flowWorkspace cannot load external data
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Entering edit mode
@brentocarrigan-21529
Last seen 23 months ago

Hi,

The external data for flowWorkspace vignettes cannot seem to be loaded. No error message generated, just a blank character string returned. The external data for flowCore loads correctly.

flowWorkspace example

> BiocManager::install('flowWorkspace')
> library(flowWorkspace)

> flowDataPath <- system.file("extdata", package = "flowWorkspaceData")
> gs <- load_gs(file.path(flowDataPath,"gs_manual"))
Error in normalizePath(path, mustWork = TRUE) : 
  path[1]="/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/extdata/gs_manual": No such file or directory

It's true: in the flowWorkspace directory /Library/Frameworks/R.framework/Resources/library/flowWorkspace/extdata there is no file called gs_manual, only empty_workspace_9.2.xml

Have tried restarting R session, re-installing flowWorkspace - no luck

flowCore comparison:

> browseVignettes('flowCore')
> file.name <- system.file("extdata","0877408774.B08", 
+                          package="flowCore")
> file.name
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowCore/extdata/0877408774.B08"
> x <- read.FCSfile.name, transformation=FALSE)
> summary(x)
            FSC-H     SSC-H    FL1-H     FL2-H    FL3-H     FL1-A     FL4-H   Time
Min.      85.0000   11.0000   0.0000    0.0000   0.0000    0.0000    0.0000   1.00
1st Qu.  385.0000  141.0000 233.0000  277.0000  90.0000    0.0000  210.0000 122.00
Median   441.0000  189.0000 545.5000  346.0000 193.0000   26.0000  279.0000 288.00
Mean     491.9644  277.9105 439.1023  366.1567 179.7122   34.0766  323.5306 294.77
3rd Qu.  518.0000  270.0000 610.0000  437.0000 264.0000   51.0000  390.0000 457.50
Max.    1023.0000 1023.0000 912.0000 1023.0000 900.0000 1023.0000 1022.0000 626.00

Session info:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] flowWorkspace_3.32.0      ncdfFlow_2.30.1           BH_1.69.0-1              
[4] RcppArmadillo_0.9.600.4.0 flowCore_1.50.0          

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5    purrr_0.3.2         lattice_0.20-38     pcaPP_1.9-73        colorspace_1.4-1   
 [6] stats4_3.6.0        yaml_2.2.0          rlang_0.4.0         hexbin_1.27.3       pillar_1.4.2       
[11] glue_1.3.1          Rgraphviz_2.28.0    BiocGenerics_0.30.0 RColorBrewer_1.1-2  matrixStats_0.54.0 
[16] robustbase_0.93-5   stringr_1.4.0       zlibbioc_1.30.0     munsell_0.5.0       gtable_0.3.0       
[21] mvtnorm_1.0-11      latticeExtra_0.6-28 Biobase_2.44.0      parallel_3.6.0      DEoptimR_1.0-8     
[26] Rcpp_1.0.2          KernSmooth_2.23-15  corpcor_1.6.9       scales_1.0.0        BiocManager_1.30.4 
[31] RcppParallel_4.4.3  graph_1.62.0        IDPmisc_1.1.19      gridExtra_2.3       digest_0.6.20      
[36] stringi_1.4.3       dplyr_0.8.3         grid_3.6.0          tools_3.6.0         magrittr_1.5       
[41] tibble_2.1.3        cluster_2.1.0       crayon_1.3.4        rrcov_1.4-7         pkgconfig_2.0.2    
[46] MASS_7.3-51.4       flowViz_1.48.0      data.table_1.12.2   assertthat_0.2.1    rstudioapi_0.10    
[51] R6_2.4.0            compiler_3.6.0     
flowWorkspace external data flowCore • 331 views
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3
Entering edit mode
@martin-morgan-1513
Last seen 3 months ago
United States

Based on this line

flowDataPath <- system.file("extdata", package = "flowWorkspaceData")

I'd guess that you would also need BiocManager::install("flowWorkspaceData")

ADD COMMENT
0
Entering edit mode

Great spot! Thanks Martin, issue solved. In the flowWorkspace vignettes there was not a call to specifically install the separate flowWorkspaceData package but that has solved the issue - thank you!

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