Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-09 12:04 -0500 (Mon, 09 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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 279/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
categoryCompare 1.50.0 (landing page) Robert M. Flight
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.50.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:categoryCompare.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings categoryCompare_1.50.0.tar.gz |
StartedAt: 2024-12-05 23:43:54 -0500 (Thu, 05 Dec 2024) |
EndedAt: 2024-12-05 23:47:55 -0500 (Thu, 05 Dec 2024) |
EllapsedTime: 240.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: categoryCompare.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:categoryCompare.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings categoryCompare_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/categoryCompare.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'categoryCompare/DESCRIPTION' ... OK * this is package 'categoryCompare' version '1.50.0' * 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 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 ... 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 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/categoryCompare.Rcheck/00check.log' for details.
categoryCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL categoryCompare ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 0.72 | 0.03 | 0.75 | |
HyperGParamsCC-class | 0 | 0 | 0 | |
HyperGResultCC-class | 0 | 0 | 0 | |
breakEdges-methods | 0.82 | 0.05 | 0.86 | |
ccCompare | 0.79 | 0.04 | 0.84 | |
ccCompareCollection-class | 0 | 0 | 0 | |
ccCompareResult-class | 0 | 0 | 0 | |
ccData | 0.60 | 0.08 | 0.67 | |
ccEnrich | 0.57 | 0.03 | 0.63 | |
ccEnrichCollection-class | 2.18 | 0.08 | 2.25 | |
ccEnrichResult-class | 3.21 | 0.06 | 3.28 | |
ccGeneList-class | 0.83 | 0.03 | 0.86 | |
ccOptions-class | 0.03 | 0.00 | 0.03 | |
ccOutCyt-methods | 0 | 0 | 0 | |
ccSigList-class | 0 | 0 | 0 | |
cytOutData-methods | 0 | 0 | 0 | |
cytOutNodes-methods | 0 | 0 | 0 | |
hyperGTestCC | 1.22 | 0.03 | 1.77 | |
mergeLists-methods | 1.17 | 0.10 | 1.26 | |
mergedData-class | 1.08 | 0.06 | 1.14 | |
minCount | 2.67 | 0.02 | 2.68 | |
minNodes | 0 | 0 | 0 | |
pvalueType | 1.72 | 0.07 | 1.80 | |
show-methods | 0.00 | 0.00 | 0.02 | |