Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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 274/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.49.0  (landing page)
Robert M. Flight
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/categoryCompare
git_branch: devel
git_last_commit: 0551947
git_last_commit_date: 2024-04-30 10:27:40 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for categoryCompare on palomino6

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.

raw results


Summary

Package: categoryCompare
Version: 1.49.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings categoryCompare_1.49.0.tar.gz
StartedAt: 2024-07-15 22:26:53 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:30:08 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 194.9 seconds
RetCode: 0
Status:   OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings categoryCompare_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/categoryCompare.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'categoryCompare/DESCRIPTION' ... OK
* this is package 'categoryCompare' version '1.49.0'
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.


Installation output

categoryCompare.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL categoryCompare
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/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)

Tests output


Example timings

categoryCompare.Rcheck/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.360.010.38
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods0.390.030.42
ccCompare0.420.000.42
ccCompareCollection-class000
ccCompareResult-class000
ccData0.330.030.36
ccEnrich0.380.000.38
ccEnrichCollection-class1.370.081.45
ccEnrichResult-class1.170.051.22
ccGeneList-class0.460.000.45
ccOptions-class0.010.000.02
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods000
cytOutNodes-methods000
hyperGTestCC0.580.090.67
mergeLists-methods1.200.091.29
mergedData-class0.550.040.58
minCount1.670.031.71
minNodes000
pvalueType1.630.041.67
show-methods000