Error: BiocParallel errors

[fang-yulo]

Hi,

Thank you very much for this wonderful package.
I follow the tutorial and use the example file provided to run the "make.projection" function.

But I met this error:

> ref <- load.reference.map()
[1] "Loading Default Reference Atlas..."
[1] "/sbgenomics/workspace/ref_TILAtlas_mouse_v1.rds"
[1] "Loaded Reference map ref_TILAtlas_mouse_v1"

> querydata <- ProjecTILs::query_example_seurat
> query.projected <- make.projection(querydata, ref=ref)

Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error: worker evaluation failed:
  option type has NULL value

Here is my session info.

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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=C
[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] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 GenomicRanges_1.46.1
[4] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3
[7] MatrixGenerics_1.6.0 matrixStats_0.61.0 GEOquery_2.62.2
[10] Biobase_2.54.0 BiocGenerics_0.40.0 ProjecTILs_2.2.1
[13] pracma_2.3.6 ggplot2_3.3.5 gridExtra_2.3
[16] BiocParallel_1.28.3 Matrix_1.4-0 umap_0.2.7.0
[19] scGate_1.0.2 reshape2_1.4.4 ggridges_0.5.3
[22] patchwork_1.1.1 dplyr_1.0.7 data.table_1.14.2
[25] SeuratObject_4.0.4 Seurat_4.0.6 UCell_1.3.1

loaded via a namespace (and not attached):
[1] plyr_1.8.6 igraph_1.2.10 lazyeval_0.2.2
[4] splines_4.1.2 listenv_0.8.0 scattermore_0.7
[7] digest_0.6.29 htmltools_0.5.2 fansi_1.0.2
[10] magrittr_2.0.1 tensor_1.5 cluster_2.1.2
[13] ROCR_1.0-11 tzdb_0.2.0 limma_3.50.0
[16] remotes_2.4.2 globals_0.14.0 readr_2.1.1
[19] askpass_1.1 spatstat.sparse_2.1-0 prettyunits_1.1.1
[22] colorspace_2.0-2 ggrepel_0.9.1 xfun_0.29
[25] RCurl_1.98-1.5 callr_3.7.0 crayon_1.4.2
[28] jsonlite_1.7.3 spatstat.data_2.1-2 survival_3.2-13
[31] zoo_1.8-9 glue_1.6.0 polyclip_1.10-0
[34] gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0
[37] leiden_0.3.9 DelayedArray_0.20.0 pkgbuild_1.3.1
[40] future.apply_1.8.1 abind_1.4-5 scales_1.1.1
[43] DBI_1.1.2 miniUI_0.1.1.1 Rcpp_1.0.8
[46] viridisLite_0.4.0 xtable_1.8-4 reticulate_1.22
[49] spatstat.core_2.3-2 htmlwidgets_1.5.4 httr_1.4.2
[52] RColorBrewer_1.1-2 ellipsis_0.3.2 ica_1.0-2
[55] pkgconfig_2.0.3 farver_2.1.0 uwot_0.1.11
[58] deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.1
[61] labeling_0.4.2 rlang_0.4.12 later_1.3.0
[64] munsell_0.5.0 tools_4.1.2 cli_3.1.1
[67] generics_0.1.1 evaluate_0.14 stringr_1.4.0
[70] fastmap_1.1.0 yaml_2.2.1 goftest_1.2-3
[73] processx_3.5.2 knitr_1.37 fitdistrplus_1.1-6
[76] purrr_0.3.4 RANN_2.6.1 pbapply_1.5-0
[79] future_1.23.0 nlme_3.1-155 mime_0.12
[82] xml2_1.3.3 compiler_4.1.2 rstudioapi_0.13
[85] plotly_4.10.0 curl_4.3.2 png_0.1-7
[88] spatstat.utils_2.3-0 tibble_3.1.6 stringi_1.7.6
[91] ps_1.6.0 RSpectra_0.16-0 lattice_0.20-45
[94] vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1
[97] BiocManager_1.30.16 spatstat.geom_2.3-1 lmtest_0.9-39
[100] RcppAnnoy_0.0.19 bitops_1.0-7 cowplot_1.1.1
[103] irlba_2.3.5 httpuv_1.6.4 R6_2.5.1
[106] promises_1.2.0.1 KernSmooth_2.23-20 parallelly_1.30.0
[109] codetools_0.2-18 MASS_7.3-55 assertthat_0.2.1
[112] openssl_1.4.6 rprojroot_2.0.2 withr_2.4.3
[115] sctransform_0.3.2 GenomeInfoDbData_1.2.7 mgcv_1.8-38
[118] parallel_4.1.2 hms_1.1.1 grid_4.1.2
[121] rpart_4.1-15 tidyr_1.1.4 rmarkdown_2.11
[124] Rtsne_0.15 shiny_1.7.1

Any help would be appreciated.

Thank you very much.

[mass-a]

Hello,

I don't think it's a problem with BiocParallel, the error seems to be "option type has NULL value". Honestly I have never seen this error before.

Can you confirm that the objects you are using are not corrupt, e.g. that you can run the following:

print(ref)
print(querydata)
DimPlot(ref)

[fang-yulo]

Hi,

Yes, I think you are right.
The objects might be a little corrupt, I restarted R and executed the code one more time and the problem was solved.

Thank you very much.

Best.