cytobank_to_gatingset path too long Error
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km_sch2002 • 0
@km_sch2002-24037
Last seen 3.5 years ago

This is my first attempt using package CytoML and function cytobanktogatingset. I am encountering this error:

      Error in basename(gs_pop_get_children(y[[1]], parent)) : path too long

Maybe there are limits to the number of characters that can be used for population/gate names? Or limits to the number of populations/gates in hierarchies? These are mass cytometry data. I don't think it's particularly large/complex. I manually replaced '/' with ':' in the XML file because the forward slashes were causing errors. These are mass cytometry data so I wasn't expecting/needing compensation so I think that Warning message is fine. Objects ce, xmlfile, and fcsFiles were made just fine. The cytobanktogatingset() function ran for awhile and sent a list of Cytobank populations/gates to the Console before stopping at the 'path too long' error.

EDIT: I exported a Public Cytobank project to .acs and successfully ran the cytobanktogatingset() function. It's something about my Cytobank Experiment that is fouled up. Just curious if anyone else has rcv this same error and whether it might point me to where the foul up is.

kurt.

ce <- open_cytobank_experiment("D:/experiment_320799_Aug-22-2020_03-27-PM.acs", exdir=tempfile())
xmlfile <- ce$gatingML
fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)
gs <<- cytobank_to_gatingset(xmlfile, fcsFiles)

Error in basename(gs_pop_get_children(y[[1]], parent)) : path too long
In addition: Warning message:
In compensate(gs, g) :
  Compensation is skipped!Because gates refer to 'FCS' for compensation but no spillover is found in FCS.

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] ggcyto_1.16.0             flowWorkspace_4.0.6       ncdfFlow_2.34.0           BH_1.72.0-3               RcppArmadillo_0.9.900.2.0 ggplot2_3.3.2             CytoML_2.0.5              flowCore_2.0.1           

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          plyr_1.8.6          compiler_4.0.2      pillar_1.4.6        cytolib_2.0.3       RColorBrewer_1.1-2  tools_4.0.2         base64enc_0.1-3     zlibbioc_1.34.0     digest_0.6.25       jsonlite_1.7.0     
[12] gtable_0.3.0        lifecycle_0.2.0     tibble_3.0.3        lattice_0.20-41     pkgconfig_2.0.3     png_0.1-7           rlang_0.4.7         graph_1.66.0        Rgraphviz_2.32.0    yaml_2.2.1          parallel_4.0.2     
[23] hexbin_1.28.1       gridExtra_2.3       withr_2.2.0         xml2_1.3.2          stringr_1.4.0       dplyr_1.0.2         generics_0.0.2      vctrs_0.3.2         stats4_4.0.2        grid_4.0.2          tidyselect_1.1.0   
[34] glue_1.4.1          data.table_1.13.0   Biobase_2.48.0      R6_2.4.1            jpeg_0.1-8.1        XML_3.99-0.5        RBGL_1.64.0         latticeExtra_0.6-29 RProtoBufLib_2.0.0  purrr_0.3.4         magrittr_1.5       
[45] scales_1.1.1        matrixStats_0.56.0  ellipsis_0.3.1      BiocGenerics_0.34.0 colorspace_1.4-1    stringi_1.4.6       munsell_0.5.0       RcppParallel_5.0.2  crayon_1.3.4       
CytoML cytobank_to_gatingset • 755 views
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Could you possibly show the output of:

str(xmlfile)
str(fcsFiles)

Also, have you tried on another OS?

Out of curiosity, don't the slashes on Windows go the other way? So, D:/experiment_320799_Aug-22-2020_03-27-PM.acs should be D:\experiment_320799_Aug-22-2020_03-27-PM.acs ?

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I'd be happy to take a quick look at the project if you send it to jpwagner@fredhutch.org. The error is arising here, but I'm not entirely sure why without seeing your particular files. It's likely something went a little awry earlier in the process before hitting the gating_graphGML call.

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