Guangchuang Yu
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/clusterProfiler |
| Branch: RELEASE_3_8 |
| Last Commit: 39927ef |
| Last Changed Date: 2018-12-20 03:15:27 -0400 (Thu, 20 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:34 -0400 (Sat, 13 Apr 2019).
| Package 279/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clusterProfiler 3.10.1 Guangchuang Yu
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: clusterProfiler |
| Version: 3.10.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings clusterProfiler_3.10.1.tar.gz |
| StartedAt: 2019-04-13 01:17:53 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:24:32 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 399.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clusterProfiler.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings clusterProfiler_3.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/clusterProfiler.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterProfiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clusterProfiler' version '3.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'clusterProfiler' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaCUdsH/R.INSTALL16684ae97bac/clusterProfiler/man/plotGOgraph.Rd:30: file link 'showSigOfNodes' in package 'topGO' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/clusterProfiler.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 ... WARNING
Duplicated \argument entries in documentation object 'simplify':
'x' 'cutoff' 'by' 'select_fun' 'measure' 'semData'
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 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
Examples with CPU or elapsed time > 5s
user system elapsed
groupGO 62.68 8.47 71.16
enrichKEGG 2.67 0.56 6.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
groupGO 67.93 3.3 71.22
enrichKEGG 2.78 0.6 5.50
* 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: 2 WARNINGs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/clusterProfiler.Rcheck/00check.log'
for details.
clusterProfiler.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/clusterProfiler_3.10.1.tar.gz && rm -rf clusterProfiler.buildbin-libdir && mkdir clusterProfiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterProfiler.buildbin-libdir clusterProfiler_3.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL clusterProfiler_3.10.1.zip && rm clusterProfiler_3.10.1.tar.gz clusterProfiler_3.10.1.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
100 4220k 100 4220k 0 0 49.9M 0 --:--:-- --:--:-- --:--:-- 52.1M
install for i386
* installing *source* package 'clusterProfiler' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'clusterProfiler'
finding HTML links ... done
DataSet html
GSEA html
Gff2GeneTable html
KEGG_path2extid html
bitr html
bitr_kegg html
browseKEGG html
buildGOmap html
clusterProfiler-package html
compareCluster html
compareClusterResult-class html
finding level-2 HTML links ... done
dotplot-methods html
download_KEGG html
dropGO html
enrichDAVID html
enrichGO html
enrichKEGG html
enrichMKEGG html
enricher html
fortify html
getGOLevel html
go2ont html
go2term html
gofilter html
groupGO html
groupGOResult-class html
gseGO html
gseKEGG html
gseMKEGG html
idType html
ko2name html
merge_result html
plotGOgraph html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaCUdsH/R.INSTALL16684ae97bac/clusterProfiler/man/plotGOgraph.Rd:30: file link 'showSigOfNodes' in package 'topGO' does not exist and so has been treated as a topic
plotting.clusterProfile html
read.gmt html
reexports html
search_kegg_organism html
simplify-methods html
uniprot_get html
viewKEGG html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'clusterProfiler' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterProfiler' as clusterProfiler_3.10.1.zip
* DONE (clusterProfiler)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'clusterProfiler' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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clusterProfiler.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(clusterProfiler)
clusterProfiler v3.10.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
>
> test_check("clusterProfiler")
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.00 2.06 18.35
|
clusterProfiler.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(clusterProfiler)
clusterProfiler v3.10.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
>
> test_check("clusterProfiler")
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.01 2.15 19.34
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clusterProfiler.Rcheck/examples_i386/clusterProfiler-Ex.timings
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clusterProfiler.Rcheck/examples_x64/clusterProfiler-Ex.timings
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