This page was generated on 2025-12-15 12:05 -0500 (Mon, 15 Dec 2025).
CHECK results for made4 on nebbiolo2
To the developers/maintainers of the made4 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/made4.git to reflect on this report. SeeTroubleshooting Build Report for more information.
- Use the followingRenviron 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. SeeRenviron.bioc for more information.
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raw results
Summary
| Package: made4 |
| Version: 1.84.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings made4_1.84.0.tar.gz |
| StartedAt: 2025-12-12 01:52:58 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 01:55:46 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 168.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: made4.Rcheck |
| Warnings: 0 |
Command output
################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings made4_1.84.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/made4.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘made4/DESCRIPTION’ ... OK* this is package ‘made4’ version ‘1.84.0’* 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 ‘made4’ 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 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 ... NOTEcheckRd: (-1) NCI60.Rd:19: Escaped LaTeX specials: \$checkRd: (-1) NCI60.Rd:19-20: Lost braces in \itemize; meant \describe ?checkRd: (-1) NCI60.Rd:22: Escaped LaTeX specials: \$checkRd: (-1) NCI60.Rd:22-23: Lost braces in \itemize; meant \describe ?checkRd: (-1) NCI60.Rd:25: Escaped LaTeX specials: \$checkRd: (-1) NCI60.Rd:25-28: Lost braces in \itemize; meant \describe ?checkRd: (-1) NCI60.Rd:30: Escaped LaTeX specials: \$checkRd: (-1) NCI60.Rd:30-33: Lost braces in \itemize; meant \describe ?checkRd: (-1) NCI60.Rd:31: Escaped LaTeX specials: \$ \$checkRd: (-1) NCI60.Rd:32: Escaped LaTeX specials: \$ \$checkRd: (-1) NCI60.Rd:33: Escaped LaTeX specials: \$ \$checkRd: (-1) NCI60.Rd:50: Escaped LaTeX specials: \$checkRd: (-1) NCI60.Rd:52: Escaped LaTeX specials: \$ \$checkRd: (-1) NCI60.Rd:60: Escaped LaTeX specials: \$checkRd: (-1) NCI60.Rd:64: Escaped LaTeX specials: \$ \$prepare_Rd: asDataFrame.Rd:30: Dropping empty section \examplescheckRd: (-1) between.graph.Rd:17: Escaped LaTeX specials: \$ \$checkRd: (-1) between.graph.Rd:25: Escaped LaTeX specials: \$checkRd: (-1) between.graph.Rd:26: Escaped LaTeX specials: \$checkRd: (-1) between.graph.Rd:32: Escaped LaTeX specials: \$ \$checkRd: (-1) between.graph.Rd:34: Escaped LaTeX specials: \$checkRd: (-1) bga.Rd:27: Escaped LaTeX specials: \$ \$ \$checkRd: (-1) bga.Rd:70: Escaped LaTeX specials: \$ \$checkRd: (-1) bga.Rd:76: Escaped LaTeX specials: \$checkRd: (-1) bga.Rd:95: Escaped LaTeX specials: \$checkRd: (-1) cia.Rd:69: Escaped LaTeX specials: \$ \$checkRd: (-1) cia.Rd:77: Escaped LaTeX specials: \$checkRd: (-1) cia.Rd:78: Escaped LaTeX specials: \$checkRd: (-1) cia.Rd:85: Escaped LaTeX specials: \$ \$checkRd: (-1) do3d.Rd:22: Escaped LaTeX specials: \$ \$checkRd: (-1) do3d.Rd:24: Escaped LaTeX specials: \$ \$checkRd: (-1) genes1d.Rd:9: Escaped LaTeX specials: \$ \$checkRd: (-1) genes1d.Rd:16: Escaped LaTeX specials: \$ \$checkRd: (-1) genes1d.Rd:22: Escaped LaTeX specials: \$ \$checkRd: (-1) html3D.Rd:19: Escaped LaTeX specials: \$ \$checkRd: (-1) html3D.Rd:20: Escaped LaTeX specials: \$ \$checkRd: (-1) jmol3D.Rd:14: Escaped LaTeX specials: \$ \$checkRd: (-1) jmol3D.Rd:15: Escaped LaTeX specials: \$ \$checkRd: (-1) khan.Rd:15: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:15-16: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:17: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:17-18: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:19: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:19-20: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:20: Escaped LaTeX specials: \$ \$checkRd: (-1) khan.Rd:21: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:21-23: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:23: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:24: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:24-26: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:26: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:27: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:27-40: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:31: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:31: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:32: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:32: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:33: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:33: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:34: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:34: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:35: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:35: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:36: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:36: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:37: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:37: Lost braces in \itemize; meant \describe ?checkRd: (-1) khan.Rd:38: Escaped LaTeX specials: \$checkRd: (-1) khan.Rd:38: Lost braces in \itemize; meant \describe ?checkRd: (-1) ord.Rd:27: Escaped LaTeX specials: \$ \$checkRd: (-1) ord.Rd:53: Escaped LaTeX specials: \$checkRd: (-1) ord.Rd:66: Escaped LaTeX specials: \$ \$checkRd: (-1) ord.Rd:74: Escaped LaTeX specials: \$checkRd: (-1) plotarrays.Rd:6: Escaped LaTeX specials: \$checkRd: (-1) plotgenes.Rd:6: Escaped LaTeX specials: \$checkRd: (-1) s.var.Rd:35: Escaped LaTeX specials: \$ \$ \$checkRd: (-1) s.var.Rd:38: Escaped LaTeX specials: \$ \$checkRd: (-1) sumstats.Rd:16: Escaped LaTeX specials: \$ \$checkRd: (-1) sumstats.Rd:17: Escaped LaTeX specials: \$checkRd: (-1) topgenes.Rd:16: Escaped LaTeX specials: \$ \$checkRd: (-1) topgenes.Rd:17: Escaped LaTeX specials: \$ \$ \$checkRd: (-1) topgenes.Rd:22: Escaped LaTeX specials: \$ \$checkRd: (-1) topgenes.Rd:33: Escaped LaTeX specials: \$ \$* checking Rd metadata ... OK* checking Rd cross-references ... NOTENon-topic package-anchored link(s) in Rd file 'isDataFrame.Rd': ‘[convert:coerce]{as}’See section 'Cross-references' in the 'Writing R Extensions' manual.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... NOTEDocumented arguments not in \usage in Rd file 'forrwcoa.Rd': ‘...’Documented arguments not in \usage in Rd file 'genes1d.Rd': ‘...’Functions with \usage entries need to have the appropriate \aliasentries, and all their arguments documented.The \usage entries must correspond to syntactically valid R code.See chapter ‘Writing R documentation files’ in the ‘Writing RExtensions’ manual.* 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 LazyData ... 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 re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 3 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/made4.Rcheck/00check.log’for details.Installation output
made4.Rcheck/00install.out
################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL made4###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘made4’ ...** this is package ‘made4’ version ‘1.84.0’** using staged installation** R** data*** moving datasets to lazyload DB** 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 (made4)
Tests output
Example timings
made4.Rcheck/made4-Ex.timings
| name | user | system | elapsed |
|
| NCI60 | 0.004 | 0.001 | 0.005 | |
|
| bet.coinertia | 0.008 | 0.001 | 0.009 | |
|
| between.graph | 0.634 | 0.015 | 0.649 | |
|
| bga | 0.268 | 0.048 | 0.315 | |
|
| bga.jackknife | 1.151 | 0.032 | 1.185 | |
|
| bga.suppl | 0.285 | 0.003 | 0.289 | |
|
| cia | 0.150 | 0.001 | 0.152 | |
|
| commonMap | 0.022 | 0.001 | 0.023 | |
|
| comparelists | 0.000 | 0.000 | 0.001 | |
|
| do3d | 0.281 | 0.001 | 0.283 | |
|
| genes1d | 0.069 | 0.001 | 0.070 | |
|
| getcol | 0.026 | 0.001 | 0.027 | |
|
| graph1D | 0.061 | 0.001 | 0.062 | |
|
| heatplot | 1.318 | 0.017 | 1.337 | |
|
| html3D | 0.155 | 0.001 | 0.155 | |
|
| isDataFrame | 0.02 | 0.00 | 0.02 | |
|
| khan | 0.005 | 0.000 | 0.004 | |
|
| ord | 0.164 | 0.005 | 0.169 | |
|
| overview | 0.102 | 0.002 | 0.103 | |
|
| plotarrays | 0.214 | 0.001 | 0.214 | |
|
| plotgenes | 0.086 | 0.003 | 0.090 | |
|
| prettyDend | 0.072 | 0.000 | 0.072 | |
|
| randomiser | 0.002 | 0.000 | 0.003 | |
|
| s.var | 0.172 | 0.002 | 0.174 | |
|
| sumstats | 0.158 | 0.003 | 0.161 | |
|
| suppl | 0.326 | 0.002 | 0.328 | |
|
| topgenes | 0.067 | 0.002 | 0.069 | |
|
