Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 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" | 4373 |
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 641/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EnrichmentBrowser 2.37.0 (landing page) Ludwig Geistlinger
| 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 EnrichmentBrowser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnrichmentBrowser.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: EnrichmentBrowser |
Version: 2.37.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EnrichmentBrowser_2.37.0.tar.gz |
StartedAt: 2024-12-23 21:44:55 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 21:59:51 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 896.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EnrichmentBrowser.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EnrichmentBrowser_2.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EnrichmentBrowser.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK * this is package ‘EnrichmentBrowser’ version ‘2.37.0’ * 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 ‘EnrichmentBrowser’ can be installed ... OK * checking installed package size ... OK * 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 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 ... NOTE Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getGOFromBiomart: no visible binding for global variable ‘go_linkage_type’ Undefined global functions or variables: go_linkage_type * 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: compileGRN.Rd: KEGGPathway-class, pathwayDatabases, pathways, parseKGML deAna.Rd: SummarizedExperiment-class, colData, filterByExpr, rowData, voom, eBayes, glmQLFit downloadPathways.Rd: keggList, keggGet, KEGGPathway-class, parseKGML eaBrowse.Rd: DataFrame-class ebrowser.Rd: SummarizedExperiment-class, assays, colData, rowData, kegg.species.code, normalizeBetweenArrays, lmFit, normalizeWithinArrays getGenesets.Rd: GeneSetCollection-class, DataFrame-class, keggList, keggLink ggeaGraph.Rd: SummarizedExperiment-class idMap.Rd: SummarizedExperiment-class, GeneSetCollection-class, rowData, mapIds, keytypes import.Rd: SummarizedExperiment-class, EList-class, DGEList-class, TopTags-class, voom, eBayes, glmQLFit isAvailable.Rd: install nbea.Rd: SummarizedExperiment-class normalize.Rd: SummarizedExperiment-class, normalizeBetweenArrays, filterByExpr, normalizeWithinArrays, cpm, estimateDisp, voom probe2gene.Rd: SummarizedExperiment-class, metadata, rowData, mapIds readSE.Rd: SummarizedExperiment-class sbea.Rd: SummarizedExperiment-class 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ebrowser 498.661 30.867 550.401 getGenesets 12.588 1.225 20.228 eaBrowse 7.557 0.573 8.137 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’ for details.
EnrichmentBrowser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL EnrichmentBrowser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘EnrichmentBrowser’ ... ** 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 (EnrichmentBrowser)
EnrichmentBrowser.Rcheck/EnrichmentBrowser-Ex.timings
name | user | system | elapsed | |
combResults | 0.454 | 0.014 | 0.468 | |
compileGRN | 3.593 | 0.081 | 3.676 | |
configEBrowser | 0 | 0 | 0 | |
deAna | 3.095 | 0.110 | 3.207 | |
downloadPathways | 0 | 0 | 0 | |
eaBrowse | 7.557 | 0.573 | 8.137 | |
ebrowser | 498.661 | 30.867 | 550.401 | |
getGenesets | 12.588 | 1.225 | 20.228 | |
ggeaGraph | 1.892 | 0.185 | 2.077 | |
idMap | 2.668 | 0.501 | 3.170 | |
import | 3.420 | 0.133 | 3.554 | |
isAvailable | 0.000 | 0.000 | 0.001 | |
makeExampleData | 0.024 | 0.000 | 0.025 | |
nbea | 0.290 | 0.025 | 0.315 | |
normalize | 0.351 | 0.005 | 0.356 | |
plots | 1.178 | 0.080 | 1.258 | |
probe2gene | 0.060 | 0.007 | 0.067 | |
readSE | 0.035 | 0.000 | 0.035 | |
sbea | 0.156 | 0.019 | 0.174 | |