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BioC 3.5: CHECK report for clusterSeq on oaxaca

This page was generated on 2017-03-04 16:53:41 -0500 (Sat, 04 Mar 2017).

Package 225/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterSeq 0.99.12
Thomas J. Hardcastle
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clusterSeq
Last Changed Rev: 126478 / Revision: 127142
Last Changed Date: 2017-02-06 08:14:28 -0500 (Mon, 06 Feb 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: clusterSeq
Version: 0.99.12
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterSeq_0.99.12.tar.gz
StartedAt: 2017-03-04 00:44:42 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 00:50:23 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 341.3 seconds
RetCode: 0
Status:  OK 
CheckDir: clusterSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterSeq_0.99.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/clusterSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clusterSeq’ version ‘0.99.12’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘clusterSeq’ 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
kCluster: no visible binding for global variable ‘normRT’
kCluster : <anonymous>: no visible binding for global variable ‘normRT’
Undefined global functions or variables:
  normRT
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
kCluster           382.422 14.259  64.920
makeClustersFF       7.482  0.384  55.651
clusterSeq-package   1.939  0.404  47.505
wallace              1.399  0.327  16.877
makeClusters         0.693  0.356  50.556
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/clusterSeq.Rcheck/00check.log’
for details.


clusterSeq.Rcheck/00install.out:

* installing *source* package ‘clusterSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clusterSeq)

clusterSeq.Rcheck/clusterSeq-Ex.timings:

nameusersystemelapsed
associatePosteriors0.4240.0931.616
clusterSeq-package 1.939 0.40447.505
kCluster382.422 14.259 64.920
makeClusters 0.693 0.35650.556
makeClustersFF 7.482 0.38455.651
plotCluster0.8600.1422.566
wallace 1.399 0.32716.877