Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:50 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE made4 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 973/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
made4 1.62.0 Aedin Culhane
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ ERROR ] | OK |
Package: made4 |
Version: 1.62.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:made4.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings made4_1.62.0.tar.gz |
StartedAt: 2020-10-17 02:35:37 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 02:38:51 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 194.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: made4.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:made4.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings made4_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/made4.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘made4/DESCRIPTION’ ... OK * this is package ‘made4’ version ‘1.62.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'ade4', 'RColorBrewer', 'gplots', 'scatterplot3d', 'Biobase', 'SummarizedExperiment' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 R 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 ... NOTE Missing or unexported object: ‘RColorBrewer::colorRampPalette’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plot.bga: warning in s.var(dudi.bga$bet$ls, xax = axis1, yax = axis2, col = as.vector(factor(dudi.bga$fac, labels = arraycol)), ...): partial argument match of 'col' to 'colpoints' plot.ord: warning in s.var(dudi.ord$co, xax = axis1, yax = axis2, col = cols.array, label = arraylabels, ...): partial argument match of 'col' to 'colpoints' plot.ord: warning in plotgenes(dudi.ord$li, genelabels = genelabels, nlab = nlab, col = genecol, axis1 = axis1, axis2 = axis2, ...): partial argument match of 'col' to 'colpoints' * checking Rd files ... NOTE prepare_Rd: array2ade4.Rd:38: Dropping empty section \references prepare_Rd: between.graph.Rd:40-42: Dropping empty section \value prepare_Rd: between.graph.Rd:47: Dropping empty section \note prepare_Rd: checkfac.Rd:15-16: Dropping empty section \details prepare_Rd: checkfac.Rd:22: Dropping empty section \note prepare_Rd: checkfac.Rd:23: Dropping empty section \seealso prepare_Rd: checkfac.Rd:24-25: Dropping empty section \examples prepare_Rd: chime3D.Rd:56: Dropping empty section \seealso prepare_Rd: chime3D.Rd:57-59: Dropping empty section \examples prepare_Rd: cia.Rd:106: Dropping empty section \note prepare_Rd: commonMap.Rd:29-30: Dropping empty section \value prepare_Rd: commonMap.Rd:31: Dropping empty section \references prepare_Rd: do3d.Rd:73: Dropping empty section \note prepare_Rd: do3d.Rd:71: Dropping empty section \references prepare_Rd: dudi.rwcoa.Rd:39-41: Dropping empty section \examples prepare_Rd: forrwcoa.Rd:38-40: Dropping empty section \examples prepare_Rd: genes.Rd:28: Dropping empty section \value prepare_Rd: genes.Rd:32-33: Dropping empty section \examples prepare_Rd: genes1d.Rd:34: Dropping empty section \references prepare_Rd: getdata.Rd:36: Dropping empty section \examples prepare_Rd: graph1D.Rd:33-34: Dropping empty section \details prepare_Rd: graph1D.Rd:35-37: Dropping empty section \value prepare_Rd: graph1D.Rd:40: Dropping empty section \note prepare_Rd: graph1D.Rd:38: Dropping empty section \references prepare_Rd: html3D.Rd:74: Dropping empty section \seealso prepare_Rd: jmol3D.Rd:37: Dropping empty section \seealso prepare_Rd: jmol3D.Rd:38-39: Dropping empty section \examples prepare_Rd: ord.Rd:93: Dropping empty section \references prepare_Rd: overview.Rd:26: Dropping empty section \value prepare_Rd: overview.Rd:29: Dropping empty section \note prepare_Rd: overview.Rd:27: Dropping empty section \references prepare_Rd: prettyDend.Rd:27: Dropping empty section \value prepare_Rd: prettyDend.Rd:30: Dropping empty section \note prepare_Rd: prettyDend.Rd:28: Dropping empty section \references prepare_Rd: sumstats.Rd:52: Dropping empty section \note prepare_Rd: sumstats.Rd:50: Dropping empty section \references prepare_Rd: sumstats.Rd:56: Dropping empty section \seealso prepare_Rd: topgenes.Rd:40: Dropping empty section \note prepare_Rd: topgenes.Rd:38: Dropping empty section \references * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'getdata.Rd': ‘[vsn:vsn]{vsn}’ 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 ... WARNING Documented arguments not in \usage in documentation object 'overview': ‘...’ 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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘made4-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: array2ade4 > ### Title: Converts microarray input data into a data frame suitable for > ### analysis in ADE4. > ### Aliases: array2ade4 > ### Keywords: manip > > ### ** Examples > > library(affy) > data(geneData) > class(geneData) [1] "matrix" "array" > dim(geneData) [1] 500 26 > dim(array2ade4(geneData)) Error in switch(class(arraydata), matrix = { : EXPR must be a length 1 vector Calls: array2ade4 -> getdata Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/made4.Rcheck/00check.log’ for details.
made4.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL made4 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘made4’ ... ** using staged installation ** R ** data ** 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 | 0.010 | 0.003 | 0.013 | |