BioC 3.6: CHECK report for ggcyto on malbec1

Package: ggcyto

Version: 1.5.3

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.5.3.tar.gz

StartedAt: 2017-08-15 23:35:23 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:37:27 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 124.0 seconds

RetCode: 0

Status:  OK

CheckDir: ggcyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.5.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ggcyto.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.3’
* 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  6.3Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
* 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       13.744  0.076  14.042
ggcyto.flowSet  6.204  0.100   6.382
* 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-3.6-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	2.044	0.012	2.205
autoplot	13.744	0.076	14.042
axis_x_inverse_trans	0.960	0.012	0.970
compute_stats	0.908	0.016	0.926
flowCore_asinht_trans	0.000	0.000	0.002
fortify.ellipsoidGate	0.008	0.000	0.006
fortify.filterList	0.028	0.000	0.026
fortify.flowSet	0.128	0.008	0.159
fortify.polygonGate	0.012	0.000	0.009
fortify.rectangleGate	0.012	0.000	0.012
fortify_fs	0.564	0.000	0.561
geom_gate	2.496	0.000	2.499
geom_hvline	0.340	0.000	0.341
geom_overlay	1.536	0.028	1.566
geom_stats	1.532	0.016	1.549
getFlowFrame	0.520	0.092	0.609
ggcyto.GatingSet	0.692	0.000	0.691
ggcyto	3.240	0.044	3.284
ggcyto.flowSet	6.204	0.100	6.382
ggcyto_GatingSet_add	0.948	0.000	0.947
ggcyto_arrange	0.000	0.000	0.001
ggcyto_flowSet_add	2.128	0.128	2.257
ggcyto_par_default	0.004	0.000	0.004
ggcyto_par_set	1.224	0.004	1.229
is.ggcyto	0.516	0.044	0.560
is.ggcyto_flowSet	0.508	0.064	0.571
is.ggcyto_par	0.000	0.000	0.001
labs_cyto	1.160	0.004	1.162
marginalFilter	1.668	0.096	1.764
plus-.ggcyto_GatingLayout	4.912	0.008	4.922
scale_x_flowCore_fasinh	0.936	0.088	1.024
scale_x_flowJo_biexp	1.092	0.108	1.198
scale_x_flowJo_fasinh	0.916	0.080	0.995
scale_x_logicle	0.912	0.104	1.019
stat_position	0.644	0.056	0.702