BioC 3.3: CHECK report for cytofkit on morelia

Package: cytofkit

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytofkit_1.3.0.tar.gz

StartedAt: 2016-04-21 01:17:26 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 01:21:48 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 261.8 seconds

RetCode: 0

Status:  OK

CheckDir: cytofkit.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 cytofkit_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/cytofkit.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytofkit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytofkit’ version ‘1.3.0’
* 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 ‘cytofkit’ can be installed ... [9s/9s] 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
cluster_gridPlot: no visible global function definition for ‘rainbow’
cluster_plot: no visible global function definition for ‘rainbow’
cytof_tsne_densvm: no visible global function definition for
  ‘read.table’
cytof_write_results: no visible global function definition for
  ‘write.table’
cytof_write_results: no visible global function definition for ‘pdf’
cytof_write_results: no visible global function definition for ‘par’
cytof_write_results: no visible global function definition for
  ‘dev.off’
sign_auto: no visible global function definition for ‘is’
Undefined global functions or variables:
  dev.off is par pdf rainbow read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "par")
  importFrom("methods", "is")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [146s/152s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
densVM_cluster 118.985 17.863 142.445
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [7s/7s] OK
* 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-3.3-bioc/meat/cytofkit.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
clust_mean_heatmap	0.226	0.006	0.249
clust_percentage_heatmap	0.065	0.007	0.071
clust_state	0.026	0.003	0.033
cluster_gridPlot	0.893	0.079	0.991
cluster_plot	0.509	0.035	0.561
cytof_dimReduction	1.657	0.004	1.708
cytof_tsne_densvm	0.001	0.000	0.002
cytof_tsne_densvm_GUI	0.000	0.000	0.001
cytof_write_results	0.002	0.001	0.004
cytofkit	0.003	0.001	0.006
densVM_cluster	118.985	17.863	142.445
fcs_lgcl	0.140	0.012	0.152
fcs_lgcl_merge	0.131	0.008	0.139
peaksGamma_plot	0.266	0.016	0.281