| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-01 11:35:50 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 501/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoPipelineGUI 1.2.0 (landing page) Philippe Hauchamps
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CytoPipelineGUI.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CytoPipelineGUI_1.2.0.tar.gz |
| StartedAt: 2024-05-01 04:33:31 -0400 (Wed, 01 May 2024) |
| EndedAt: 2024-05-01 04:36:49 -0400 (Wed, 01 May 2024) |
| EllapsedTime: 197.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoPipelineGUI.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CytoPipelineGUI.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CytoPipelineGUI_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CytoPipelineGUI.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CytoPipelineGUI/DESCRIPTION’ ... OK
* this is package ‘CytoPipelineGUI’ version ‘1.2.0’
* 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 loading without being on the library search path ... 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 11.319 0.259 11.585
plotSelectedFlowFrame 9.957 0.169 10.114
CytoPipelineCheckApp 9.668 0.343 10.012
plotScaleTransformedChannel 8.708 0.204 8.899
plotSelectedWorkflow 8.403 0.140 8.551
ScaleTransformApp 7.672 0.180 8.004
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/CytoPipelineGUI.Rcheck/00check.log’
for details.
CytoPipelineGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CytoPipelineGUI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 beta (2024-04-15 r86425) -- "Puppy Cup"
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.
> # 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] ...
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/site-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] ...
Compensating file : Donor1.fcs
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 /home/biocbuild/bbs-3.19-bioc/R/site-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] ...
Compensating file : Donor2.fcs
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) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-plots.R:218:1'
• On CRAN (1): 'test-plots.R:101:5'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
Deleting unused snapshots:
• plots/pltselff-allc-tran.svg
>
> proc.time()
user system elapsed
19.222 1.100 20.278
CytoPipelineGUI.Rcheck/CytoPipelineGUI-Ex.timings
| name | user | system | elapsed | |
| CytoPipelineCheckApp | 9.668 | 0.343 | 10.012 | |
| ScaleTransformApp | 7.672 | 0.180 | 8.004 | |
| plotDiffFlowFrame | 11.319 | 0.259 | 11.585 | |
| plotScaleTransformedChannel | 8.708 | 0.204 | 8.899 | |
| plotSelectedFlowFrame | 9.957 | 0.169 | 10.114 | |
| plotSelectedWorkflow | 8.403 | 0.140 | 8.551 | |