Error: could not find function "loadMethod"

[nyudanin]

Hi all, I'm trying to run the script on two FCS files, and both cytoscape and R keep hanging up because of this "loadMethod" issue. I've included the output (until where it hangs up). Does anyone know how to fix this? Thanks! Naomi

BEGIN AUTOGENERATED DATA

FILE_TO_PROCESS="." CLUSTERING_MARKERS=c("APC-Cy7-A","Alexa Fluor 700-A","FSC-A","PE-A","Pacific Blue-A","Qdot 655-A","SSC-A") PANELS=list(

• list(
• panel_files=c(),
• median_cols=NULL,
• reference_files=NULL,
• fold_cols=NULL
• ),
• list(
• panel_files=c("LungWT1.fcs","SpleenWT1.fcs"),
• median_cols=NULL,
• reference_files=c("SpleenWT1.fcs"),
• fold_cols=c("FITC-A","PE-Cy7-A","PerCP-Cy5-5-A")
• )) TRANSFORMS=flowCore::arcsinhTransform(a=0, b=0.007) Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

DOWNSAMPLED_EVENTS=5000 DOWNSAMPLING_TARGET_PCTILE=NULL TARGET_CLUSTERS=200 CLUSTERING_SAMPLES=50000 DOWNSAMPLING_EXCLUDE_PCTILE=0.01 NODE_SIZE_SCALE_FACTOR=1.2 NORMALIZE="global" OUTPUT_DIR="output/"

END AUTOGENERATED DATA

LIBRARY_PATH=NULL NUM_THREADS <- 1 for (e in commandArgs()) {

• ta <- strsplit(e,"=",fixed=TRUE)
• if( ta[[1]][1] == "-num_threads") {
• NUM_THREADS <- ta[[1]][2]
• }
• if( ta[[1]][1] == "-file_to_process") {
• FILE_TO_PROCESS <- ta[[1]][2]
• }
• } Sys.setenv("OMP_NUM_THREADS"=NUM_THREADS) library("spade",lib.loc=LIBRARY_PATH) Loading required package: igraph0 LAYOUT_FUNCTION=layout.kamada.kawai SPADE.driver(FILE_TO_PROCESS, file_pattern="*.fcs", out_dir=OUTPUT_DIR, cluster_cols=CLUSTERING_MARKERS, panels=PANELS, transforms=TRANSFORMS, layout=LAYOUT_FUNCTION, downsampling_samples=DOWNSAMPLED_EVENTS, downsampling_target_pctile=DOWNSAMPLING_TARGET_PCTILE, downsampling_exclude_pctile=DOWNSAMPLING_EXCLUDE_PCTILE, k=TARGET_CLUSTERS, clustering_samples=CLUSTERING_SAMPLES) Downsampling file: ./LungWT1.fcs

[zbjornson]

Sorry that no one responded to this. If you're still having the issue, please click "reopen." Note that in the past this has been caused by a particular version of FlowJo writing bad files.