Mike Jiang
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ggcyto |
| git_branch: RELEASE_3_17 |
| git_last_commit: ae9e242 |
| git_last_commit_date: 2023-07-14 15:23:13 -0400 (Fri, 14 Jul 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 833/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggcyto 1.28.1 (landing page) Mike Jiang
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the ggcyto package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ggcyto |
| Version: 1.28.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggcyto_1.28.1.tar.gz |
| StartedAt: 2023-10-17 22:19:22 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 22:24:26 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 304.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggcyto.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggcyto_1.28.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ggcyto.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.28.1’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file path:
ggcyto/docs/articles/advanced/ggplot.flowSet.overlay_files/accessible-code-block-0.0.1/empty-anchor.js
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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:::gh_pop_is_negated’
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’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
grid.draw:
function(x, recording)
grid.draw.ggcyto_GatingLayout:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* 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 ‘count’
as.ggplot: no visible global function definition for ‘densCols’
as.ggplot: no visible global function definition for ‘colorRampPalette’
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.cytoframe: no visible global function definition for
‘getS3method’
autoplot.cytoset: 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’
faust_gating_plot: no visible global function definition for ‘gray’
fortify.GatingSetList: no visible global function definition for
‘getS3method’
fortify.cytoframe: no visible global function definition for
‘getS3method’
fortify.cytoset: 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.cytoset: 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.cytoset: 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’
stat_position.filter: no visible global function definition for
‘setNames’
Undefined global functions or variables:
axis colorRampPalette count densCols density desc getS3method gray
modifyList name setNames
Consider adding
importFrom("grDevices", "colorRampPalette", "densCols", "gray")
importFrom("graphics", "axis")
importFrom("stats", "density", "setNames")
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 ... WARNING
Undocumented arguments in documentation object 'faust_gating_plot'
‘gh’ ‘...’
Documented arguments not in \usage in documentation object 'fortify.multiRangeGate':
‘nPoints’
Undocumented arguments in documentation object 'geom_multi_range'
‘stat’ ‘linejoin’ ‘na.rm’ ‘inherit.aes’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
autoplot 13.746 0.347 19.789
ggcyto 12.159 0.220 18.681
ggcyto_add 11.186 0.249 17.113
getFlowFrame 5.645 0.169 8.760
geom_gate 4.586 0.080 7.122
scales_flowjo_fasinh 3.269 0.047 5.034
* 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 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ggcyto.Rcheck/00check.log’
for details.
ggcyto.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggcyto ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘ggcyto’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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: BH
Loading required package: flowWorkspace
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
> library(vdiffr)
>
> test_check("ggcyto")
Coordinate system already present. Adding new coordinate system, which will
replace the existing one.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
[ FAIL 0 | WARN 0 | SKIP 8 | PASS 1 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (8): 'test-autoplot.R:9:3', 'test-autoplot.R:14:3',
'test-autoplot.R:25:3', 'test-ggcyto-fs.R:17:3', 'test-ggcyto-gs.R:31:3',
'test-ggcyto-gs.R:83:3', 'test-ggcyto-gs.R:99:3',
'test-multiRangeGate.R:14:3'
[ FAIL 0 | WARN 0 | SKIP 8 | PASS 1 ]
Deleting unused snapshots:
• autoplot/autoplot-fr-2d.svg
• autoplot/autoplot-fs-2d.svg
• autoplot/autoplot-gs-2-gate.svg
• autoplot/autoplot-gs-bool-gate.svg
• ggcyto-fs/ggcyto-fs-1d-den-stats.svg
• ggcyto-fs/ggcyto-fs-1d-density-alpha.svg
• ggcyto-fs/ggcyto-fs-1d-density-black.svg
• ggcyto-fs/ggcyto-fs-1d-density.svg
• ggcyto-fs/ggcyto-fs-1d-facet.svg
• ggcyto-fs/ggcyto-fs-2d-hex-1dgate-static-stats.svg
• ggcyto-fs/ggcyto-fs-2d-hex-1dgate.svg
• ggcyto-fs/ggcyto-fs-2d-hex-gradien.svg
• ggcyto-fs/ggcyto-fs-2d-hex-lim.svg
• ggcyto-fs/ggcyto-fs-2d-hex-polygates.svg
• ggcyto-fs/ggcyto-fs-2d-hex-rectgate-stats.svg
• ggcyto-fs/ggcyto-fs-2d-hex-rectgate.svg
• ggcyto-fs/ggcyto-fs-2d-hex.svg
• ggcyto-fs/ggcyto-fs-2d-multi-gates-single-stats.svg
• ggcyto-fs/ggcyto-fs-2d-multi-gates.svg
• ggcyto-gs/gate-null-2gates-geom-gate.svg
• ggcyto-gs/ggcyto-gs-1-gate.svg
• ggcyto-gs/ggcyto-gs-2-gate.svg
• ggcyto-gs/ggcyto-gs-all-children.svg
• ggcyto-gs/ggcyto-gs-axis-x-inverse-trans.svg
• ggcyto-gs/ggcyto-gs-custom-range.svg
• ggcyto-gs/ggcyto-gs-instrument-range.svg
• ggcyto-gs/ggcyto-gs-overlay-1d.svg
• ggcyto-gs/ggcyto-gs-overlay-2d.svg
• ggcyto-gs/ggcyto-gs-root.svg
• ggcyto-gs/ggcyto-gs-stats-all.svg
• ggcyto-gs/ggcyto-gs-stats-custom.svg
• ggcyto-gs/ggcyto-gs-stats.svg
• ggcyto-gs/stats-null-1gate-geom-stats.svg
• ggcyto-gs/stats-null-2gates-geom-stats.svg
• ggcyto-gs/stats-null-2gates.svg
• multiRangeGate/ggcyto-fs-2d-multirangegate-flip.svg
• multiRangeGate/ggcyto-fs-2d-multirangegate.svg
>
> proc.time()
user system elapsed
13.188 0.587 21.126
ggcyto.Rcheck/ggcyto-Ex.timings
| name | user | system | elapsed | |
| as.ggplot | 3.083 | 0.063 | 4.525 | |
| autoplot | 13.746 | 0.347 | 19.789 | |
| axis_x_inverse_trans | 0.869 | 0.033 | 1.215 | |
| compute_stats | 2.785 | 0.038 | 4.088 | |
| faust_gating_plot | 0.000 | 0.001 | 0.000 | |
| flowCore_asinht_trans | 0.002 | 0.000 | 0.002 | |
| fortify.ellipsoidGate | 0.007 | 0.001 | 0.011 | |
| fortify.filterList | 0.021 | 0.003 | 0.032 | |
| fortify.flowSet | 0.131 | 0.020 | 0.216 | |
| fortify.multiRangeGate | 0.006 | 0.000 | 0.009 | |
| fortify.polygonGate | 0.003 | 0.000 | 0.004 | |
| fortify.rectangleGate | 0.009 | 0.001 | 0.013 | |
| fortify_fs | 2.558 | 0.032 | 3.914 | |
| gate_null | 0.512 | 0.021 | 0.821 | |
| geom_gate | 4.586 | 0.080 | 7.122 | |
| geom_hvline | 0.370 | 0.009 | 0.580 | |
| geom_overlay | 1.422 | 0.052 | 2.249 | |
| geom_stats | 1.964 | 0.061 | 3.168 | |
| getFlowFrame | 5.645 | 0.169 | 8.760 | |
| ggcyto | 12.159 | 0.220 | 18.681 | |
| ggcyto_add | 11.186 | 0.249 | 17.113 | |
| ggcyto_arrange | 0 | 0 | 0 | |
| ggcyto_par_default | 0.012 | 0.001 | 0.020 | |
| ggcyto_par_set | 1.050 | 0.032 | 1.652 | |
| is.ggcyto | 2.304 | 0.028 | 3.525 | |
| is.ggcyto_flowSet | 2.356 | 0.025 | 3.549 | |
| is.ggcyto_par | 0.002 | 0.000 | 0.004 | |
| labs_cyto | 1.087 | 0.032 | 1.582 | |
| marginalFilter | 3.394 | 0.054 | 4.578 | |
| merge.quad.gates | 0.128 | 0.004 | 0.174 | |
| replace_data | 1.231 | 0.050 | 1.629 | |
| scale_x_flowCore_fasinh | 2.899 | 0.034 | 3.791 | |
| scale_x_logicle | 2.987 | 0.035 | 4.439 | |
| scales_flowjo_biexp | 2.867 | 0.035 | 4.462 | |
| scales_flowjo_fasinh | 3.269 | 0.047 | 5.034 | |
| stat_position | 2.494 | 0.031 | 3.858 | |
| stats_null | 0.180 | 0.009 | 0.292 | |