[Bioc-devel] Broken pathway in graphite package?

[Ryan C. Thompson]

Hello,

I was attempting to run SPIA through the graphite package and ran into 
an odd error when running prepareSPIA on the human Reactome pathways. 
You can reproduce the error simply and quickly by:

 > library(graphite)
 > prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor 
signalling cascade"], "test", TRUE)
Insulin receptor signalling cascade
Error in Filter(Negate(is.null), lapply(db, function(p) { :
   error in evaluating the argument 'x' in selecting a method for 
function 'Filter': Error in if (e[1] <= e[2]) paste(e[1], e[2], sep = 
"|") else paste(e[2],  :
   missing value where TRUE/FALSE needed

The traceback is not particularly informative. I don't actually see the 
line of code from the error message in the traceback:

 > traceback()
4: Filter(Negate(is.null), lapply(db, function(p) {
        if (print.names)
            cat(p at title, "\n")
        p <- convertIdentifiers(p, "entrez")
        es <- edges(p)
        if (NROW(es) == 0 || NROW(unique(es[, 1:2])) < 5)
            return(NULL)
        ns <- nodes(p)
        es <- merge(es, spiaConv, all.x = TRUE)[c("src", "dest",
            "direction", "spiaType")]
        l <- sapply(spiaAttributes, simplify = FALSE, USE.NAMES = TRUE,
            function(edgeType) {
                est <- es[es[, 4] == edgeType, , drop = FALSE]
                gnl <- buildGraphNEL(ns, est, TRUE)
                t(as(gnl, "matrix"))
            })
        l$title <- p at title
        l$nodes <- ns
        l$NumberOfReactions <- 0
        return(l)
    }))
3: .prepareSPIA(db at entries, pathwaySetName, print.names)
2: prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor 
signalling cascade"],
        "test", TRUE)
1: prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor 
signalling cascade"],
        "test", TRUE)

I guess for now I will remove the offending pathway, but it seems 
unexpected that graphite cannot handle a pathway included in its own 
package.

-Ryan Thompson

 > sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grDevices datasets  parallel  graphics  stats4    stats utils
[8] methods   base

other attached packages:
  [1] org.Hs.eg.db_3.1.2        GSEABase_1.30.2
  [3] graph_1.46.0              annotate_1.46.0
  [5] XML_3.98-1.2              graphite_1.14.0
  [7] openxlsx_2.5.10           DESeq2_1.8.1
  [9] RcppArmadillo_0.5.200.1.0 Rcpp_0.11.6
[11] edgeR_3.10.2              limma_3.24.10
[13] magrittr_1.5              dplyr_0.4.1
[15] biomaRt_2.24.0            functional_0.6
[17] sqldf_0.4-10              RSQLite_1.0.0
[19] DBI_0.3.1                 gsubfn_0.6-6
[21] proto_0.3-10              GenomicFeatures_1.20.1
[23] AnnotationDbi_1.30.1      chipseq_1.18.0
[25] BSgenome_1.36.0           inline_0.3.14
[27] affy_1.46.1               rtracklayer_1.28.4
[29] Biobase_2.28.0            ShortRead_1.26.0
[31] GenomicAlignments_1.4.1   BiocParallel_1.3.16
[33] Rsamtools_1.20.4          Biostrings_2.36.1
[35] XVector_0.8.0             GenomicRanges_1.20.5
[37] GenomeInfoDb_1.4.0        doParallel_1.0.8
[39] iterators_1.0.7           foreach_1.4.2
[41] plyr_1.8.3                stringr_1.0.0
[43] IRanges_2.2.4             ggplot2_1.0.1
[45] S4Vectors_0.6.0           BiocGenerics_0.14.0
[47] BiocInstaller_1.18.3

loaded via a namespace (and not attached):
  [1] splines_3.2.0         assertthat_0.1 Formula_1.2-1
  [4] latticeExtra_0.6-26   lattice_0.20-31 chron_2.3-45
  [7] digest_0.6.8          RColorBrewer_1.1-2 colorspace_1.2-6
[10] preprocessCore_1.30.0 genefilter_1.50.0 zlibbioc_1.14.0
[13] xtable_1.7-4          scales_0.2.5 affyio_1.36.0
[16] lazyeval_0.1.10       nnet_7.3-9 survival_2.38-2
[19] MASS_7.3-40           hwriter_1.3.2 foreign_0.8-63
[22] tools_3.2.0           munsell_0.4.2 locfit_1.5-9.1
[25] cluster_2.0.1         lambda.r_1.1.7 compiler_3.2.0
[28] futile.logger_1.4.1   grid_3.2.0 RCurl_1.96-0
[31] bitops_1.0-6          gtable_0.1.2 codetools_0.2-11
[34] reshape2_1.4.1        gridExtra_0.9.1 Hmisc_3.16-0
[37] futile.options_1.0.0  stringi_0.4-1 geneplotter_1.46.0
[40] rpart_4.1-9           acepack_1.3-3.3
 >