Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ChAMP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChAMP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 283/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChAMP 2.22.0 (landing page) Yuan Tian
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: ChAMP |
Version: 2.22.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChAMP_2.22.0.tar.gz |
StartedAt: 2021-10-14 09:13:12 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:20:04 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 412.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChAMP.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChAMP_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ChAMP.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChAMP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChAMP’ version ‘2.22.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db', 'IlluminaHumanMethylationEPICmanifest', 'DT', 'RPMM' 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 ‘ChAMP’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' See ‘/home/biocbuild/bbs-3.13-bioc/meat/ChAMP.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘rmarkdown’ A package should be listed in only one of these fields. * 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 Namespace in Imports field not imported from: 'prettydoc' All declared Imports should be used. Package in Depends field not imported from: 'DT' 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 champ.DMR: possible error in dmrcate(myannotation, min.cpgs = minProbes, lambda = lambda, C = C, mc.cores = cores): unused argument (mc.cores = cores) champ.ebGSEA : gseaWTfn: no visible global function definition for 'wilcox.test' champ.ebGSEA: no visible global function definition for 'stopCluster' champ.norm: no visible global function definition for 'stopCluster' champ.process: no visible global function definition for 'champ.EpiMod' Undefined global functions or variables: champ.EpiMod stopCluster wilcox.test Consider adding importFrom("stats", "wilcox.test") 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 ... WARNING Duplicated \argument entries in documentation object 'champ.SVD': ‘Rplot’ 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 2 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/ChAMP.Rcheck/00check.log’ for details.
ChAMP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChAMP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘ChAMP’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** testing if installed package can be loaded from final location Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** testing if installed package keeps a record of temporary installation path * DONE (ChAMP)
ChAMP.Rcheck/ChAMP-Ex.timings
name | user | system | elapsed | |
Block.GUI | 0.000 | 0.000 | 0.001 | |
ChAMP-package | 0 | 0 | 0 | |
CpG.GUI | 0 | 0 | 0 | |
DMP.GUI | 0 | 0 | 0 | |
DMR.GUI | 0.000 | 0.000 | 0.001 | |
QC.GUI | 0.000 | 0.000 | 0.001 | |
champ.Block | 0.001 | 0.000 | 0.000 | |
champ.CNA | 0 | 0 | 0 | |
champ.DMP | 0 | 0 | 0 | |
champ.DMR | 0.000 | 0.001 | 0.000 | |
champ.GSEA | 0.000 | 0.001 | 0.000 | |
champ.QC | 0.000 | 0.000 | 0.001 | |
champ.SVD | 0 | 0 | 0 | |
champ.ebGSEA | 0 | 0 | 0 | |
champ.filter | 0 | 0 | 0 | |
champ.import | 0.000 | 0.001 | 0.000 | |
champ.impute | 0.000 | 0.000 | 0.001 | |
champ.load | 0 | 0 | 0 | |
champ.norm | 0.001 | 0.000 | 0.000 | |
champ.process | 0 | 0 | 0 | |
champ.refbase | 0 | 0 | 0 | |
champ.runCombat | 0.000 | 0.000 | 0.001 | |