Back to Build/check report for BioC 3.15 experimental data |
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This page was generated on 2022-10-18 14:50:12 -0400 (Tue, 18 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
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 |
To the developers/maintainers of the Hiiragi2013 package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 179/410 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
Hiiragi2013 1.32.0 (landing page) Andrzej Oles
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||
Package: Hiiragi2013 |
Version: 1.32.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Hiiragi2013_1.32.0.tar.gz |
StartedAt: 2022-10-18 11:26:03 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 11:28:31 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 148.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Hiiragi2013.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Hiiragi2013_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/Hiiragi2013.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Hiiragi2013’ version ‘1.32.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'affy', 'Biobase', 'boot', 'clue', 'cluster', 'genefilter', 'geneplotter', 'gplots', 'gtools', 'KEGGREST', 'MASS', 'mouse4302.db', 'RColorBrewer', 'xtable' 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 ‘Hiiragi2013’ can be installed ... OK * checking installed package size ... NOTE installed size is 136.6Mb sub-directories of 1Mb or more: data 136.4Mb * 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 Packages in Depends field not imported from: ‘KEGGREST’ ‘affy’ ‘boot’ ‘clue’ ‘geneplotter’ ‘gtools’ ‘mouse4302.db’ ‘xtable’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MDSplot: no visible global function definition for ‘dist’ MDSplot: no visible global function definition for ‘par’ MDSplot: no visible global function definition for ‘points’ MDSplot: no visible global function definition for ‘grey’ MDSplot: no visible global function definition for ‘text’ getDifferentialExpressedGenes: no visible global function definition for ‘quantile’ getDifferentialExpressedGenes: no visible global function definition for ‘p.adjust’ myHeatmap: no visible global function definition for ‘as.dendrogram’ myHeatmap: no visible global function definition for ‘hclust’ myHeatmap: no visible global function definition for ‘dist’ myHeatmap: no visible global function definition for ‘order.dendrogram’ myHeatmap2: no visible global function definition for ‘colorRampPalette’ ordermat : <anonymous>: no visible global function definition for ‘order.dendrogram’ ordermat : <anonymous>: no visible global function definition for ‘as.dendrogram’ ordermat : <anonymous>: no visible global function definition for ‘hclust’ ordermat : <anonymous>: no visible global function definition for ‘dist’ pamCluster: no visible global function definition for ‘dist’ Undefined global functions or variables: as.dendrogram colorRampPalette dist grey hclust order.dendrogram p.adjust par points quantile text Consider adding importFrom("grDevices", "colorRampPalette", "grey") importFrom("graphics", "par", "points", "text") importFrom("stats", "as.dendrogram", "dist", "hclust", "order.dendrogram", "p.adjust", "quantile") to your NAMESPACE file. * checking Rd files ... OK * 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed a 9.638 0.468 10.109 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’ for details.
Hiiragi2013.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Hiiragi2013 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘Hiiragi2013’ ... ** 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 (Hiiragi2013)
Hiiragi2013.Rcheck/Hiiragi2013-Ex.timings
name | user | system | elapsed | |
MDSplot | 3.206 | 0.152 | 3.359 | |
a | 9.638 | 0.468 | 10.109 | |
getDifferentialExpressedGenes | 2.760 | 0.096 | 2.855 | |
myHeatmap | 3.132 | 0.152 | 3.284 | |
myHeatmap2 | 0.000 | 0.001 | 0.001 | |
pamCluster | 2.487 | 0.055 | 2.541 | |
plotProjection | 0 | 0 | 0 | |
x | 2.455 | 0.068 | 2.523 | |
xq | 0.010 | 0.004 | 0.013 | |
xql | 0.006 | 0.000 | 0.005 | |