Aedin Culhane
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 1143/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| made4 1.78.0 (landing page) Aedin Culhane
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.78.0 |
| 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: 2024-06-09 21:14:45 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 21:17:30 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 165.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: made4.Rcheck |
| Warnings: 0 |
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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
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/made4.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* 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: \$
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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: \$ \$
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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 ?
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checkRd: (-1) khan.Rd:33: Lost braces in \itemize; meant \describe ?
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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: \$ \$
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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.
made4.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
made4.Rcheck/made4-Ex.timings
| name | user | system | elapsed | |
| NCI60 | 0.006 | 0.002 | 0.009 | |
| bet.coinertia | 0.013 | 0.001 | 0.015 | |
| between.graph | 0.360 | 0.014 | 0.375 | |
| bga | 0.777 | 0.024 | 0.806 | |
| bga.jackknife | 1.380 | 0.063 | 1.447 | |
| bga.suppl | 0.330 | 0.013 | 0.345 | |
| cia | 0.168 | 0.008 | 0.177 | |
| commonMap | 0.026 | 0.002 | 0.028 | |
| comparelists | 0.001 | 0.001 | 0.001 | |
| do3d | 0.300 | 0.012 | 0.314 | |
| genes1d | 0.064 | 0.010 | 0.074 | |
| getcol | 0.033 | 0.002 | 0.036 | |
| graph1D | 0.058 | 0.006 | 0.065 | |
| heatplot | 1.416 | 0.089 | 1.518 | |
| html3D | 0.215 | 0.014 | 0.230 | |
| isDataFrame | 0.016 | 0.003 | 0.020 | |
| khan | 0.005 | 0.002 | 0.008 | |
| ord | 0.210 | 0.016 | 0.229 | |
| overview | 0.126 | 0.006 | 0.134 | |
| plotarrays | 0.248 | 0.010 | 0.261 | |
| plotgenes | 0.123 | 0.007 | 0.131 | |
| prettyDend | 0.096 | 0.006 | 0.103 | |
| randomiser | 0.002 | 0.001 | 0.003 | |
| s.var | 0.257 | 0.018 | 0.275 | |
| sumstats | 0.187 | 0.005 | 0.193 | |
| suppl | 0.383 | 0.012 | 0.397 | |
| topgenes | 0.083 | 0.009 | 0.092 | |