Philippe Hauchamps
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/CytoPipelineGUI |
| git_branch: devel |
| git_last_commit: 8e614da |
| git_last_commit_date: 2024-04-30 11:51:15 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 486/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoPipelineGUI 1.3.0 (landing page) Philippe Hauchamps
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.3.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CytoPipelineGUI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CytoPipelineGUI_1.3.0.tar.gz |
| StartedAt: 2024-06-10 01:36:03 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 01:40:12 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 249.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoPipelineGUI.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CytoPipelineGUI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CytoPipelineGUI_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CytoPipelineGUI.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CytoPipelineGUI/DESCRIPTION' ... OK
* this is package 'CytoPipelineGUI' version '1.3.0'
* 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 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 ... 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 (user + system) or elapsed time > 5s
user system elapsed
plotDiffFlowFrame 13.45 1.93 15.64
plotSelectedFlowFrame 12.40 1.49 14.14
CytoPipelineCheckApp 10.87 2.00 13.17
plotScaleTransformedChannel 10.24 1.40 11.89
plotSelectedWorkflow 9.97 1.36 11.55
ScaleTransformApp 8.91 0.90 10.05
* 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: 1 NOTE
See
'F:/biocbuild/bbs-3.20-bioc/meat/CytoPipelineGUI.Rcheck/00check.log'
for details.
CytoPipelineGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CytoPipelineGUI ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'CytoPipelineGUI' ... ** 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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
>
> 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 F:/biocbuild/bbs-3.20-bioc/R/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%
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|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 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 F:/biocbuild/bbs-3.20-bioc/R/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%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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
22.85 4.60 29.39
CytoPipelineGUI.Rcheck/CytoPipelineGUI-Ex.timings
| name | user | system | elapsed | |
| CytoPipelineCheckApp | 10.87 | 2.00 | 13.17 | |
| ScaleTransformApp | 8.91 | 0.90 | 10.05 | |
| plotDiffFlowFrame | 13.45 | 1.93 | 15.64 | |
| plotScaleTransformedChannel | 10.24 | 1.40 | 11.89 | |
| plotSelectedFlowFrame | 12.40 | 1.49 | 14.14 | |
| plotSelectedWorkflow | 9.97 | 1.36 | 11.55 | |