Mike Jiang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ggcyto |
| Branch: master |
| Last Commit: d28ee68 |
| Last Changed Date: 2019-01-18 19:02:03 -0400 (Fri, 18 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:44:30 -0400 (Tue, 09 Apr 2019).
| Package 667/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggcyto 1.11.4 Mike Jiang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: ggcyto |
| Version: 1.11.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ggcyto_1.11.4.tar.gz |
| StartedAt: 2019-04-09 00:51:57 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:55:40 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 223.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ggcyto.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ggcyto_1.11.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.11.4’
* 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 55.658 0.253 17.978
plus-.ggcyto_GatingLayout 34.317 0.168 10.026
ggcyto.flowSet 10.903 0.051 7.417
ggcyto 9.128 0.061 5.688
geom_stats 8.872 0.056 3.204
replace_data 6.980 0.063 2.486
geom_gate 6.559 0.068 3.916
geom_overlay 5.882 0.017 1.837
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck/00check.log’
for details.
ggcyto.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ggcyto ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
ggcyto.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 7 SKIPPED: 33 FAILED: 0
>
> proc.time()
user system elapsed
97.254 1.818 56.920
ggcyto.Rcheck/ggcyto-Ex.timings
| name | user | system | elapsed | |
| as.ggplot | 2.287 | 0.027 | 1.264 | |
| autoplot | 55.658 | 0.253 | 17.978 | |
| axis_x_inverse_trans | 3.784 | 0.016 | 1.428 | |
| compute_stats | 2.902 | 0.040 | 1.580 | |
| flowCore_asinht_trans | 0.011 | 0.000 | 0.003 | |
| fortify.ellipsoidGate | 0.012 | 0.000 | 0.009 | |
| fortify.filterList | 0.131 | 0.000 | 0.043 | |
| fortify.flowSet | 2.192 | 0.019 | 0.468 | |
| fortify.polygonGate | 0.001 | 0.003 | 0.005 | |
| fortify.rectangleGate | 0.010 | 0.000 | 0.011 | |
| fortify_fs | 0.694 | 0.031 | 0.724 | |
| geom_gate | 6.559 | 0.068 | 3.916 | |
| geom_hvline | 0.359 | 0.000 | 0.360 | |
| geom_overlay | 5.882 | 0.017 | 1.837 | |
| geom_stats | 8.872 | 0.056 | 3.204 | |
| getFlowFrame | 0.765 | 0.036 | 0.801 | |
| ggcyto.GatingSet | 2.386 | 0.004 | 1.051 | |
| ggcyto | 9.128 | 0.061 | 5.688 | |
| ggcyto.flowSet | 10.903 | 0.051 | 7.417 | |
| ggcyto_GatingSet_add | 4.262 | 0.024 | 1.856 | |
| ggcyto_arrange | 0.001 | 0.000 | 0.000 | |
| ggcyto_flowSet_add | 4.582 | 0.040 | 2.655 | |
| ggcyto_par_default | 0.006 | 0.000 | 0.006 | |
| ggcyto_par_set | 3.385 | 0.011 | 1.690 | |
| is.ggcyto | 0.968 | 0.032 | 0.758 | |
| is.ggcyto_flowSet | 0.568 | 0.036 | 0.547 | |
| is.ggcyto_par | 0.001 | 0.000 | 0.001 | |
| labs_cyto | 3.52 | 0.04 | 1.43 | |
| marginalFilter | 4.158 | 0.048 | 2.350 | |
| merge.quad.gates | 0.141 | 0.000 | 0.143 | |
| plus-.ggcyto_GatingLayout | 34.317 | 0.168 | 10.026 | |
| replace_data | 6.980 | 0.063 | 2.486 | |
| scale_x_flowCore_fasinh | 2.231 | 0.028 | 1.567 | |
| scale_x_flowJo_biexp | 2.109 | 0.016 | 1.407 | |
| scale_x_flowJo_fasinh | 1.944 | 0.024 | 1.258 | |
| scale_x_logicle | 2.123 | 0.028 | 1.396 | |
| stat_position | 0.928 | 0.032 | 0.866 | |