Yuan Tian
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ChAMP |
| Branch: RELEASE_3_9 |
| Last Commit: d180295 |
| Last Changed Date: 2019-05-02 11:53:46 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:51 -0400 (Wed, 16 Oct 2019).
| Package 246/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChAMP 2.14.0 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 | |
| Package: ChAMP |
| Version: 2.14.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChAMP_2.14.0.tar.gz |
| StartedAt: 2019-10-16 02:35:02 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:44:30 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 568.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChAMP.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChAMP_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChAMP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChAMP' version '2.14.0'
* 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 whether package 'ChAMP' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' 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'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck/00install.out' for details.
* 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): C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck/00check.log'
for details.
ChAMP.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChAMP_2.14.0.tar.gz && rm -rf ChAMP.buildbin-libdir && mkdir ChAMP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChAMP.buildbin-libdir ChAMP_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChAMP_2.14.0.zip && rm ChAMP_2.14.0.tar.gz ChAMP_2.14.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
73 5890k 73 4320k 0 0 42.3M 0 --:--:-- --:--:-- --:--:-- 44.8M
100 5890k 100 5890k 0 0 23.2M 0 --:--:-- --:--:-- --:--:-- 23.7M
install for i386
* installing *source* package 'ChAMP' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM'
2: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
3: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
4: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
5: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
6: replacing previous import 'Matrix::which' by 'BiocGenerics::which' when loading 'FEM'
7: replacing previous import 'igraph::path' by 'BiocGenerics::path' when loading 'FEM'
8: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' 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
converting help for package 'ChAMP'
finding HTML links ... done
Block.GUI html
ChAMP-package html
CpG.GUI html
DMP.GUI html
DMR.GUI html
QC.GUI html
champ.Block html
champ.CNA html
champ.DMP html
champ.DMR html
champ.EpiMod html
champ.GSEA html
champ.QC html
champ.SVD html
champ.ebGSEA html
champ.filter html
champ.import html
champ.impute html
champ.load html
champ.norm html
champ.process html
champ.refbase html
champ.runCombat html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
Warning: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
Warning: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
Warning: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import 'Matrix::which' by 'BiocGenerics::which' when loading 'FEM'
Warning: replacing previous import 'igraph::path' by 'BiocGenerics::path' when loading 'FEM'
Warning: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' 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::intersection' by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
Warning: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
Warning: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
Warning: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import 'Matrix::which' by 'BiocGenerics::which' when loading 'FEM'
Warning: replacing previous import 'igraph::path' by 'BiocGenerics::path' when loading 'FEM'
Warning: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' 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
install for x64
* installing *source* package 'ChAMP' ...
** 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 'igraph::path' by 'BiocGenerics::path' 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'
* MD5 sums
packaged installation of 'ChAMP' as ChAMP_2.14.0.zip
* DONE (ChAMP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ChAMP' successfully unpacked and MD5 sums checked
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ChAMP.Rcheck/examples_i386/ChAMP-Ex.timings
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ChAMP.Rcheck/examples_x64/ChAMP-Ex.timings
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