Problems with RefNet
I am getting timeout and other errors when sending a group of genes to RefNet. In summary, simple queries work, more complex ones hang and return errors. The worst part is that my browser becomes dysfunctional for a while afterwards. Even if R is not showing activity after an escape, the internet connection is tied up somehow for 10-15 min or longer.
Session info pasted below.
Thanks for your help,
Mark
Queries with single genes work. Queries with 10 genes that retrieve no interactions also do not produce errors.
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Examples of Failures
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> genes
[1] "TMEM25" "TAMM41" "LOC619574" "HMGN3" "ZFAND2B" "CDK5RAP1" "AHI1" "TDP2" "CPOX" "MRPL16"
[11] "DNM1L" "CSNK1A1" "RAB40B" "GPC4" "KBTBD11" "RGD1563863" "CYP51" "RB1" "MEF2A" "TCF15"
[21] "CNO" "LOC100174910" "FAM69A" "SPHK2" "SCYL1" "SPARC" "EPHA5" "RGD1560433" "LOC501282" "ANKRD10"
[31] "ZFP821"
#
# After failures, Try removing orfs with names unlikely to possess interaction information:
> genes.1 <- genes[-grep("LOC", genes)]
> genes.2 <- genes.1[-grep("RGD", genes.1)]
> tbl.2 <- interactions(refnet, species="9606", id=genes.2, speciesExclusive=FALSE, provider=c("gerstein-2012", "BioGrid"))
List of 2
$ message: chr "Failed connect to tyersrest.tyerslab.com:8805; Operation timed out"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_CONNECT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:%28CPOX%20AND%20ANKRD10%29%20AND%20species:9606"
List of 2
$ message: chr "Failed connect to tyersrest.tyerslab.com:8805; Operation timed out"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_CONNECT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:%28MRPL16%20AND%20ANKRD10%29%20AND%20species:9606"
List of 2
$ message: chr "Failed connect to tyersrest.tyerslab.com:8805; Operation timed out"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_CONNECT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:%28DNM1L%20AND%20ANKRD10%29%20AND%20species:9606"
<ESC>
traceback()
>
>
> traceback()
18: match.fun(FUN)
17: lapply(X = X, FUN = FUN, ...)
16: sapply(paste("str", cl, sep = "."), function(ob) exists(ob, mode = "function",
inherits = TRUE))
15: str.default(err)
14: str(err)
13: sprintf("%s, %s", str(err), "server not responding")
12: print(sprintf("%s, %s", str(err), "server not responding"))
11: value[[3L]](cond)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch({
txt <- getURL(query.url)
if (nchar(txt) == 0)
return(data.frame(stringsAsFactors = FALSE))
ftmp <- tempfile()
write(txt, file = ftmp)
result <- read.table(file = ftmp, , sep = "\t", header = FALSE,
fill = TRUE, quote = "\"", stringsAsFactors = FALSE)
if (!quiet)
.printf("--- %s result: %d %d", query.url, nrow(result),
ncol(result))
return(result)
}, error = function(err) {
print(sprintf("%s, %s", str(err), "server not responding"))
print(sprintf("failed url: %s", query.url))
return(data.frame(stringsAsFactors = FALSE))
})
7: .retrieveData(query.url, quiet)
6: .runQuery(base.url, a, b, species, speciesExclusive, type, detectionMethod,
publicationID, quiet)
5: interactions(object@psicquic, id, species, speciesExclusive,
type, psicquic.providers, detectionMethod, publicationID,
quiet)
4: interactions(object@psicquic, id, species, speciesExclusive,
type, psicquic.providers, detectionMethod, publicationID,
quiet)
3: .interactions(object, id, species, speciesExclusive, type, provider,
detectionMethod, publicationID, quiet)
2: interactions(refnet, species = "9606", id = genes.2, speciesExclusive = FALSE,
provider = c("gerstein-2012", "BioGrid"))
1: interactions(refnet, species = "9606", id = genes.2, speciesExclusive = FALSE,
provider = c("gerstein-2012", "BioGrid"))
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel splines grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.16.0 rgl_0.93.1098 plyr_1.8.1 RefNet_1.0.4 RCurl_1.95-4.3 bitops_1.0-6 AnnotationHub_1.4.0
[8] PSICQUIC_1.2.1 biomaRt_2.20.0 Biostrings_2.32.1 XVector_0.4.0 IRanges_1.22.10 GOstats_2.30.0 Category_2.30.0
[15] Matrix_1.1-4 GO.db_2.14.0 org.Hs.eg.db_2.14.0 RSQLite_1.0.0 DBI_0.3.1 AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2
[22] Biobase_2.24.0 BiocGenerics_0.10.0 RCytoscape_1.14.0 XMLRPC_0.3-0 graph_1.42.0 devtools_1.6.1 gplots_2.14.2
[29] Rtsne_0.9 tsne_0.1-2 vegan_2.0-10 permute_0.8-3 RUnit_0.4.27 adegenet_1.4-2 ade4_1.6-2
[36] cluster_1.15.3 Hmisc_3.14-5 Formula_1.1-2 survival_2.37-7 lattice_0.20-29 stringr_0.6.2 fdrtool_1.2.12
[43] qgraph_1.2.5
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 annotate_1.42.1 AnnotationForge_1.6.1 ape_3.1-4 caTools_1.17.1 colorspace_1.2-4
[7] corpcor_1.6.7 digest_0.6.4 ellipse_0.3-8 foreign_0.8-61 gdata_2.13.3 genefilter_1.46.1
[13] GenomicRanges_1.16.4 ggplot2_1.0.0 glasso_1.8 gridSVG_1.4-0 GSEABase_1.26.0 gtable_0.1.2
[19] gtools_3.4.1 htmltools_0.2.6 httpuv_1.3.2 httr_0.5 huge_1.2.6 igraph_0.7.1
[25] interactiveDisplay_1.2.0 jpeg_0.1-8 KernSmooth_2.23-13 latticeExtra_0.6-26 lavaan_0.5-17 MASS_7.3-35
[31] matrixcalc_1.0-3 mime_0.2 mnormt_1.5-1 munsell_0.4.2 nlme_3.1-118 nnet_7.3-8
[37] pbivnorm_0.5-1 png_0.1-7 proto_0.3-10 psych_1.4.8.11 quadprog_1.5-5 R6_2.0.1
[43] RBGL_1.40.1 RColorBrewer_1.0-5 Rcpp_0.11.3 reshape2_1.4 rjson_0.2.14 RJSONIO_1.3-0
[49] rpart_4.1-8 scales_0.2.4 sem_3.1-5 shiny_0.10.2.1 sna_2.3-2 stats4_3.1.1
[55] tools_3.1.1 XML_3.98-1.1 xtable_1.7-4 zlibbioc_1.10.0
tbl.1 <- interactions(refnet, species="9606", id=genes[1:20], speciesExclusive=FALSE, provider=c( "STRING" ))
List of 2
$ message: chr "Failed connect to string.uzh.ch:80; Operation timed out"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_CONNECT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://string.uzh.ch/psicquic/webservices/current/search/query/identifier:%28DNM1L%20AND%20CSNK1A1%29%20AND%20species:9606"
… (error messages like this repeat with different proteins and providers)
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# This problem ties up my computer for some time afterwards. I got this:
> mapper <- IDMapper("9606")
connecting to biomart...
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:
??? Internet problem??? My browser becomes dysfunctional for a while afterwards. Even if R is not showing activity.
# A bit later, after the browser starts working again:
> mapper <- IDMapper("9606")
connecting to biomart...
> mapper
An object of class "IDMapper"
Slot "species":
[1] "9606"
Slot "mart":
Object of class 'Mart':
Using the ensembl BioMart database
Using the hsapiens_gene_ensembl dataset