Yuan Tian
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ChAMP |
| Branch: master |
| Last Commit: 0f600f3 |
| Last Changed Date: 2019-02-05 17:12:44 -0400 (Tue, 05 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:09:13 -0400 (Tue, 09 Apr 2019).
| Package 241/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChAMP 2.13.5 Yuan Tian
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: ChAMP |
| Version: 2.13.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChAMP_2.13.5.tar.gz |
| StartedAt: 2019-04-09 00:32:47 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:43:20 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 633.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChAMP.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChAMP_2.13.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.13.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'minfi', 'ChAMPdata', 'FEM', 'DMRcate',
'Illumina450ProbeVariants.db', 'IlluminaHumanMethylationEPICmanifest'
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 ... OK
* 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 ... WARNING
Problems with news in ‘inst/NEWS.Rd’:
inst/NEWS.Rd:81: unexpected END_OF_INPUT '
'
Invalid citation information in ‘inst/CITATION’:
Error in parse(file = cfile): /Users/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck/00_pkg_src/ChAMP/inst/CITATION:10:12: unexpected symbol
9: person("Stephan", "Beck")
10: person
^
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
champ.ebGSEA : gseaWTfn: no visible global function definition for
'wilcox.test'
Undefined global functions or variables:
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* 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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck/00check.log’
for details.
ChAMP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChAMP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ChAMP’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading There were 12 warnings (use warnings() to see them) 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 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ 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 '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 ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ 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 '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 | 0.001 | 0.000 | 0.001 | |
| CpG.GUI | 0.001 | 0.000 | 0.000 | |
| DMP.GUI | 0.001 | 0.001 | 0.001 | |
| DMR.GUI | 0.001 | 0.000 | 0.001 | |
| QC.GUI | 0.001 | 0.000 | 0.000 | |
| champ.Block | 0.001 | 0.000 | 0.001 | |
| champ.CNA | 0.000 | 0.000 | 0.001 | |
| champ.DMP | 0.000 | 0.001 | 0.000 | |
| champ.DMR | 0.000 | 0.000 | 0.001 | |
| champ.EpiMod | 0 | 0 | 0 | |
| champ.GSEA | 0.000 | 0.001 | 0.001 | |
| champ.QC | 0 | 0 | 0 | |
| champ.SVD | 0.000 | 0.000 | 0.001 | |
| champ.ebGSEA | 0.000 | 0.001 | 0.001 | |
| champ.filter | 0 | 0 | 0 | |
| champ.import | 0 | 0 | 0 | |
| champ.impute | 0.000 | 0.000 | 0.001 | |
| champ.load | 0.001 | 0.000 | 0.001 | |
| champ.norm | 0.001 | 0.001 | 0.001 | |
| champ.process | 0.001 | 0.000 | 0.000 | |
| champ.refbase | 0.000 | 0.000 | 0.001 | |
| champ.runCombat | 0.000 | 0.001 | 0.001 | |