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BioC 3.1: CHECK report for clusterProfiler on moscato2

This page was generated on 2015-10-09 09:29:08 -0700 (Fri, 09 Oct 2015).

Package 179/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterProfiler 2.2.7
Guangchuang Yu
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/clusterProfiler
Last Changed Rev: 108732 / Revision: 109384
Last Changed Date: 2015-09-22 18:47:06 -0700 (Tue, 22 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterProfiler
Version: 2.2.7
Command: rm -rf clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && mkdir clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterProfiler.buildbin-libdir clusterProfiler_2.2.7.tar.gz >clusterProfiler.Rcheck\00install.out 2>&1 && cp clusterProfiler.Rcheck\00install.out clusterProfiler-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clusterProfiler.buildbin-libdir --install="check:clusterProfiler-install.out" --force-multiarch --no-vignettes --timings clusterProfiler_2.2.7.tar.gz
StartedAt: 2015-10-09 00:28:03 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:33:52 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 349.4 seconds
RetCode: 0
Status:  OK  
CheckDir: clusterProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && mkdir clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterProfiler.buildbin-libdir clusterProfiler_2.2.7.tar.gz >clusterProfiler.Rcheck\00install.out 2>&1 && cp clusterProfiler.Rcheck\00install.out clusterProfiler-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clusterProfiler.buildbin-libdir --install="check:clusterProfiler-install.out" --force-multiarch --no-vignettes --timings clusterProfiler_2.2.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/clusterProfiler.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '2.2.7'
* 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 'clusterProfiler' can be installed ... OK
* 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 ... NOTE
plot,compareClusterResult-ANY : .local: no visible binding for global
  variable 'ID'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [92s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
compareCluster 8.72   0.16   48.22
enrichKEGG     0.97   0.00   36.90
** running examples for arch 'x64' ... [90s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
compareCluster 11.84   0.27   46.94
enrichKEGG      0.80   0.03   35.81
* 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 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/clusterProfiler.Rcheck/00check.log'
for details.


clusterProfiler.Rcheck/00install.out:


install for i386

* installing *source* package 'clusterProfiler' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'clusterProfiler' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'clusterProfiler' as clusterProfiler_2.2.7.zip
* DONE (clusterProfiler)

clusterProfiler.Rcheck/examples_i386/clusterProfiler-Ex.timings:

nameusersystemelapsed
compareCluster 8.72 0.1648.22
enrichGO000
enrichKEGG 0.97 0.0036.90
groupGO1.590.081.67

clusterProfiler.Rcheck/examples_x64/clusterProfiler-Ex.timings:

nameusersystemelapsed
compareCluster11.84 0.2746.94
enrichGO000
enrichKEGG 0.80 0.0335.81
groupGO1.750.091.84