BioC 3.5: CHECK report for clusterSeq on oaxaca

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

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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_0.99.12.tar.gz
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* 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.

* 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	0.424	0.093	1.616
clusterSeq-package	1.939	0.404	47.505
kCluster	382.422	14.259	64.920
makeClusters	0.693	0.356	50.556
makeClustersFF	7.482	0.384	55.651
plotCluster	0.860	0.142	2.566
wallace	1.399	0.327	16.877