue Nov 8 15:17:55 2022: Iteration: 9 loss: 6.71699801668689"

[1] "Tue Nov 8 15:18:28 2022: Iteration: 10 loss: 6.71672009727248"

[1] "Tue Nov 8 15:19:01 2022: Iteration: 11 loss: 6.71651699889295"

[1] "Tue Nov 8 15:19:34 2022: Iteration: 12 loss: 6.71635916723858"

[1] "Tue Nov 8 15:20:06 2022: Iteration: 13 loss: 6.71623831491149"

[1] "Tue Nov 8 15:20:40 2022: Iteration: 14 loss: 6.71614050976445"

[1] "Tue Nov 8 15:21:11 2022: Iteration: 15 loss: 6.71608078863923"

Error: BiocParallel errors

element index: 1, 2, 3

first error: unable to find an inherited method for function ‘bpbackend’ for signature ‘"SerialParam"’

In addition: Warning messages:

1: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading

2: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

3: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

4: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

5: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

6: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

7: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

8: In serialize(data, node$con, xdr = FALSE) :

'package:stats' may not be available when loading

9: stop worker failed:

attempt to select less than one element in OneIndex

sessionInfo()

R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Ventura 13.0

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] tibble_3.1.8 readr_2.1.3 magrittr_2.0.3 dplyr_1.0.10
[5] ggplot2_3.3.6 OUTRIDER_1.14.0 data.table_1.14.4 SummarizedExperiment_1.26.1 [9] MatrixGenerics_1.8.1 matrixStats_0.62.0 GenomicFeatures_1.48.4 AnnotationDbi_1.58.0
[13] Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4 IRanges_2.30.1
[17] S4Vectors_0.34.0 BiocGenerics_0.42.0 BiocParallel_1.17.9.1

loaded via a namespace (and not attached): [1] colorspace_2.0-3 rjson_0.2.21 ellipsis_0.3.2 XVector_0.36.0
[5] rstudioapi_0.14 farver_2.1.1 bit64_4.0.5 fansi_1.0.3
[9] xml2_1.3.3 codetools_0.2-18 splines_4.2.1 PRROC_1.3.1
[13] cachem_1.0.6 geneplotter_1.74.0 jsonlite_1.8.3 Rsamtools_2.12.0
[17] annotate_1.74.0 dbplyr_2.2.1 png_0.1-7 pheatmap_1.0.12
[21] compiler_4.2.1 httr_1.4.4 backports_1.4.1 assertthat_0.2.1
[25] Matrix_1.5-1 fastmap_1.1.0 lazyeval_0.2.2 cli_3.4.1
[29] htmltools_0.5.3 prettyunits_1.1.1 tools_4.2.1 gtable_0.3.1
[33] glue_1.6.2 GenomeInfoDbData_1.2.8 reshape2_1.4.4 rappdirs_0.3.3
[37] Rcpp_1.0.9 vctrs_0.5.0 Biostrings_2.64.1 rtracklayer_1.56.1
[41] iterators_1.0.14 stringr_1.4.1 lifecycle_1.0.3 restfulr_0.0.15
[45] XML_3.99-0.12 dendextend_1.16.0 ca_0.71.1 zlibbioc_1.42.0
[49] scales_1.2.1 TSP_1.2-1 pcaMethods_1.88.0 hms_1.1.2
[53] parallel_4.2.1 RColorBrewer_1.1-3 BBmisc_1.13 yaml_2.3.6
[57] curl_4.3.3 memoise_2.0.1 heatmaply_1.4.0 gridExtra_2.3
[61] biomaRt_2.52.0 stringi_1.7.8 RSQLite_2.2.18 genefilter_1.78.0
[65] BiocIO_1.6.0 foreach_1.5.2 checkmate_2.1.0 seriation_1.4.0
[69] filelock_1.0.2 rlang_1.0.6 pkgconfig_2.0.3 bitops_1.0-7
[73] lattice_0.20-45 purrr_0.3.5 GenomicAlignments_1.32.1 htmlwidgets_1.5.4
[77] bit_4.0.4 tidyselect_1.2.0 plyr_1.8.7 DESeq2_1.36.0
[81] R6_2.5.1 snow_0.4-4 generics_0.1.3 DelayedArray_0.22.0
[85] DBI_1.1.3 withr_2.5.0 pillar_1.8.1 survival_3.4-0
[89] KEGGREST_1.36.3 RCurl_1.98-1.9 crayon_1.5.2 utf8_1.2.2
[93] BiocFileCache_2.4.0 plotly_4.10.0 tzdb_0.3.0 viridis_0.6.2
[97] progress_1.2.2 locfit_1.5-9.6 grid_4.2.1 blob_1.2.3
[101] digest_0.6.30 webshot_0.5.4 xtable_1.8-4 tidyr_1.2.1
[105] munsell_0.5.0 registry_0.5-1 viridisLite_0.4.1

I would be soooo happy if anyone could help me because I didn't find anything in the internet.

Thank you in advance!