BioC 3.2: CHECK report for flowCHIC on oaxaca

Package: flowCHIC

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowCHIC_1.4.0.tar.gz

StartedAt: 2016-04-23 00:06:07 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:08:24 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 136.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowCHIC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowCHIC_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowCHIC.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCHIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowCHIC’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘flowCHIC’ can be installed ... [9s/10s] OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
fcs_to_img,character : .local: warning in hexbin(x, y, xbin = 128):
  partial argument match of 'xbin' to 'xbins'
img_sub,character : .local: warning in hexbin(x, y, xbin = xbin):
  partial argument match of 'xbin' to 'xbins'
fcs_to_img,character : .local: no visible binding for global variable
  ‘count’
img_sub,character : .local: no visible binding for global variable
  ‘count’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘flowCyBar’
* 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 ... [34s/37s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
calculate_overlaps_xor 14.588  0.794  16.838
plot_nmds               7.664  0.451   8.344
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowCHIC.Rcheck/00check.log’
for details.

* installing *source* package ‘flowCHIC’ ...
** 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 (flowCHIC)

name	user	system	elapsed
calculate_overlaps_xor	14.588	0.794	16.838
fcs_to_img	2.112	0.086	2.314
img_sub	4.112	0.102	4.523
plot_nmds	7.664	0.451	8.344