I am working on a Mac from 2017 (should support all assembler instructions)
have downloaded the latest docker image:
>docker pull public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest
latest: Pulling from x4k5d9i7/cytoverse/gs-to-wsp
Digest: sha256:fd76daee4a3c198880e99c2f50a75cc43880ab6da468c81300e833809b05b7ae
Status: Image is up to date for public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest
public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest
protobuf should be the latest version as well (2.3.5)
library(flowWorkspace)
#> As part of improvements to flowWorkspace, some behavior of
#> GatingSet objects has changed. For details, please read the section
#> titled "The cytoframe and cytoset classes" in the package vignette:
#>
#> vignette("flowWorkspace-Introduction", "flowWorkspace")
library(CytoML)
path <- system.file("extdata",package="flowWorkspaceData")
gs_path <- list.files(path, pattern = "gs_manual",full = TRUE)
gs <- load_gs(gs_path)
#output to flowJo
outFile <- tempfile(fileext = ".wsp")
gatingset_to_flowjo(gs, outFile)
#> Using docker image public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest to write FlowJo workspace...
#> Error in gatingset_to_flowjo(gs, outFile): [libprotobuf ERROR external/com_google_protobuf/src/google/protobuf/message_lite.cc:133] Can't parse message of type "pb.GatingHierarchy" because it is missing required fields: tree.node[0].node.hidden, tree.node[1].node.hidden, tree.node[1].node.indices.indtype, tree.node[2].node.hidden, tree.node[2].node.indices.indtype, tree.node[2].node.thisGate.neg, tree.node[3].node.hidden, tree.node[3].node.indices.indtype, tree.node[3].node.thisGate.neg, tree.node[4].node.hidden, tree.node[4].node.indices.indtype, tree.node[4].node.thisGate.neg, tree.node[5].node.hidden, tree.node[5].node.thisGate.neg, tree.node[6].node.hidden, tree.node[6].node.thisGate.neg, tree.node[7].node.hidden, tree.node[7].node.indices.indtype, tree.node[7].node.thisGate.neg, tree.node[8].node.hidden, tree.node[8].node.indices.indtype, tree.node[8].node.thisGate.neg, tree.node[9].node.hidden, tree.node[9].node.thisGate.neg, tree.node[10].node.hidden, tree.node[10].node.indices.indtype, tree.node[10].node.thisGate.neg, tree.node[11].node.hidden, tree.node[11].node.indices.indtype, tree.node[11].node.thisGate.neg, tree.node[12].node.hidden, tree.node[12].node.indices.indtype, tree.node[12].node.thisGate.neg, tree.node[13].node.hidden, tree.node[13].node.indices.indtype, tree.node[13].node.thisGate.neg, tree.node[14].node.hidden, tree.node[14].node.thisGate.neg, tree.node[15].node.hidden, tree.node[15].node.thisGate.neg, tree.node[16].node.hidden, tree.node[16].node.indices.indtype, tree.node[16].node.thisGate.neg, tree.node[17].node.hidden, tree.node[17].node.indices.indtype, tree.node[17].node.thisGate.neg, tree.node[18].node.hidden, tree.node[18].node.indices.indtype, tree.node[18].node.thisGate.neg, tree.node[19].node.hidden, tree.node[19].node.indices.indtype, tree.node[19].node.thisGate.neg, tree.node[20].node.hidden, tree.node[20].node.thisGate.neg, tree.node[21].node.hidden, tree.node[21].node.thisGate.neg, tree.node[22].node.hidden, tree.node[22].node.thisGate.neg, tree.node[23].node.hidden, tree.node[23].node.thisGate.negterminate called after throwing an instance of 'std::domain_error' what(): Failed to parse GatingHierarchy CytoTrol_CytoTrol_1.fcs
sessionInfo()
#> R version 4.0.4 (2021-02-15)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] CytoML_2.3.4 flowWorkspace_4.3.8
#>
#> loaded via a namespace (and not attached):
#> [1] Biobase_2.50.0 httr_1.4.2 jsonlite_1.7.2
#> [4] RcppParallel_5.1.2 assertthat_0.2.1 highr_0.9
#> [7] stats4_4.0.4 latticeExtra_0.6-29 RBGL_1.66.0
#> [10] yaml_2.2.1 pillar_1.6.0 backports_1.2.1
#> [13] lattice_0.20-41 glue_1.4.2 digest_0.6.27
#> [16] RColorBrewer_1.1-2 colorspace_2.0-0 ggcyto_1.18.0
#> [19] htmltools_0.5.1.1 plyr_1.8.6 XML_3.99-0.6
#> [22] pkgconfig_2.0.3 zlibbioc_1.36.0 purrr_0.3.4
#> [25] flowCore_2.3.2 scales_1.1.1 jpeg_0.1-8.1
#> [28] tibble_3.1.1 aws.s3_0.3.21 styler_1.4.1
#> [31] generics_0.1.0 ggplot2_3.3.3 ellipsis_0.3.1
#> [34] withr_2.4.2 BiocGenerics_0.36.1 hexbin_1.28.2
#> [37] magrittr_2.0.1 crayon_1.4.1 evaluate_0.14
#> [40] fs_1.5.0 fansi_0.4.2 xml2_1.3.2
#> [43] graph_1.68.0 tools_4.0.4 data.table_1.14.0
#> [46] ncdfFlow_2.36.0 lifecycle_1.0.0 matrixStats_0.58.0
#> [49] stringr_1.4.0 S4Vectors_0.28.1 munsell_0.5.0
#> [52] reprex_2.0.0 compiler_4.0.4 rlang_0.4.10
#> [55] grid_4.0.4 aws.signature_0.6.0 base64enc_0.1-3
#> [58] rmarkdown_2.7 cytolib_2.3.9 gtable_0.3.0
#> [61] DBI_1.1.1 curl_4.3 R6_2.5.0
#> [64] RProtoBufLib_2.3.5 gridExtra_2.3 knitr_1.33
#> [67] dplyr_1.0.5 utf8_1.2.1 Rgraphviz_2.34.0
#> [70] stringi_1.5.3 parallel_4.0.4 Rcpp_1.0.6
#> [73] vctrs_0.3.7 png_0.1-7 tidyselect_1.1.0
#> [76] xfun_0.22
I am working on a Mac from 2017 (should support all assembler instructions) have downloaded the latest docker image:
protobuf should be the latest version as well (2.3.5)
Created on 2021-04-27 by the reprex package (v2.0.0)