Closed AMAKIRI-AUGUSTINE closed 3 years ago
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¡Gracias!
Alejandro Ramos Gutiérrez
Enviado desde mi iPhone
El 24 oct 2020, a la(s) 11:35 p.m., AMAKIRI-AUGUSTINE notifications@github.com escribió:
Hello, I am trying to use enrichDavid to perform an analysis on a set with about 2000 proteins but I keep getting the following error message.
R version 4.0.2 (2020-06-22) -- "Taking Off Again" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
load("~/serine_threonine_tyrosine/serine_threonine_tyrosine.RData")
library("msigdbr", "enrichplot") ?enrichDavid No documentation for ‘enrichDavid’ in specified packages and libraries: you could try ‘??enrichDavid’ ??enrichDavid library("org.Hs.eg.db", "topGO", "clusterProfiler") Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
Warning message: In library("org.Hs.eg.db", "topGO", "clusterProfiler") : ‘clusterProfiler’ not found on search path, using pos = 2
library("clusterProfiler", lib.loc="/R/win-library/4.0") Error: package or namespace load failed for ‘clusterProfiler’: .onLoad failed in loadNamespace() for 'farver', details: call: load_colour_names() error: cannot open file '/R/win-library/4.0/farver/R/sysdata.rdb': No such file or directory library("RDAVIDWebService") Loading required package: graph Loading required package: GOstats Loading required package: Category Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Attaching package: ‘GOstats’
The following object is masked from ‘package:AnnotationDbi’:
makeGOGraph
Loading required package: ggplot2
Attaching package: ‘RDAVIDWebService’
The following object is masked from ‘package:AnnotationDbi’:
species
The following object is masked from ‘package:IRanges’:
members
The following objects are masked from ‘package:BiocGenerics’:
counts, species, type
library("clusterProfiler") clusterProfiler v3.16.1 For help: https://guangchuangyu.github.io/software/clusterProfilerhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fguangchuangyu.github.io%2Fsoftware%2FclusterProfiler&data=04%7C01%7C%7C756551049f7144452a7408d8789f742d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637391973522254497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4oYn6gFX9zU4nizF5IYoqtG9SZj2UL7BrLCfCkH28WQ%3D&reserved=0
If you use clusterProfiler in published research, please cite: Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Attaching package: ‘clusterProfiler’
The following object is masked from ‘package:AnnotationDbi’:
select
The following object is masked from ‘package:IRanges’:
slice
The following object is masked from ‘package:S4Vectors’:
rename
The following object is masked from ‘package:stats’:
filter
packages<- c("readr", "tidyr", "data.table", "openxlsx", "dplyr", "org.Hs.eg.db", "topGO", "clusterProfiler", "DOSE",
*
"pathview","magrittr", "tidyr","msigdbr", "enrichplot", "ggplot2",
*
"clusterProfiler","RDAVIDWebService")
outlining the packages neccessary for this analysis
lapply(packages, require, character.only = TRUE) Loading required package: readr Loading required package: tidyr
Attaching package: ‘tidyr’
The following objects are masked from ‘package:Matrix’:
expand, pack, unpack
The following object is masked from ‘package:S4Vectors’:
expand
Loading required package: data.table data.table 1.13.0 using 4 threads (see ?getDTthreads). Latest news: r-datatable.com
Attaching package: ‘data.table’
The following object is masked from ‘package:IRanges’:
shift
The following objects are masked from ‘package:S4Vectors’:
first, second
Loading required package: openxlsx Loading required package: dplyr
Attaching package: ‘dplyr’
The following objects are masked from ‘package:data.table’:
between, first, last
The following object is masked from ‘package:graph’:
union
The following object is masked from ‘package:AnnotationDbi’:
select
The following objects are masked from ‘package:IRanges’:
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from ‘package:S4Vectors’:
first, intersect, rename, setdiff, setequal, union
The following object is masked from ‘package:Biobase’:
combine
The following objects are masked from ‘package:BiocGenerics’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: topGO Loading required package: GO.db Loading required package: SparseM
Attaching package: ‘SparseM’
The following object is masked from ‘package:base’:
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: ‘topGO’
The following objects are masked from ‘package:RDAVIDWebService’:
genes, members
The following object is masked from ‘package:GOstats’:
testName
The following objects are masked from ‘package:Category’:
ontology, ontology<-, testName
The following object is masked from ‘package:IRanges’:
members
Loading required package: DOSE DOSE v3.14.0 For help: https://guangchuangyu.github.io/software/DOSEhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fguangchuangyu.github.io%2Fsoftware%2FDOSE&data=04%7C01%7C%7C756551049f7144452a7408d8789f742d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637391973522254497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2FV1k7M4v0QD80zCF%2Bs%2BFw%2BuvSGny9zxbKVHvCcKtV0k%3D&reserved=0
If you use DOSE in published research, please cite: Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609
Loading required package: pathview ############################################################################## Pathview is an open source software package distributed under GNU General Public License version 3 (GPLv3). Details of GPLv3 is available at http://www.gnu.org/licenses/gpl-3.0.htmlhttps://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gnu.org%2Flicenses%2Fgpl-3.0.html&data=04%7C01%7C%7C756551049f7144452a7408d8789f742d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637391973522264491%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1sOTlHfkWxnvXKVSaCayMtjdeBpzQBtTxnvJBa85SZk%3D&reserved=0. Particullary, users are required to formally cite the original Pathview paper (not just mention it) in publications or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG license agreement (details at http://www.kegg.jp/kegg/legal.htmlhttps://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kegg.jp%2Fkegg%2Flegal.html&data=04%7C01%7C%7C756551049f7144452a7408d8789f742d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637391973522264491%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Q5gE8u7XRN%2Fi77vlVZg8Gifr0VZdT39ODEvc%2BZi2j7k%3D&reserved=0). ############################################################################## Loading required package: magrittr
Attaching package: ‘magrittr’
The following object is masked from ‘package:tidyr’:
extract
Loading required package: enrichplot [[1]] [1] TRUE
[[2]] [1] TRUE
[[3]] [1] TRUE
[[4]] [1] TRUE
[[5]] [1] TRUE
[[6]] [1] TRUE
[[7]] [1] TRUE
[[8]] [1] TRUE
[[9]] [1] TRUE
[[10]] [1] TRUE
[[11]] [1] TRUE
[[12]] [1] TRUE
[[13]] [1] TRUE
[[14]] [1] TRUE
[[15]] [1] TRUE
[[16]] [1] TRUE
[[17]] [1] TRUE
View(Y_DAVID) View(sig_ST[[1]]) View(ST_counts_above) View(ST_DAVID[["CDK2"]]) test_CDK2<- enrichDAVID(ST_DAVID[["CDK2"]], idType = "UNIPROT_ACCESSION", universe = ST_back,
*
annotation = c("GOTERM_MF_DIRECT", "GOTERM_BP_FAT", "UP_KEYWORDS"),
*
david.user = "hlaamaki@liverpool.ac.uk")
[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(Unknown Source) at sun.security.ssl.SSLSocketImpl.readApplicationRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.access$300(Unknown Source) at sun.security.ssl.SSLSocketImpl$AppInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:78) at org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:106) at org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1116) at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.readLine(MultiThreadedHttpConnectionManager.java:1413) at org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:1973) at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1735) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1098) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.addList(DAVIDWebServiceStub.java:2773) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at RJavaTools.invokeMethod(RJavaTools.java:386) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Read timed out
test_CDK2<- enrichDAVID(ST_DAVID[["CDK2"]], idType = "UNIPROT_ACCESSION", universe = ST_back,
*
annotation = c("GOTERM_MF_DIRECT", "GOTERM_BP_FAT", "UP_KEYWORDS"),
*
david.user = "hlaamaki@liverpool.ac.uk")
[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(Unknown Source) at sun.security.ssl.SSLSocketImpl.readApplicationRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.access$300(Unknown Source) at sun.security.ssl.SSLSocketImpl$AppInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:78) at org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:106) at org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1116) at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.readLine(MultiThreadedHttpConnectionManager.java:1413) at org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:1973) at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1735) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1098) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.addList(DAVIDWebServiceStub.java:2773) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at RJavaTools.invokeMethod(RJavaTools.java:386) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Read timed out
test_CDK2<- enrichDAVID(ST_DAVID[["CDK2"]], idType = "UNIPROT_ACCESSION",
*
annotation = c("GOTERM_MF_DIRECT", "GOTERM_BP_FAT", "UP_KEYWORDS"),
*
david.user = "hlaamaki@liverpool.ac.uk")
[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(Unknown Source) at sun.security.ssl.SSLSocketImpl.readApplicationRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.access$300(Unknown Source) at sun.security.ssl.SSLSocketImpl$AppInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:78) at org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:106) at org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1116) at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.readLine(MultiThreadedHttpConnectionManager.java:1413) at org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:1973) at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1735) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1098) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.addList(DAVIDWebServiceStub.java:2773) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at RJavaTools.invokeMethod(RJavaTools.java:386) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Read timed out
?enrichDAVID test_CDK2<- enrichDAVID(ST_DAVID[["CDK2"]], idType = "UNIPROT_ACCESSION", maxGSSize = 3000,
*
annotation = c("GOTERM_MF_DIRECT", "GOTERM_BP_FAT", "UP_KEYWORDS"),
*
david.user = "hlaamaki@liverpool.ac.uk")
[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(Unknown Source) at sun.security.ssl.SSLSocketImpl.readApplicationRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.access$300(Unknown Source) at sun.security.ssl.SSLSocketImpl$AppInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:78) at org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:106) at org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1116) at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.readLine(MultiThreadedHttpConnectionManager.java:1413) at org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:1973) at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1735) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1098) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.addList(DAVIDWebServiceStub.java:2773) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at RJavaTools.invokeMethod(RJavaTools.java:386) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Read timed out
View(ST_DAVID[["CDK2"]][1:500]) test_CDK2<- enrichDAVID(ST_DAVID, idType = "UNIPROT_ACCESSION",
*
annotation = c("GOTERM_MF_DIRECT", "GOTERM_BP_FAT", "UP_KEYWORDS"),
*
david.user = "useremail@email.org")
[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(Unknown Source) at sun.security.ssl.SSLSocketImpl.readApplicationRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.access$300(Unknown Source) at sun.security.ssl.SSLSocketImpl$AppInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:78) at org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:106) at org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1116) at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.readLine(MultiThreadedHttpConnectionManager.java:1413) at org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:1973) at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1735) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1098) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.addList(DAVIDWebServiceStub.java:2773) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at RJavaTools.invokeMethod(RJavaTools.java:386) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Read timed out
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Hello, I am trying to use enrichDavid to perform an analysis on a set with about 2000 proteins but I keep getting the following error message. [INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(Unknown Source) at sun.security.ssl.SSLSocketImpl.readApplicationRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.access$300(Unknown Source) at sun.security.ssl.SSLSocketImpl$AppInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:78) at org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:106) at org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1116) at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.readLine(MultiThreadedHttpConnectionManager.java:1413) at org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:1973) at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1735) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1098) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.addList(DAVIDWebServiceStub.java:2773) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at RJavaTools.invokeMethod(RJavaTools.java:386) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Read timed out