Package: ggcyto

Version: 1.11.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.11.4.tar.gz

StartedAt: 2019-04-09 01:12:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:15:58 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 183.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: ggcyto.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.11.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.4’
* 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 ... 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
':::' call which should be '::': ‘flowWorkspace:::isNegated’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’
  ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’
  ‘ggplot2:::as_gg_data_frame’ ‘ggplot2:::check_aesthetics’
  ‘ggplot2:::hex_binwidth’ ‘ggplot2:::is.waive’
  ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’
  ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’
  ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’
  ‘ggplot2:::scales_list’ ‘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 global function definition for ‘modifyList’
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’
as.ggplot : <anonymous>: no visible binding for global variable ‘axis’
as.ggplot : <anonymous>: no visible binding for global variable ‘name’
as.ggplot: no visible binding for global variable ‘density’
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_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:
  axis density desc getS3method gray modifyList name
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis")
  importFrom("stats", "density")
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
autoplot                  33.145 18.575  15.548
plus-.ggcyto_GatingLayout 15.689  9.882   6.435
ggcyto.flowSet            12.901  6.793   8.331
ggcyto                     9.727  4.605   5.864
geom_stats                 6.621  5.478   2.804
geom_overlay               5.329  4.904   2.080
ggcyto_flowSet_add         5.735  3.209   3.298
geom_gate                  5.618  3.065   3.396
replace_data               4.240  4.077   1.460
labs_cyto                  4.094  3.930   1.562
marginalFilter             4.453  3.337   2.279
ggcyto_par_set             4.309  3.387   2.023
ggcyto.GatingSet           2.934  2.803   1.136
axis_x_inverse_trans       3.046  2.617   1.225
ggcyto_GatingSet_add       3.111  2.226   1.462
scale_x_flowCore_fasinh    2.773  2.379   1.411
scale_x_flowJo_biexp       3.080  2.015   1.682
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(ggcyto)
  Loading required package: ggplot2
  Loading required package: flowCore
  Loading required package: ncdfFlow
  Loading required package: RcppArmadillo
  Loading required package: BH
  Loading required package: flowWorkspace
  > library(vdiffr)
  Error: package or namespace load failed for 'vdiffr' in dyn.load(file, DLLpath = DLLpath, ...):
   unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so':
    dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so, 6): Symbol not found: _FT_Done_Face
    Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
    Expected in: flat namespace
   in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggcyto
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ggcyto’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘%+%’ from package ‘ggplot2’ in package ‘ggcyto’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggcyto)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ggcyto)
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
> library(vdiffr)
Error: package or namespace load failed for 'vdiffr' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so, 6): Symbol not found: _FT_Done_Face
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
Execution halted

name	user	system	elapsed
as.ggplot	1.912	1.082	1.228
autoplot	33.145	18.575	15.548
axis_x_inverse_trans	3.046	2.617	1.225
compute_stats	1.490	0.518	1.180
flowCore_asinht_trans	0.011	0.011	0.003
fortify.ellipsoidGate	0.042	0.037	0.012
fortify.filterList	0.135	0.110	0.035
fortify.flowSet	1.218	0.904	0.477
fortify.polygonGate	0.023	0.019	0.006
fortify.rectangleGate	0.053	0.037	0.014
fortify_fs	1.263	0.554	0.855
geom_gate	5.618	3.065	3.396
geom_hvline	0.380	0.002	0.390
geom_overlay	5.329	4.904	2.080
geom_stats	6.621	5.478	2.804
getFlowFrame	0.634	0.068	0.728
ggcyto.GatingSet	2.934	2.803	1.136
ggcyto	9.727	4.605	5.864
ggcyto.flowSet	12.901	6.793	8.331
ggcyto_GatingSet_add	3.111	2.226	1.462
ggcyto_arrange	0.000	0.000	0.001
ggcyto_flowSet_add	5.735	3.209	3.298
ggcyto_par_default	0.012	0.000	0.012
ggcyto_par_set	4.309	3.387	2.023
is.ggcyto	0.750	0.174	0.734
is.ggcyto_flowSet	1.386	1.012	0.826
is.ggcyto_par	0.009	0.011	0.002
labs_cyto	4.094	3.930	1.562
marginalFilter	4.453	3.337	2.279
merge.quad.gates	0.123	0.001	0.130
plus-.ggcyto_GatingLayout	15.689	9.882	6.435
replace_data	4.240	4.077	1.460
scale_x_flowCore_fasinh	2.773	2.379	1.411
scale_x_flowJo_biexp	3.080	2.015	1.682
scale_x_flowJo_fasinh	2.756	2.172	1.271
scale_x_logicle	2.746	2.202	1.308
stat_position	0.730	0.058	0.783