Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 492/2255 | 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 | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.3.0 |
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: 2024-08-20 23:57:29 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-21 00:01:01 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 211.6 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 4.4.1 (2024-06-14 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 14.36 1.50 16.54 plotSelectedFlowFrame 12.56 1.28 14.20 CytoPipelineCheckApp 11.70 1.16 13.12 plotScaleTransformedChannel 11.05 0.86 12.38 plotSelectedWorkflow 10.58 0.95 11.89 ScaleTransformApp 10.17 0.82 11.23 * 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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% | |++ | 5% | |+++++ | 10% | |++++++++ | 15% | |++++++++++ | 20% | |++++++++++++ | 25% | |+++++++++++++++ | 30% | |++++++++++++++++++ | 35% | |++++++++++++++++++++ | 40% | |++++++++++++++++++++++ | 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 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 23.95 2.32 26.59
CytoPipelineGUI.Rcheck/CytoPipelineGUI-Ex.timings
name | user | system | elapsed | |
CytoPipelineCheckApp | 11.70 | 1.16 | 13.12 | |
ScaleTransformApp | 10.17 | 0.82 | 11.23 | |
plotDiffFlowFrame | 14.36 | 1.50 | 16.54 | |
plotScaleTransformedChannel | 11.05 | 0.86 | 12.38 | |
plotSelectedFlowFrame | 12.56 | 1.28 | 14.20 | |
plotSelectedWorkflow | 10.58 | 0.95 | 11.89 | |