Error using enrichDavid

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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.

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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/clusterProfiler https://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/DOSE https://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.html https://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.html https://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")

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")

?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")

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")

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YuLab-SMU / clusterProfiler

Error using enrichDavid #297