Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1135/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
made4 1.80.0 (landing page) Aedin Culhane
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.80.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:made4.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings made4_1.80.0.tar.gz |
StartedAt: 2024-12-20 03:01:15 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:04:23 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 188.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: made4.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:made4.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings made4_1.80.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/made4.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'made4/DESCRIPTION' ... OK * this is package 'made4' version '1.80.0' * 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 '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 'F:/biocbuild/bbs-3.20-bioc/meat/made4.Rcheck/00check.log' for details.
made4.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL made4 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 0.00 | 0.01 | 0.01 | |
bet.coinertia | 0.02 | 0.00 | 0.01 | |
between.graph | 0.81 | 0.03 | 0.84 | |
bga | 0.27 | 0.05 | 0.31 | |
bga.jackknife | 1.64 | 0.06 | 1.70 | |
bga.suppl | 0.49 | 0.00 | 0.49 | |
cia | 0.17 | 0.03 | 0.20 | |
commonMap | 0.02 | 0.00 | 0.01 | |
comparelists | 0 | 0 | 0 | |
do3d | 0.33 | 0.03 | 0.36 | |
genes1d | 0.11 | 0.02 | 0.12 | |
getcol | 0.03 | 0.00 | 0.03 | |
graph1D | 0.07 | 0.01 | 0.08 | |
heatplot | 1.73 | 0.04 | 1.78 | |
html3D | 0.19 | 0.01 | 0.21 | |
isDataFrame | 0.01 | 0.02 | 0.07 | |
khan | 0.02 | 0.00 | 0.02 | |
ord | 0.25 | 0.03 | 0.28 | |
overview | 0.12 | 0.00 | 0.12 | |
plotarrays | 0.3 | 0.0 | 0.3 | |
plotgenes | 0.13 | 0.00 | 0.13 | |
prettyDend | 0.12 | 0.00 | 0.12 | |
randomiser | 0 | 0 | 0 | |
s.var | 0.28 | 0.00 | 0.29 | |
sumstats | 0.19 | 0.00 | 0.18 | |
suppl | 0.58 | 0.01 | 0.60 | |
topgenes | 0.09 | 0.00 | 0.09 | |