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 02:21:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:24:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 232.0 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) (2019-03-18 r76245)
* 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                  38.094 18.384  18.907
plus-.ggcyto_GatingLayout 18.106  8.157   8.166
ggcyto.flowSet            13.777  4.334  10.499
ggcyto                    11.374  3.679   6.532
geom_stats                 8.354  4.424   3.397
geom_gate                  7.370  2.510   3.988
ggcyto_flowSet_add         6.233  1.924   3.831
geom_overlay               4.887  3.103   2.431
labs_cyto                  5.368  2.202   2.133
marginalFilter             5.326  2.198   3.093
replace_data               3.956  2.498   1.943
ggcyto_par_set             3.711  2.179   2.163
ggcyto.GatingSet           3.559  1.758   1.512
ggcyto_GatingSet_add       4.050  1.024   1.808
* 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’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘%+%’ from package ‘ggplot2’ in package ‘ggcyto’
** help
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggcyto)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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	1.971	0.838	1.618
autoplot	38.094	18.384	18.907
axis_x_inverse_trans	3.333	1.456	1.505
compute_stats	1.688	0.461	1.555
flowCore_asinht_trans	0.017	0.011	0.006
fortify.ellipsoidGate	0.044	0.030	0.018
fortify.filterList	0.133	0.101	0.044
fortify.flowSet	2.323	0.418	0.337
fortify.polygonGate	0.018	0.010	0.006
fortify.rectangleGate	0.055	0.026	0.017
fortify_fs	1.154	0.487	0.924
geom_gate	7.370	2.510	3.988
geom_hvline	0.434	0.015	0.449
geom_overlay	4.887	3.103	2.431
geom_stats	8.354	4.424	3.397
getFlowFrame	0.825	0.146	0.971
ggcyto.GatingSet	3.559	1.758	1.512
ggcyto	11.374	3.679	6.532
ggcyto.flowSet	13.777	4.334	10.499
ggcyto_GatingSet_add	4.050	1.024	1.808
ggcyto_arrange	0.001	0.000	0.000
ggcyto_flowSet_add	6.233	1.924	3.831
ggcyto_par_default	0.014	0.001	0.014
ggcyto_par_set	3.711	2.179	2.163
is.ggcyto	0.883	0.205	0.962
is.ggcyto_flowSet	1.134	0.587	0.766
is.ggcyto_par	0.011	0.008	0.003
labs_cyto	5.368	2.202	2.133
marginalFilter	5.326	2.198	3.093
merge.quad.gates	0.201	0.019	0.220
plus-.ggcyto_GatingLayout	18.106	8.157	8.166
replace_data	3.956	2.498	1.943
scale_x_flowCore_fasinh	2.582	1.231	1.634
scale_x_flowJo_biexp	2.401	1.012	1.563
scale_x_flowJo_fasinh	3.082	1.567	1.864
scale_x_logicle	3.032	1.388	1.484
stat_position	0.721	0.100	0.811