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Unable to reattach to a session #54

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lev-kuznetsov opened this issue Jan 12, 2016 · 0 comments
Open

Unable to reattach to a session #54

lev-kuznetsov opened this issue Jan 12, 2016 · 0 comments

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@lev-kuznetsov
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I'm having a weird issue with reattaching to a detached session created with RSevalDetach using the RSclient (issue also pops up using the java client with voidEvalDetach()), when I try to reattach the server closes connection with garbage message. This only seems to happen when I'm doing something with one of bioconductor's annotation packages and happens every time. Here's a simple snippet to reproduce my issue:

RSattach(RSevalDetach (RSconnect(),
  "rr<-(function (geneList, minGSSize, pvalueCutoff, pAdjustMethod, organism='human') {
    library (org.Hs.eg.db);
    GStoEG_map <- as.list (org.Hs.egALIAS2EG);
    require(ReactomePA);
    EntrezList = lapply (na.omit (geneList), function (GS, GStoEG_map) GStoEG_map[[GS]][1], GStoEG_map = GStoEG_map);
    enrichPways <- enrichPathway (gene = EntrezList, minGSSize = minGSSize, organism = organism, pvalueCutoff = pvalueCutoff, pAdjustMethod = pAdjustMethod, readable = T);
    summary (enrichPways);
  }) (c ('C1S', 'IDO1', 'IL8', 'HLA-DRA', 'NLRC5', 'TNF', 'CD274', 'COL4A1', 'CLIC2', 'SECTM1', 'GBP4','SOCS3', 'UBE2L6', 'IL18BP', 'EPSTI1', 'SLC6A14','SAMD9L', 'CCL22', 'DRAM1', 'HLA-DPA1', 'CX3CL1'), 20, .25, 'fdr');"))

The error message on the server with debug on is:

session: resuming session, waiting for connections.
session: accepted
OUT.sendRespData
HEAD DUMP [16]: 01 00 01 00 00 00 00 00 00 00 00 00 00 00 00 00  |................
(no body)
reply sent.
malformed packet (n=-1). closing socket to prevent garbage.
done.

This is all with R version 3.2.0; CRAN's version of Rserve, the libraries needed from bioc are org.Hs.eg.db and ReactomePA; Rserve is running on locahlost at port 6311

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