| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 506/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoPipelineGUI 1.6.0 (landing page) Philippe Hauchamps
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CytoPipelineGUI package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoPipelineGUI.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: CytoPipelineGUI |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoPipelineGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoPipelineGUI_1.6.0.tar.gz |
| StartedAt: 2025-04-21 20:06:00 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:09:12 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 191.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoPipelineGUI.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoPipelineGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoPipelineGUI_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CytoPipelineGUI.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoPipelineGUI/DESCRIPTION’ ... OK
* this is package ‘CytoPipelineGUI’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘CytoPipelineGUI’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
CytoPipelineGUI.Rd: CytoPipeline
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 (user + system) or elapsed time > 5s
user system elapsed
plotDiffFlowFrame 12.564 0.705 13.394
CytoPipelineCheckApp 10.827 0.700 11.621
plotSelectedFlowFrame 10.906 0.604 11.628
plotScaleTransformedChannel 9.431 0.534 10.039
plotSelectedWorkflow 9.112 0.534 9.722
ScaleTransformApp 8.812 0.525 9.415
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-bioc/meat/CytoPipelineGUI.Rcheck/00check.log’
for details.
CytoPipelineGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoPipelineGUI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘CytoPipelineGUI’ ... ** this is package ‘CytoPipelineGUI’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** 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 (CytoPipelineGUI)
CytoPipelineGUI.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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.
> # CytoPipelineGUI - Copyright (C) <2022-2024>
> # <Université catholique de Louvain (UCLouvain), Belgique>
> #
> # Description and complete License: see LICENSE file.
> #
> # This program (CytoPipelineGUI) is free software:
> # you can redistribute it and/or modify it under the terms of the GNU
> # General Public License as published by the Free Software Foundation,
> # either version 3 of the License, or (at your option) any later version.
> #
> # This program is distributed in the hope that it will be useful,
> # but WITHOUT ANY WARRANTY; without even the implied warranty of
> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> # GNU General Public License for more details (<http://www.gnu.org/licenses/>).
>
> library(testthat)
> library(CytoPipelineGUI)
Loading required package: CytoPipeline
>
> # launch CytoPipelineGUI tests
> test_check("CytoPipelineGUI")
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor1.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
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|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor2.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
no sample file passed as argument => defaulting to first sample file
displaying flow frame plot...
displaying flow frame comparison plot...
displaying flow frame comparison plot...
displaying flow frame comparison plot...
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-plots.R:101:5'
• empty test (1): 'test-plots.R:218:1'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
Deleting unused snapshots:
• plots/pltselff-allc-tran.svg
>
> proc.time()
user system elapsed
21.431 1.313 22.878
CytoPipelineGUI.Rcheck/CytoPipelineGUI-Ex.timings
| name | user | system | elapsed | |
| CytoPipelineCheckApp | 10.827 | 0.700 | 11.621 | |
| ScaleTransformApp | 8.812 | 0.525 | 9.415 | |
| plotDiffFlowFrame | 12.564 | 0.705 | 13.394 | |
| plotScaleTransformedChannel | 9.431 | 0.534 | 10.039 | |
| plotSelectedFlowFrame | 10.906 | 0.604 | 11.628 | |
| plotSelectedWorkflow | 9.112 | 0.534 | 9.722 | |