| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the paxtoolsr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/paxtoolsr.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1439/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.33.0 (landing page) Augustin Luna
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: paxtoolsr |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings paxtoolsr_1.33.0.tar.gz |
| StartedAt: 2023-02-28 10:51:06 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 10:57:11 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 364.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings paxtoolsr_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/paxtoolsr.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.33.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘paxtoolsr’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 32.1Mb
sub-directories of 1Mb or more:
extdata 7.3Mb
java 24.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
splitSifnxByPathway: no visible global function definition for
‘%dopar%’
Undefined global functions or variables:
%dopar%
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘paxtoolsr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPcDatabaseNames
> ### Title: Get a Pathway Commons Databases
> ### Aliases: getPcDatabaseNames
>
> ### ** Examples
>
> getPcDatabaseNames(version=10)
Error: failed to load external entity "http://www.pathwaycommons.org/archives/PC2/"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('test_paxtools.R:41'): validate ──────────────────────────────────────
<XMLParserErrorList/simpleError/error/condition>
Error: 1: Start tag expected, '<' not found
Backtrace:
▆
1. ├─paxtoolsr::validate(...) at test_paxtools.R:41:4
2. │ └─XML::xmlTreeParse(outputFile, useInternalNodes = TRUE)
3. └─XML (local) `<fn>`(`<chr>`)
[ FAIL 2 | WARN 0 | SKIP 10 | PASS 36 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘using_paxtoolsr.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL paxtoolsr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘paxtoolsr’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (paxtoolsr)
paxtoolsr.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.
> library(testthat)
> library(paxtoolsr)
Loading required package: rJava
Loading required package: XML
Consider citing this package: Luna A, et al. PaxtoolsR: pathway analysis in R using Pathway Commons. PMID: 26685306; citation("paxtoolsr")
>
> test_check("paxtoolsr")
2023-02-28 10:53:11,849 469 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2023-02-28 10:53:11,866 486 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2023-02-28 10:53:11,873 493 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2023-02-28 10:53:11,873 493 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2023-02-28 10:53:11,884 504 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2023-02-28 10:53:11,887 507 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2023-02-28 10:53:11,890 510 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2023-02-28 10:53:11,890 510 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2023-02-28 10:55:21,941 130561 [main] WARN org.biopax.paxtools.client.BiopaxValidatorClient - Failed to resolve to actual web service URL using: null (if there is a 301/302/307 HTTP redirect, then validation requests (using HTTP POST method) will probably fail...)
org.apache.http.conn.HttpHostConnectException: Connect to www.biopax.org:80 [www.biopax.org/142.150.84.100] failed: Connection timed out (Connection timed out)
at org.apache.http.impl.conn.HttpClientConnectionOperator.connect(HttpClientConnectionOperator.java:138)
at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:314)
at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:357)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:218)
at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:194)
at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:85)
at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:108)
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:186)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.http.client.fluent.Request.execute(Request.java:143)
at org.biopax.paxtools.client.BiopaxValidatorClient.location(BiopaxValidatorClient.java:220)
at org.biopax.paxtools.client.BiopaxValidatorClient.<init>(BiopaxValidatorClient.java:108)
at org.biopax.paxtools.client.BiopaxValidatorClient.<init>(BiopaxValidatorClient.java:124)
at org.biopax.paxtools.PaxtoolsMain.validate(PaxtoolsMain.java:309)
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:412)
at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:255)
at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:237)
at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.base/java.net.Socket.connect(Socket.java:609)
at org.apache.http.conn.socket.PlainConnectionSocketFactory.connectSocket(PlainConnectionSocketFactory.java:72)
at org.apache.http.impl.conn.HttpClientConnectionOperator.connect(HttpClientConnectionOperator.java:118)
... 15 more
130561 [main] WARN org.biopax.paxtools.client.BiopaxValidatorClient - Failed to resolve to actual web service URL using: null (if there is a 301/302/307 HTTP redirect, then validation requests (using HTTP POST method) will probably fail...)
org.apache.http.conn.HttpHostConnectException: Connect to www.biopax.org:80 [www.biopax.org/142.150.84.100] failed: Connection timed out (Connection timed out)
at org.apache.http.impl.conn.HttpClientConnectionOperator.connect(HttpClientConnectionOperator.java:138)
at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:314)
at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:357)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:218)
at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:194)
at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:85)
at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:108)
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:186)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.http.client.fluent.Request.execute(Request.java:143)
at org.biopax.paxtools.client.BiopaxValidatorClient.location(BiopaxValidatorClient.java:220)
at org.biopax.paxtools.client.BiopaxValidatorClient.<init>(BiopaxValidatorClient.java:108)
at org.biopax.paxtools.client.BiopaxValidatorClient.<init>(BiopaxValidatorClient.java:124)
at org.biopax.paxtools.PaxtoolsMain.validate(PaxtoolsMain.java:309)
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:412)
at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:255)
at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:237)
at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.base/java.net.Socket.connect(Socket.java:609)
at org.apache.http.conn.socket.PlainConnectionSocketFactory.connectSocket(PlainConnectionSocketFactory.java:72)
at org.apache.http.impl.conn.HttpClientConnectionOperator.connect(HttpClientConnectionOperator.java:118)
... 15 more
2023-02-28 10:55:23,929 132549 [main] ERROR org.biopax.paxtools.PaxtoolsMain - Unable to check with the biopax-validator web service:
org.apache.http.client.HttpResponseException: Moved Temporarily
Fall-back: trying to parse the file(s) with paxtools (up to the first syntax error in each file)...
org.apache.http.client.HttpResponseException: Moved Temporarily
at org.apache.http.client.fluent.ContentResponseHandler.handleResponse(ContentResponseHandler.java:47)
at org.apache.http.client.fluent.ContentResponseHandler.handleResponse(ContentResponseHandler.java:40)
at org.apache.http.client.fluent.Response.handleResponse(Response.java:85)
at org.apache.http.client.fluent.Response.returnContent(Response.java:92)
at org.biopax.paxtools.client.BiopaxValidatorClient.validate(BiopaxValidatorClient.java:176)
at org.biopax.paxtools.PaxtoolsMain.validate(PaxtoolsMain.java:310)
132549 [main] ERROR org.biopax.paxtools.PaxtoolsMain - Unable to check with the biopax-validator web service:
org.apache.http.client.HttpResponseException: Moved Temporarily
Fall-back: trying to parse the file(s) with paxtools (up to the first syntax error in each file)...
org.apache.http.client.HttpResponseException: Moved Temporarily
at org.apache.http.client.fluent.ContentResponseHandler.handleResponse(ContentResponseHandler.java:47)
at org.apache.http.client.fluent.ContentResponseHandler.handleResponse(ContentResponseHandler.java:40)
at org.apache.http.client.fluent.Response.handleResponse(Response.java:85)
at org.apache.http.client.fluent.Response.returnContent(Response.java:92)
at org.biopax.paxtools.client.BiopaxValidatorClient.validate(BiopaxValidatorClient.java:176)
at org.biopax.paxtools.PaxtoolsMain.validate(PaxtoolsMain.java:310)
Start tag expected, '<' not found
2023-02-28 10:55:24,285 132905 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 1.0
enhanced ratio: 1.0
Total execution time: 40 miliseconds.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1 (file:/home/biocbuild/bbs-3.17-bioc/R/library/paxtoolsr/java/paxtools-4.3.1.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int)
WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2023-02-28 10:55:24,841 133461 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2023-02-28 10:55:25,331 133951 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2023-02-28 10:55:25,846 134466 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
[ FAIL 2 | WARN 0 | SKIP 10 | PASS 36 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (7)
• empty test (3)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_pathwayCommons.R:27'): getPc ───────────────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.pathwaycommons.org] Connection timeout after 10000 ms
Backtrace:
▆
1. └─paxtoolsr::getPc("http://identifiers.org/uniprot/Q06609") at test_pathwayCommons.R:27:4
2. └─paxtoolsr:::getPcRequest(url, verbose)
3. └─httr::HEAD(url)
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error ('test_paxtools.R:41'): validate ──────────────────────────────────────
<XMLParserErrorList/simpleError/error/condition>
Error: 1: Start tag expected, '<' not found
Backtrace:
▆
1. ├─paxtoolsr::validate(...) at test_paxtools.R:41:4
2. │ └─XML::xmlTreeParse(outputFile, useInternalNodes = TRUE)
3. └─XML (local) `<fn>`(`<chr>`)
[ FAIL 2 | WARN 0 | SKIP 10 | PASS 36 ]
Error: Test failures
Execution halted
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.018 | 0.000 | 0.019 | |
| convertDataFrameListsToVectors | 0.010 | 0.000 | 0.009 | |
| convertSifToGmt | 0.208 | 0.000 | 0.208 | |
| downloadFile | 0.036 | 0.000 | 0.431 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 3.685 | 0.236 | 0.900 | |
| filterSif | 0.381 | 0.029 | 0.098 | |
| getCacheFiles | 0 | 0 | 0 | |
| getErrorMessage | 0.008 | 0.000 | 0.000 | |
| getNeighbors | 0.577 | 0.040 | 0.108 | |
| getPc | 0.001 | 0.000 | 0.000 | |