Yuan Tian
| Snapshot Date: 2018-02-19 17:00:21 -0500 (Mon, 19 Feb 2018) |
| URL: https://git.bioconductor.org/packages/ChAMP |
| Branch: RELEASE_3_6 |
| Last Commit: 52901fe |
| Last Changed Date: 2018-01-08 06:35:24 -0500 (Mon, 08 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-02-20 15:03:13 -0500 (Tue, 20 Feb 2018).
| Package 208/1473 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChAMP 2.9.10 Yuan Tian
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| Package: ChAMP |
| Version: 2.9.10 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMP_2.9.10.tar.gz |
| StartedAt: 2018-02-20 01:33:46 -0500 (Tue, 20 Feb 2018) |
| EndedAt: 2018-02-20 01:41:01 -0500 (Tue, 20 Feb 2018) |
| EllapsedTime: 435.4 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 --no-vignettes --timings ChAMP_2.9.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ChAMP.Rcheck’
* using R version 3.4.3 (2017-11-30)
* 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 ‘2.9.10’
* 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 ... NOTE
installed size is 11.7Mb
sub-directories of 1Mb or more:
doc 9.6Mb
extdata 1.9Mb
* 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:74: unexpected END_OF_INPUT '
'
* 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 loading without being on the library search path ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... 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-3.6-bioc/meat/ChAMP.Rcheck/00check.log’
for details.
ChAMP.Rcheck/00install.out
* installing *source* package ‘ChAMP’ ... ** R ** inst ** preparing package for lazy loading 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 ‘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' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded 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 ‘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' * DONE (ChAMP)
ChAMP.Rcheck/ChAMP-Ex.timings
| name | user | system | elapsed | |
| Block.GUI | 0.001 | 0.000 | 0.001 | |
| ChAMP-package | 0 | 0 | 0 | |
| CpG.GUI | 0.001 | 0.000 | 0.001 | |
| DMP.GUI | 0.000 | 0.000 | 0.001 | |
| DMR.GUI | 0.001 | 0.000 | 0.001 | |
| QC.GUI | 0.001 | 0.001 | 0.001 | |
| champ.Block | 0.000 | 0.000 | 0.001 | |
| champ.CNA | 0 | 0 | 0 | |
| champ.DMP | 0.001 | 0.000 | 0.001 | |
| champ.DMR | 0.000 | 0.000 | 0.001 | |
| champ.EpiMod | 0.001 | 0.000 | 0.001 | |
| champ.GSEA | 0.001 | 0.000 | 0.001 | |
| champ.QC | 0.000 | 0.000 | 0.001 | |
| champ.SVD | 0.001 | 0.000 | 0.001 | |
| champ.filter | 0.000 | 0.001 | 0.001 | |
| champ.import | 0.001 | 0.000 | 0.000 | |
| champ.impute | 0.001 | 0.000 | 0.001 | |
| champ.load | 0.000 | 0.001 | 0.001 | |
| champ.norm | 0.001 | 0.000 | 0.001 | |
| champ.process | 0 | 0 | 0 | |
| champ.refbase | 0.001 | 0.001 | 0.001 | |
| champ.runCombat | 0.001 | 0.000 | 0.001 | |