| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-15 11:32:18 -0400 (Mon, 15 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 | ||||
| Package 1511/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.36.0 (landing page) Augustin Luna
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the paxtoolsr package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: paxtoolsr |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.36.0.tar.gz |
| StartedAt: 2024-04-14 22:11:51 -0400 (Sun, 14 Apr 2024) |
| EndedAt: 2024-04-14 22:14:14 -0400 (Sun, 14 Apr 2024) |
| EllapsedTime: 142.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.36.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/paxtoolsr.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.36.0’
* 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 startup messages can be suppressed ... 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 in UseMethod("xmlNamespaceDefinitions") :
no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"
Calls: getPcDatabaseNames ... xpathApply.XMLInternalDocument -> getDefaultNamespace -> xmlNamespaceDefinitions
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 9993 Segmentation fault: 11 ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
26: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
27: source_file(path, env = env(env), desc = desc, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("paxtoolsr")
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/paxtoolsr.Rcheck/00check.log’
for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL paxtoolsr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")
2024-04-14 22:12:47,507 701 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2024-04-14 22:12:47,523 717 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2024-04-14 22:12:47,528 722 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2024-04-14 22:12:47,529 723 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2024-04-14 22:12:47,538 732 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2024-04-14 22:12:47,540 734 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2024-04-14 22:12:47,542 736 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2024-04-14 22:12:47,542 736 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2024-04-14 22:12:48,370 1564 [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.client.ClientProtocolException
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:188)
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: org.apache.http.ProtocolException: The server failed to respond with a valid HTTP response
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:151)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:57)
at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:260)
at org.apache.http.impl.DefaultBHttpClientConnection.receiveResponseHeader(DefaultBHttpClientConnection.java:161)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
at org.apache.http.impl.conn.CPoolProxy.invoke(CPoolProxy.java:138)
at jdk.proxy2/jdk.proxy2.$Proxy3.receiveResponseHeader(Unknown Source)
at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:271)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:123)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:253)
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)
... 8 more
1564 [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.client.ClientProtocolException
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:188)
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: org.apache.http.ProtocolException: The server failed to respond with a valid HTTP response
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:151)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:57)
at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:260)
at org.apache.http.impl.DefaultBHttpClientConnection.receiveResponseHeader(DefaultBHttpClientConnection.java:161)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
at org.apache.http.impl.conn.CPoolProxy.invoke(CPoolProxy.java:138)
at jdk.proxy2/jdk.proxy2.$Proxy3.receiveResponseHeader(Unknown Source)
at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:271)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:123)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:253)
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)
... 8 more
*** caught segfault ***
address 0x100004, cause 'invalid permissions'
Traceback:
1: .jcheck(silent = TRUE)
2: .jnew("java/lang/String", command)
3: getNeighbors(system.file("extdata", "raf_map_kinase_cascade_reactome.owl", package = "paxtoolsr"), outFile, c("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606", "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606"))
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
14: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
15: test_that("getNeighbors", { outFile <- tempfile() results <- getNeighbors(system.file("extdata", "raf_map_kinase_cascade_reactome.owl", package = "paxtoolsr"), outFile, c("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606", "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606")) expect_is(results, "XMLInternalDocument")})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
26: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
27: source_file(path, env = env(env), desc = desc, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("paxtoolsr")
An irrecoverable exception occurred. R is aborting now ...
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.094 | 0.003 | 0.097 | |
| convertDataFrameListsToVectors | 0.001 | 0.000 | 0.002 | |
| convertSifToGmt | 0.261 | 0.023 | 0.287 | |
| downloadFile | 0.172 | 0.010 | 0.368 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 2.923 | 0.166 | 1.159 | |
| filterSif | 0.192 | 0.023 | 0.120 | |
| getCacheFiles | 0.000 | 0.000 | 0.001 | |
| getErrorMessage | 0.001 | 0.001 | 0.000 | |
| getNeighbors | 0.556 | 0.030 | 0.196 | |
| getPc | 0.000 | 0.000 | 0.001 | |