BioC 3.5: CHECK report for ggcyto on oaxaca

Package: ggcyto

Version: 1.3.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggcyto_1.3.6.tar.gz

StartedAt: 2017-03-04 03:41:12 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:43:47 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 154.8 seconds

RetCode: 0

Status:  OK

CheckDir: ggcyto.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 ggcyto_1.3.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ggcyto.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 ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.3.6’
* 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 ‘ggcyto’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’
  ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’
  ‘ggplot2:::check_aesthetics’ ‘ggplot2:::ggplot.data.frame’
  ‘ggplot2:::is.waive’ ‘ggplot2:::is_calculated_aes’
  ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’
  ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’
  ‘ggplot2:::update_theme’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fs2dt: no visible binding for global variable ‘name’
add_ggcyto: no visible binding for global variable ‘name’
add_ggcyto: no visible binding for global variable ‘density’
add_ggcyto: no visible binding for global variable ‘axis’
add_ggcyto: no visible binding for global variable ‘desc’
add_par: no visible global function definition for ‘modifyList’
as.ggplot: no visible binding for global variable ‘axis’
as.ggplot: no visible binding for global variable ‘name’
autoplot.GatingHierarchy : <anonymous>: no visible global function
  definition for ‘gray’
autoplot.GatingSetList: no visible global function definition for
  ‘getS3method’
autoplot.ncdfFlowList: no visible global function definition for
  ‘getS3method’
density_fr_all : <anonymous>: no visible global function definition for
  ‘gray’
fortify.GatingSetList: no visible global function definition for
  ‘getS3method’
fortify.ncdfFlowList: no visible global function definition for
  ‘getS3method’
fortify.polygonGate : <anonymous>: no visible global function
  definition for ‘dist’
fortify.polygonGate : <anonymous>: no visible global function
  definition for ‘approx’
fortify_fs.GatingSetList: no visible global function definition for
  ‘getS3method’
getFlowFrame.GatingSetList: no visible global function definition for
  ‘getS3method’
getFlowFrame.ncdfFlowList: no visible global function definition for
  ‘getS3method’
ggcyto.GatingSetList: no visible global function definition for
  ‘getS3method’
ggcyto.flowSet: no visible binding for global variable ‘name’
ggcyto.flowSet: no visible binding for global variable ‘axis’
ggcyto.ncdfFlowList: no visible global function definition for
  ‘getS3method’
ggcyto_arrange: no visible binding for global variable ‘name’
Undefined global functions or variables:
  approx axis density desc dist getS3method gray modifyList name
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis")
  importFrom("stats", "approx", "density", "dist")
  importFrom("utils", "getS3method", "modifyList")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
autoplot                  13.252  0.613  21.356
plus-.ggcyto_GatingLayout  5.891  0.412  11.743
ggcyto.flowSet             5.736  0.320   6.156
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ggcyto.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
as.ggplot	1.946	0.057	2.025
autoplot	13.252	0.613	21.356
axis_x_inverse_trans	0.978	0.083	1.400
compute_stats	1.009	0.068	1.078
fortify.ellipsoidGate	0.011	0.001	0.012
fortify.filterList	0.031	0.002	0.032
fortify.flowSet	0.127	0.037	0.297
fortify.polygonGate	0.010	0.000	0.011
fortify.rectangleGate	0.013	0.000	0.013
fortify_fs	0.743	0.065	0.896
geom_gate	2.788	0.188	3.580
geom_hvline	0.496	0.004	0.615
geom_overlay	1.873	0.217	2.566
geom_stats	1.743	0.185	1.938
getFlowFrame	0.560	0.057	0.618
ggcyto.GatingSet	0.927	0.109	1.038
ggcyto	4.103	0.113	4.323
ggcyto.flowSet	5.736	0.320	6.156
ggcyto_GatingSet_add	1.267	0.097	1.384
ggcyto_arrange	0.001	0.000	0.001
ggcyto_flowSet_add	2.495	0.159	2.681
ggcyto_par_default	0.006	0.000	0.006
ggcyto_par_set	1.707	0.184	1.981
is.ggcyto	0.598	0.057	0.655
is.ggcyto_flowSet	0.547	0.027	0.575
is.ggcyto_par	0.001	0.000	0.001
labs_cyto	1.438	0.153	1.595
marginalFilter	2.198	0.164	2.365
plus-.ggcyto_GatingLayout	5.891	0.412	11.743
scale_x_flowJo_biexp	0.971	0.045	1.167
scale_x_flowJo_fasinh	1.252	0.040	1.347
scale_x_logicle	1.051	0.034	1.085
stat_position	0.697	0.027	0.724