Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-19 17:40 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 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 1143/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.78.0  (landing page)
Aedin Culhane
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/made4
git_branch: RELEASE_3_19
git_last_commit: 981e55a
git_last_commit_date: 2024-04-30 10:13:40 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for made4 on merida1

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.

raw results


Summary

Package: made4
Version: 1.78.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:made4.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings made4_1.78.0.tar.gz
StartedAt: 2024-07-18 07:45:40 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 07:52:21 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 400.9 seconds
RetCode: 0
Status:   OK  
CheckDir: made4.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:made4.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings made4_1.78.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/made4.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.78.0’
* 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 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 ... OK
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/made4.Rcheck/00check.log’
for details.


Installation output

made4.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL made4
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘made4’ ...
** 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

nameusersystemelapsed
NCI600.0300.0070.048
bet.coinertia0.0170.0020.027
between.graph0.7770.0251.032
bga1.2770.0501.725
bga.jackknife3.6110.2044.959
bga.suppl0.9690.0251.252
cia0.3660.0160.525
commonMap0.0630.0050.081
comparelists0.0010.0010.003
do3d0.8610.0251.142
genes1d0.2030.0210.284
getcol0.0470.0030.061
graph1D0.1610.0090.213
heatplot3.3090.1874.608
html3D0.5240.0210.696
isDataFrame0.0290.0060.052
khan0.0090.0050.013
ord0.4040.0270.559
overview0.2380.0140.314
plotarrays0.6210.0180.848
plotgenes0.2560.0150.364
prettyDend0.1760.0130.267
randomiser0.0050.0020.007
s.var0.5950.0150.783
sumstats0.5460.0140.731
suppl1.0440.0201.373
topgenes0.1890.0190.256