BioC 3.5: CHECK report for clusterSeq on veracruz2

Package: clusterSeq

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterSeq_1.0.0.tar.gz

StartedAt: 2017-10-18 01:51:11 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:56:38 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 326.9 seconds

RetCode: 0

Status:  OK

CheckDir: clusterSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterSeq_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/clusterSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.0’
* 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
makeClustersFF     6.942  0.320  55.019
clusterSeq-package 2.000  0.458  52.066
kCluster           1.549  0.506  60.586
wallace            1.578  0.348  15.989
makeClusters       0.648  0.294  49.171
* 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.

* 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)

name	user	system	elapsed
associatePosteriors	0.628	0.113	2.124
clusterSeq-package	2.000	0.458	52.066
kCluster	1.549	0.506	60.586
makeClusters	0.648	0.294	49.171
makeClustersFF	6.942	0.320	55.019
plotCluster	0.609	0.103	2.159
wallace	1.578	0.348	15.989