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 11:44 -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 273/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
categoryCompare 1.51.0 (landing page) Robert M. Flight
| 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 categoryCompare package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/categoryCompare.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: categoryCompare |
Version: 1.51.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings categoryCompare_1.51.0.tar.gz |
StartedAt: 2024-12-23 18:29:52 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:31:05 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 72.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: categoryCompare.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings categoryCompare_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/categoryCompare.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘categoryCompare/DESCRIPTION’ ... OK * this is package ‘categoryCompare’ version ‘1.51.0’ * 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 ‘categoryCompare’ 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 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 .ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOTERM’ .ccCompareGO: no visible binding for global variable ‘Term’ .cytOutNodes: ... may be used in an incorrect context: exportImage(filename = fileName, type = "png", network = cwObj, ...) .getDesc : <anonymous>: no visible global function definition for ‘Term’ show,HyperGResultCC: no visible global function definition for ‘description’ Undefined global functions or variables: GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM Term description * checking Rd files ... NOTE checkRd: (-1) ccData.Rd:21: Lost braces 21 | \code{table10}{: Log-ratio output from \pkg{limma} for the comparison of presence-absence of estrogen at 10 hours} | ^ checkRd: (-1) ccData.Rd:23: Lost braces 23 | \code{table48}{: Log-ratio output from \pkg{limma} for the comparison of presence-absence of estrogen at 48 hours} | ^ checkRd: (-1) ccData.Rd:25: Lost braces 25 | \code{gUniverse}{: All of the genes measured on the chip} | ^ checkRd: (-1) ccData.Rd:27: Lost braces 27 | \code{gseaRes}{: Toy results of GSEA analysis of 3 different tissues} | ^ checkRd: (-1) ccData.Rd:29: Lost braces 29 | \code{enrichLists}{: Apply \code{\link{ccEnrich}} to a ccGeneList from \code{table10} and \code{table48}} | ^ checkRd: (-1) ccData.Rd:31: Lost braces 31 | \code{ccResults}{: Apply \code{\link{ccCompare}} to \code{enrichLists}} | ^ checkRd: (-1) ccData.Rd:33: Lost braces 33 | \code{ccResultsBPHier}{: Modify \code{enrichLists$BP} to use a "hierarchical" layout} | ^ checkRd: (-1) ccData.Rd:35: Lost braces 35 | \code{geneLists}{: a \code{ccGeneList} generated from genes in table10 and table48} | ^ checkRd: (-1) ccData.Rd:37: Lost braces 37 | \code{ccOpts}{: a \code{ccOptions} object describing what we are going to do as far as feature list comparisons} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GENccEnrichResult-class.Rd: AssayData-class HyperGResultCC-class.Rd: HyperGParams-class, HyperGResult-class, HyperGResultBase-class ccCompareCollection-class.Rd: AssayData-class ccEnrichCollection-class.Rd: AssayData-class ccEnrichResult-class.Rd: AssayData-class mergedData-class.Rd: data.frameOrNULL-class resetColors-methods.Rd: setNodeColorMapping 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/categoryCompare.Rcheck/00check.log’ for details.
categoryCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL categoryCompare ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘categoryCompare’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** 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 (categoryCompare)
categoryCompare.Rcheck/categoryCompare-Ex.timings
name | user | system | elapsed | |
GENccEnrichResult-class | 0.180 | 0.003 | 0.183 | |
HyperGParamsCC-class | 0.001 | 0.000 | 0.001 | |
HyperGResultCC-class | 0.001 | 0.000 | 0.001 | |
breakEdges-methods | 0.475 | 0.004 | 0.484 | |
ccCompare | 0.174 | 0.002 | 0.176 | |
ccCompareCollection-class | 0.000 | 0.000 | 0.001 | |
ccCompareResult-class | 0 | 0 | 0 | |
ccData | 0.176 | 0.002 | 0.178 | |
ccEnrich | 0.178 | 0.002 | 0.180 | |
ccEnrichCollection-class | 0.671 | 0.013 | 0.686 | |
ccEnrichResult-class | 0.657 | 0.018 | 0.674 | |
ccGeneList-class | 0.467 | 0.004 | 0.474 | |
ccOptions-class | 0.005 | 0.000 | 0.005 | |
ccOutCyt-methods | 0 | 0 | 0 | |
ccSigList-class | 0 | 0 | 0 | |
cytOutData-methods | 0 | 0 | 0 | |
cytOutNodes-methods | 0.001 | 0.000 | 0.000 | |
hyperGTestCC | 0.269 | 0.008 | 0.281 | |
mergeLists-methods | 0.278 | 0.009 | 0.288 | |
mergedData-class | 0.232 | 0.006 | 0.238 | |
minCount | 0.566 | 0.017 | 0.584 | |
minNodes | 0 | 0 | 0 | |
pvalueType | 0.584 | 0.013 | 0.596 | |
show-methods | 0 | 0 | 0 | |