Mike Jiang
| Snapshot Date: 2024-10-02 13:40 -0400 (Wed, 02 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/ggcyto |
| git_branch: devel |
| git_last_commit: 09c942f |
| git_last_commit_date: 2024-04-30 10:47:37 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-03 11:41 -0400 (Thu, 03 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 845/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggcyto 1.33.0 (landing page) Mike Jiang
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the ggcyto package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggcyto.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.33.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggcyto_1.33.0.tar.gz |
| StartedAt: 2024-10-02 22:02:11 -0400 (Wed, 02 Oct 2024) |
| EndedAt: 2024-10-02 22:06:17 -0400 (Wed, 02 Oct 2024) |
| EllapsedTime: 245.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ggcyto.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggcyto_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ggcyto.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.33.0’
* 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 code 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 loading without being on the library search path ... 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:::guides_list’ ‘ggplot2:::hex_binwidth’ ‘ggplot2:::is.waive’
‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’
‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’
‘ggplot2:::print.ggplot’ ‘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
.fr2dt: no visible binding for global variable ‘axis’
.fr2dt: no visible binding for global variable ‘name’
.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 ‘axis’
ggcyto.flowSet: no visible binding for global variable ‘name’
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 Rd file 'faust_gating_plot.Rd'
‘gh’ ‘...’
Documented arguments not in \usage in Rd file 'fortify.multiRangeGate.Rd':
‘nPoints’
Undocumented arguments in Rd file 'geom_multi_range.Rd'
‘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 10.786 0.304 10.814
ggcyto 10.291 0.375 10.494
ggcyto_add 9.036 0.161 9.094
* 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:
• 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
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/ggcyto.Rcheck/00check.log’
for details.
ggcyto.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ggcyto ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
[ FAIL 2 | WARN 6 | SKIP 4 | PASS 0 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-ggcyto-gs.R:31:3', 'test-ggcyto-gs.R:83:3',
'test-ggcyto-gs.R:99:3', 'test-multiRangeGate.R:14:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoplot.R:6:1'): (code run outside of `test_that()`) ──────────
Error in `file(filename, open = "wb")`: cannot open the connection
Backtrace:
▆
1. └─flowWorkspace::flowSet_to_cytoset(fs) at test-autoplot.R:6:1
2. └─flowCore::write.flowSet(fs, tmp, filename = sampleNames(fs))
3. └─flowCore::write.FCS(...)
4. └─base::file(filename, open = "wb")
── Error ('test-ggcyto-fs.R:7:1'): (code run outside of `test_that()`) ─────────
Error in `file(filename, open = "wb")`: cannot open the connection
Backtrace:
▆
1. └─flowWorkspace::flowSet_to_cytoset(fs) at test-ggcyto-fs.R:7:1
2. └─flowCore::write.flowSet(fs, tmp, filename = sampleNames(fs))
3. └─flowCore::write.FCS(...)
4. └─base::file(filename, open = "wb")
[ FAIL 2 | WARN 6 | SKIP 4 | PASS 0 ]
Deleting unused snapshots:
• autoplot/autoplot-fr-1d.svg
• autoplot/autoplot-fr-2d.svg
• autoplot/autoplot-fs-1d.svg
• autoplot/autoplot-fs-2d.svg
• autoplot/autoplot-gs-1-gate.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-1d.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
Error: Test failures
Execution halted
ggcyto.Rcheck/ggcyto-Ex.timings
| name | user | system | elapsed | |
| as.ggplot | 1.847 | 0.028 | 1.868 | |
| autoplot | 10.786 | 0.304 | 10.814 | |
| axis_x_inverse_trans | 0.744 | 0.006 | 0.733 | |
| compute_stats | 1.453 | 0.001 | 1.454 | |
| faust_gating_plot | 0 | 0 | 0 | |
| flowCore_asinht_trans | 0.002 | 0.000 | 0.001 | |
| fortify.ellipsoidGate | 0.005 | 0.001 | 0.005 | |
| fortify.filterList | 0.017 | 0.000 | 0.017 | |
| fortify.flowSet | 0.169 | 0.019 | 0.144 | |
| fortify.multiRangeGate | 0.009 | 0.000 | 0.005 | |
| fortify.polygonGate | 0.005 | 0.000 | 0.003 | |
| fortify.rectangleGate | 0.009 | 0.000 | 0.007 | |
| fortify_fs | 1.351 | 0.023 | 1.374 | |
| gate_null | 0.448 | 0.021 | 0.459 | |
| geom_gate | 3.177 | 0.096 | 3.252 | |
| geom_hvline | 0.286 | 0.004 | 0.290 | |
| geom_overlay | 1.346 | 0.014 | 1.317 | |
| geom_stats | 1.427 | 0.004 | 1.395 | |
| getFlowFrame | 4.486 | 0.081 | 4.567 | |
| ggcyto | 10.291 | 0.375 | 10.494 | |
| ggcyto_add | 9.036 | 0.161 | 9.094 | |
| ggcyto_arrange | 0 | 0 | 0 | |
| ggcyto_par_default | 0.019 | 0.001 | 0.019 | |
| ggcyto_par_set | 1.003 | 0.009 | 0.977 | |
| is.ggcyto | 1.518 | 0.014 | 1.532 | |
| is.ggcyto_flowSet | 1.456 | 0.003 | 1.459 | |
| is.ggcyto_par | 0.002 | 0.001 | 0.004 | |
| labs_cyto | 0.931 | 0.006 | 0.910 | |
| marginalFilter | 2.185 | 0.042 | 2.210 | |
| merge.quad.gates | 0.096 | 0.000 | 0.096 | |
| replace_data | 1.025 | 0.019 | 1.006 | |
| scale_x_flowCore_fasinh | 1.758 | 0.003 | 1.748 | |
| scale_x_logicle | 2.405 | 0.061 | 2.452 | |
| scales_flowjo_biexp | 1.717 | 0.006 | 1.708 | |
| scales_flowjo_fasinh | 1.650 | 0.004 | 1.640 | |
| stat_position | 1.359 | 0.002 | 1.362 | |
| stats_null | 0.143 | 0.002 | 0.145 | |