Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1739/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rGREAT 2.8.0 (landing page) Zuguang Gu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the rGREAT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rGREAT.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: rGREAT |
Version: 2.8.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rGREAT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rGREAT_2.8.0.tar.gz |
StartedAt: 2024-11-20 11:38:18 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:44:44 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 386.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rGREAT.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:rGREAT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rGREAT_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rGREAT.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rGREAT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rGREAT’ version ‘2.8.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘BioMartGOGeneSets’ * 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 ‘rGREAT’ can be installed ... OK * used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING Error: .onLoad failed in loadNamespace() for 'Rsamtools', details: call: h(simpleError(msg, call)) error: error in evaluating the argument 'x' in selecting a method for function 'levels': unable to find an inherited method for function ‘strand’ for signature ‘x = "<unknown>"’ Call sequence: 11: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 10: runHook(".onLoad", env, package.lib, package) 9: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 8: asNamespace(ns) 7: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 5: asNamespace(ns) 4: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), Execution halted See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed submitGreatJob 0.368 0.051 10.02 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/rGREAT.Rcheck/00check.log’ for details.
rGREAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rGREAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘rGREAT’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c reduce_by_start_and_end.cpp -o reduce_by_start_and_end.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o rGREAT.so RcppExports.o reduce_by_start_and_end.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-rGREAT/00new/rGREAT/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rGREAT)
rGREAT.Rcheck/tests/test-all.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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) > suppressWarnings(suppressPackageStartupMessages(library(rGREAT))) > > test_check("rGREAT") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 17.767 1.018 18.825
rGREAT.Rcheck/rGREAT-Ex.timings
name | user | system | elapsed | |
GreatJob-class | 0 | 0 | 0 | |
GreatJob | 0 | 0 | 0 | |
GreatObject-class | 0 | 0 | 0 | |
GreatObject | 0 | 0 | 0 | |
availableCategories-GreatJob-method | 0.144 | 0.004 | 0.150 | |
availableOntologies-GreatJob-method | 0.082 | 0.008 | 0.091 | |
extendTSS | 0.000 | 0.000 | 0.001 | |
extendTSSFromDataFrame | 0 | 0 | 0 | |
extendTSSFromOrgDb | 0 | 0 | 0 | |
extendTSSFromTxDb | 0 | 0 | 0 | |
getEnrichmentTable-GreatJob-method | 0.097 | 0.000 | 0.097 | |
getEnrichmentTable-GreatObject-method | 0.066 | 0.000 | 0.067 | |
getEnrichmentTable-dispatch | 0 | 0 | 0 | |
getEnrichmentTables-GreatJob-method | 0.138 | 0.000 | 0.139 | |
getEnrichmentTables-GreatObject-method | 0 | 0 | 0 | |
getEnrichmentTables-dispatch | 0 | 0 | 0 | |
getGREATDefaultTSS | 0.000 | 0.000 | 0.001 | |
getGapFromUCSC | 0.089 | 0.000 | 0.090 | |
getGeneSetsFromBioMart | 0 | 0 | 0 | |
getGeneSetsFromOrgDb | 0 | 0 | 0 | |
getGenesFromGencode | 0 | 0 | 0 | |
getGenomeDataFromNCBI | 0.001 | 0.000 | 0.000 | |
getKEGGGenome | 0 | 0 | 0 | |
getKEGGPathways | 0 | 0 | 0 | |
getRefSeqGenesFromUCSC | 0 | 0 | 0 | |
getRegionGeneAssociations-GreatJob-method | 0.518 | 0.004 | 0.524 | |
getRegionGeneAssociations-GreatObject-method | 3.190 | 0.140 | 3.336 | |
getRegionGeneAssociations-dispatch | 0 | 0 | 0 | |
getTSS | 0 | 0 | 0 | |
great | 0.000 | 0.000 | 0.001 | |
great_opt | 0.018 | 0.004 | 0.023 | |
plotRegionGeneAssociationGraphs-GreatJob-method | 0.000 | 0.000 | 0.001 | |
plotRegionGeneAssociations-GreatJob-method | 1.165 | 0.028 | 1.196 | |
plotRegionGeneAssociations-GreatObject-method | 4.187 | 0.036 | 4.232 | |
plotRegionGeneAssociations-dispatch | 0 | 0 | 0 | |
plotVolcano-GreatJob-method | 0 | 0 | 0 | |
plotVolcano-GreatObject-method | 0.000 | 0.001 | 0.000 | |
plotVolcano-dispatch | 0 | 0 | 0 | |
randomRegions | 0.270 | 0.038 | 0.308 | |
randomRegionsFromBioMartGenome | 0 | 0 | 0 | |
read_gmt | 0.034 | 0.024 | 2.349 | |
reduce_by_start_and_end | 0 | 0 | 0 | |
shinyReport-GreatJob-method | 0 | 0 | 0 | |
shinyReport-GreatObject-method | 0 | 0 | 0 | |
shinyReport-dispatch | 0 | 0 | 0 | |
submitGreatJob | 0.368 | 0.051 | 10.020 | |