BioC 3.5: CHECK report for ggcyto on malbec2

Package: ggcyto

Version: 1.4.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.4.1.tar.gz

StartedAt: 2017-10-17 23:37:13 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:39:18 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 124.7 seconds

RetCode: 0

Status:  OK

CheckDir: ggcyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ggcyto.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.1’
* 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  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
* 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                  14.252  0.140  14.497
ggcyto.flowSet             5.416  0.092   5.512
plus-.ggcyto_GatingLayout  5.060  0.004   5.068
* 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
  ‘/home/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	2.040	0.128	2.178
autoplot	14.252	0.140	14.497
axis_x_inverse_trans	0.928	0.004	0.930
compute_stats	0.716	0.048	0.766
fortify.ellipsoidGate	0.004	0.000	0.006
fortify.filterList	0.028	0.000	0.027
fortify.flowSet	0.160	0.076	0.260
fortify.polygonGate	0.008	0.000	0.010
fortify.rectangleGate	0.016	0.000	0.013
fortify_fs	0.752	0.100	0.856
geom_gate	2.656	0.096	2.762
geom_hvline	0.344	0.000	0.344
geom_overlay	1.832	0.024	1.859
geom_stats	1.276	0.012	1.289
getFlowFrame	0.500	0.076	0.574
ggcyto.GatingSet	0.684	0.000	0.684
ggcyto	3.444	0.076	3.524
ggcyto.flowSet	5.416	0.092	5.512
ggcyto_GatingSet_add	1.248	0.000	1.248
ggcyto_arrange	0.000	0.000	0.001
ggcyto_flowSet_add	2.400	0.052	2.455
ggcyto_par_default	0.004	0.000	0.004
ggcyto_par_set	1.672	0.004	1.675
is.ggcyto	0.508	0.084	0.590
is.ggcyto_flowSet	0.576	0.072	0.651
is.ggcyto_par	0.000	0.000	0.001
labs_cyto	1.120	0.000	1.121
marginalFilter	1.504	0.084	1.587
plus-.ggcyto_GatingLayout	5.060	0.004	5.068
scale_x_flowJo_biexp	0.956	0.060	1.017
scale_x_flowJo_fasinh	1.068	0.088	1.153
scale_x_logicle	0.900	0.052	0.955
stat_position	0.520	0.036	0.557