BioC 3.1: CHECK report for flowCHIC on zin2

Package: flowCHIC

Version: 1.2.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings flowCHIC_1.2.0.tar.gz

StartedAt: 2015-10-09 01:08:42 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:10:31 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 108.9 seconds

RetCode: 0

Status:  OK

CheckDir: flowCHIC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings flowCHIC_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/flowCHIC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 ... [7s/8s] OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  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 ... [21s/24s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
calculate_overlaps_xor 8.951  0.055  10.408
plot_nmds              5.308  0.024   5.883
* 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
  ‘/home/biocbuild/bbs-3.1-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	8.951	0.055	10.408
fcs_to_img	1.147	0.004	1.412
img_sub	2.710	0.011	2.853
plot_nmds	5.308	0.024	5.883