Guangchuang Yu
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ChIPseeker |
| Branch: RELEASE_3_11 |
| Last Commit: 9f4a2d8 |
| Last Changed Date: 2020-04-27 14:40:23 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:15 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE ChIPseeker PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 284/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPseeker 1.24.0 Guangchuang Yu
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: ChIPseeker |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPseeker_1.24.0.tar.gz |
| StartedAt: 2020-10-17 02:31:15 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:40:22 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 547.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChIPseeker.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPseeker_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseeker.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChIPseeker/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChIPseeker' version '1.24.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 'ChIPseeker' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkFzxgU/R.INSTALL2e9884f51d5/ChIPseeker/man/enrichPeakOverlap.Rd:34: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkFzxgU/R.INSTALL2e9884f51d5/ChIPseeker/man/reexports.Rd:14: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseeker.Rcheck/00install.out' for details. * checking installed package size ... OK * 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 * 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 ... OK * 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 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' 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 See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseeker.Rcheck/00check.log' for details.
ChIPseeker.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ChIPseeker_1.24.0.tar.gz && rm -rf ChIPseeker.buildbin-libdir && mkdir ChIPseeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseeker.buildbin-libdir ChIPseeker_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ChIPseeker_1.24.0.zip && rm ChIPseeker_1.24.0.tar.gz ChIPseeker_1.24.0.zip
###
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install for i386
* installing *source* package 'ChIPseeker' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ChIPseeker'
finding HTML links ... done
ChIPseeker-package html
annotatePeak html
as.GRanges html
as.data.frame.csAnno html
covplot html
csAnno-class html
dotFun html
downloadGEObedFiles html
downloadGSMbedFiles html
dropAnno html
enrichAnnoOverlap html
enrichPeakOverlap html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkFzxgU/R.INSTALL2e9884f51d5/ChIPseeker/man/enrichPeakOverlap.Rd:34: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
getBioRegion html
getGEOInfo html
getGEOgenomeVersion html
getGEOspecies html
getGeneAnno html
getGenomicAnnotation html
getNearestFeatureIndicesAndDistances html
getPromoters html
getSampleFiles html
getTagMatrix html
info html
overlap html
peakHeatmap html
plotAnnoBar-methods html
plotAnnoBar.data.frame html
plotAnnoPie-methods html
plotAnnoPie.csAnno html
plotAvgProf html
plotAvgProf2 html
plotDistToTSS-methods html
plotDistToTSS.data.frame html
readPeakFile html
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkFzxgU/R.INSTALL2e9884f51d5/ChIPseeker/man/reexports.Rd:14: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
seq2gene html
show-methods html
shuffle html
tagHeatmap html
upsetplot-methods html
vennpie-methods html
vennplot html
vennplot.peakfile html
** 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
install for x64
* installing *source* package 'ChIPseeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseeker' as ChIPseeker_1.24.0.zip
* DONE (ChIPseeker)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ChIPseeker' successfully unpacked and MD5 sums checked
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ChIPseeker.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ChIPseeker)
ChIPseeker v1.24.0 For help: https://guangchuangyu.github.io/software/ChIPseeker
If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
>
> test_check("ChIPseeker")
== testthat results ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.98 1.45 20.61
|
ChIPseeker.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ChIPseeker)
ChIPseeker v1.24.0 For help: https://guangchuangyu.github.io/software/ChIPseeker
If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
>
> test_check("ChIPseeker")
== testthat results ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.79 0.95 23.92
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ChIPseeker.Rcheck/examples_i386/ChIPseeker-Ex.timings
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ChIPseeker.Rcheck/examples_x64/ChIPseeker-Ex.timings
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