Mike Jiang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ggcyto |
| Branch: RELEASE_3_7 |
| Last Commit: ad88ca1 |
| Last Changed Date: 2018-07-13 03:07:15 -0400 (Fri, 13 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:55:49 -0400 (Wed, 17 Oct 2018).
| Package 614/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggcyto 1.8.2 Mike Jiang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ggcyto |
| Version: 1.8.2 |
| 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_1.8.2.tar.gz |
| StartedAt: 2018-10-16 21:43:47 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:47:43 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 236.5 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 --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.8.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ggcyto.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.2’
* 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.
Unexported objects imported by ':::' calls:
‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’
‘flowWorkspace:::fix_y_axis’ ‘flowWorkspace:::isNegated’
‘ggplot2:::+.gg’ ‘ggplot2:::add_group’ ‘ggplot2:::as_gg_data_frame’
‘ggplot2:::check_aesthetics’ ‘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 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: 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.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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot 16.002 0.971 17.193
ggcyto.flowSet 7.286 0.513 7.867
plus-.ggcyto_GatingLayout 6.716 0.573 7.332
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/ggcyto.Rcheck/00check.log’
for details.
ggcyto.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggcyto ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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)
ggcyto.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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)
>
> test_check("ggcyto")
loading R object...
loading tree object...
Done
══ testthat results ═══════════════════════════════════════════════════════════
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
62.763 5.269 68.737
ggcyto.Rcheck/ggcyto-Ex.timings
| name | user | system | elapsed | |
| as.ggplot | 1.210 | 0.084 | 1.306 | |
| autoplot | 16.002 | 0.971 | 17.193 | |
| axis_x_inverse_trans | 1.310 | 0.120 | 1.458 | |
| compute_stats | 0.910 | 0.071 | 1.001 | |
| flowCore_asinht_trans | 0.004 | 0.000 | 0.005 | |
| fortify.ellipsoidGate | 0.010 | 0.001 | 0.012 | |
| fortify.filterList | 0.035 | 0.002 | 0.037 | |
| fortify.flowSet | 0.142 | 0.044 | 0.189 | |
| fortify.polygonGate | 0.008 | 0.001 | 0.009 | |
| fortify.rectangleGate | 0.014 | 0.001 | 0.014 | |
| fortify_fs | 0.737 | 0.062 | 0.812 | |
| geom_gate | 3.419 | 0.255 | 3.751 | |
| geom_hvline | 0.417 | 0.002 | 0.428 | |
| geom_overlay | 1.940 | 0.196 | 2.192 | |
| geom_stats | 2.734 | 0.259 | 3.023 | |
| getFlowFrame | 0.696 | 0.067 | 0.765 | |
| ggcyto.GatingSet | 1.159 | 0.131 | 1.305 | |
| ggcyto | 4.340 | 0.115 | 4.481 | |
| ggcyto.flowSet | 7.286 | 0.513 | 7.867 | |
| ggcyto_GatingSet_add | 1.323 | 0.113 | 1.448 | |
| ggcyto_arrange | 0.002 | 0.000 | 0.002 | |
| ggcyto_flowSet_add | 2.981 | 0.204 | 3.205 | |
| ggcyto_par_default | 0.010 | 0.001 | 0.011 | |
| ggcyto_par_set | 1.751 | 0.186 | 1.950 | |
| is.ggcyto | 0.644 | 0.055 | 0.707 | |
| is.ggcyto_flowSet | 0.649 | 0.032 | 0.689 | |
| is.ggcyto_par | 0.002 | 0.000 | 0.002 | |
| labs_cyto | 1.500 | 0.208 | 1.723 | |
| marginalFilter | 1.786 | 0.189 | 1.988 | |
| merge.quad.gates | 0.146 | 0.001 | 0.148 | |
| plus-.ggcyto_GatingLayout | 6.716 | 0.573 | 7.332 | |
| replace_data | 1.550 | 0.085 | 1.649 | |
| scale_x_flowCore_fasinh | 1.301 | 0.067 | 1.374 | |
| scale_x_flowJo_biexp | 1.255 | 0.042 | 1.306 | |
| scale_x_flowJo_fasinh | 1.285 | 0.052 | 1.350 | |
| scale_x_logicle | 1.373 | 0.051 | 1.429 | |
| stat_position | 0.692 | 0.042 | 0.737 | |