Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:42 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1726/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rGREAT 2.9.0 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: rGREAT |
Version: 2.9.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rGREAT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings rGREAT_2.9.0.tar.gz |
StartedAt: 2024-12-23 04:10:35 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 04:16:37 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 361.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rGREAT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rGREAT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings rGREAT_2.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/rGREAT.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'rGREAT/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rGREAT' version '2.9.0' * checking package namespace information ... OK * checking package dependencies ... INFO 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 whether package 'rGREAT' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * 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 whether 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: getRefSeqGenesFromUCSC.Rd: GenomicRanges Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/rGREAT/libs/x64/rGREAT.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotRegionGeneAssociations-GreatObject-method 5.18 0.05 5.23 submitGreatJob 0.37 0.06 9.92 * 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: 3 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/rGREAT.Rcheck/00check.log' for details.
rGREAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL rGREAT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'rGREAT' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reduce_by_start_and_end.cpp -o reduce_by_start_and_end.o g++ -std=gnu++17 -shared -s -static-libgcc -o rGREAT.dll tmp.def RcppExports.o reduce_by_start_and_end.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-rGREAT/00new/rGREAT/libs/x64 ** 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 (rGREAT)
rGREAT.Rcheck/tests/test-all.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 14.82 0.76 15.59
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 | 0.11 | 0.00 | 0.11 | |
availableOntologies-GreatJob-method | 0.08 | 0.00 | 0.08 | |
extendTSS | 0 | 0 | 0 | |
extendTSSFromDataFrame | 0 | 0 | 0 | |
extendTSSFromOrgDb | 0 | 0 | 0 | |
extendTSSFromTxDb | 0 | 0 | 0 | |
getEnrichmentTable-GreatJob-method | 0.08 | 0.01 | 0.10 | |
getEnrichmentTable-GreatObject-method | 0.07 | 0.00 | 0.07 | |
getEnrichmentTable-dispatch | 0 | 0 | 0 | |
getEnrichmentTables-GreatJob-method | 0.16 | 0.02 | 0.18 | |
getEnrichmentTables-GreatObject-method | 0 | 0 | 0 | |
getEnrichmentTables-dispatch | 0 | 0 | 0 | |
getGREATDefaultTSS | 0 | 0 | 0 | |
getGapFromUCSC | 0.08 | 0.02 | 0.09 | |
getGeneSetsFromBioMart | 0 | 0 | 0 | |
getGeneSetsFromOrgDb | 0 | 0 | 0 | |
getGenesFromGencode | 0 | 0 | 0 | |
getGenomeDataFromNCBI | 0 | 0 | 0 | |
getKEGGGenome | 0 | 0 | 0 | |
getKEGGPathways | 0 | 0 | 0 | |
getRefSeqGenesFromUCSC | 0 | 0 | 0 | |
getRegionGeneAssociations-GreatJob-method | 0.47 | 0.01 | 0.48 | |
getRegionGeneAssociations-GreatObject-method | 2.80 | 0.14 | 2.94 | |
getRegionGeneAssociations-dispatch | 0 | 0 | 0 | |
getTSS | 0 | 0 | 0 | |
great | 0 | 0 | 0 | |
great_opt | 0.02 | 0.00 | 0.01 | |
plotRegionGeneAssociationGraphs-GreatJob-method | 0 | 0 | 0 | |
plotRegionGeneAssociations-GreatJob-method | 0.89 | 0.06 | 0.96 | |
plotRegionGeneAssociations-GreatObject-method | 5.18 | 0.05 | 5.23 | |
plotRegionGeneAssociations-dispatch | 0 | 0 | 0 | |
plotVolcano-GreatJob-method | 0 | 0 | 0 | |
plotVolcano-GreatObject-method | 0 | 0 | 0 | |
plotVolcano-dispatch | 0 | 0 | 0 | |
randomRegions | 0.24 | 0.03 | 0.27 | |
randomRegionsFromBioMartGenome | 0 | 0 | 0 | |
read_gmt | 0.06 | 0.02 | 0.51 | |
reduce_by_start_and_end | 0 | 0 | 0 | |
shinyReport-GreatJob-method | 0 | 0 | 0 | |
shinyReport-GreatObject-method | 0.02 | 0.00 | 0.02 | |
shinyReport-dispatch | 0 | 0 | 0 | |
submitGreatJob | 0.37 | 0.06 | 9.92 | |