Aedin Culhane
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/made4 |
| git_branch: RELEASE_3_21 |
| git_last_commit: af8e708 |
| git_last_commit_date: 2025-04-15 09:35:56 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1160/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| made4 1.82.0 (landing page) Aedin Culhane
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. 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: made4 |
| Version: 1.82.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings made4_1.82.0.tar.gz |
| StartedAt: 2025-10-16 00:37:33 -0400 (Thu, 16 Oct 2025) |
| EndedAt: 2025-10-16 00:40:15 -0400 (Thu, 16 Oct 2025) |
| EllapsedTime: 162.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: made4.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings made4_1.82.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/made4.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.82.0’
* 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 ... NOTE
checkRd: (-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 \examples
checkRd: (-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 ... NOTE
Non-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 ... NOTE
Documented 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 \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ 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
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/made4.Rcheck/00check.log’
for details.
made4.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL made4 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘made4’ ... ** this is package ‘made4’ version ‘1.82.0’ ** 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)
made4.Rcheck/made4-Ex.timings
| name | user | system | elapsed | |
| NCI60 | 0.004 | 0.001 | 0.006 | |
| bet.coinertia | 0.008 | 0.000 | 0.009 | |
| between.graph | 0.644 | 0.011 | 0.656 | |
| bga | 0.267 | 0.033 | 0.300 | |
| bga.jackknife | 1.143 | 0.048 | 1.191 | |
| bga.suppl | 0.293 | 0.006 | 0.299 | |
| cia | 0.150 | 0.002 | 0.152 | |
| commonMap | 0.022 | 0.001 | 0.024 | |
| comparelists | 0.000 | 0.001 | 0.001 | |
| do3d | 0.275 | 0.003 | 0.278 | |
| genes1d | 0.066 | 0.005 | 0.071 | |
| getcol | 0.027 | 0.001 | 0.027 | |
| graph1D | 0.059 | 0.001 | 0.059 | |
| heatplot | 1.371 | 0.027 | 1.402 | |
| html3D | 0.158 | 0.004 | 0.162 | |
| isDataFrame | 0.014 | 0.000 | 0.014 | |
| khan | 0.005 | 0.001 | 0.005 | |
| ord | 0.168 | 0.004 | 0.172 | |
| overview | 0.103 | 0.001 | 0.105 | |
| plotarrays | 0.183 | 0.002 | 0.185 | |
| plotgenes | 0.096 | 0.002 | 0.099 | |
| prettyDend | 0.071 | 0.002 | 0.074 | |
| randomiser | 0.001 | 0.002 | 0.003 | |
| s.var | 0.171 | 0.000 | 0.172 | |
| sumstats | 0.156 | 0.002 | 0.159 | |
| suppl | 0.326 | 0.001 | 0.327 | |
| topgenes | 0.076 | 0.006 | 0.082 | |