Arnaud Wolfer
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: RELEASE_3_18 |
| git_last_commit: 8a9ba02 |
| git_last_commit_date: 2024-02-26 17:51:10 -0400 (Mon, 26 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:13 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1520/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.16.1 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the peakPantheR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakPantheR.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: peakPantheR |
| Version: 1.16.1 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings peakPantheR_1.16.1.tar.gz |
| StartedAt: 2024-04-16 02:12:17 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 02:33:11 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 1253.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: peakPantheR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings peakPantheR_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/peakPantheR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.16.1’
* 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 ‘peakPantheR’ 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 R 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 startup messages can be suppressed ... 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
peakPantheR_ROIStatistics 19.577 0.344 19.925
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.353 0.572 15.938
peakPantheR_parallelAnnotation 15.207 0.188 15.395
outputAnnotationResult-peakPantheRAnnotation-method 13.893 0.244 14.137
EICs-peakPantheRAnnotation-method 12.563 0.928 13.497
retentionTimeCorrection-peakPantheRAnnotation-method 10.470 0.140 10.610
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘getting-started.Rmd’ using ‘UTF-8’... failed
‘parallel-annotation.Rmd’ using ‘UTF-8’... failed
‘peakPantheR-GUI.Rmd’ using ‘UTF-8’... failed
‘real-time-annotation.Rmd’ using ‘UTF-8’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘getting-started.Rmd’
...
sigma
> library(pander)
> knitr::include_graphics("../man/figures/example-UI.png")
When sourcing ‘getting-started.R’:
Error: Cannot find the file(s): "../man/figures/example-UI.png"
Execution halted
when running code in ‘parallel-annotation.Rmd’
...
Loading required package: iterators
Loading required package: parallel
> library(foreach)
> knitr::include_graphics("../man/figures/parallelAnnotation.png")
When sourcing ‘parallel-annotation.R’:
Error: Cannot find the file(s): "../man/figures/parallelAnnotation.png"
Execution halted
when running code in ‘peakPantheR-GUI.Rmd’
...
sigma
> library(pander)
> knitr::include_graphics("../man/figures/01-import_RData.png")
When sourcing ‘peakPantheR-GUI.R’:
Error: Cannot find the file(s): "../man/figures/01-import_RData.png"
Execution halted
when running code in ‘real-time-annotation.Rmd’
...
95 3435.655 496.2 86408
96 3437.220 496.2 81288
97 3438.785 496.2 78144
> knitr::include_graphics("../man/figures/singleFileSearch_EICsPlot.png")
When sourcing ‘real-time-annotation.R’:
Error: Cannot find the file(s): "../man/figures/singleFileSearch_EICsPlot.png"
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.18-bioc/meat/peakPantheR.Rcheck/00check.log’
for details.
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘peakPantheR’ ... ** 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 (peakPantheR)
peakPantheR.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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(peakPantheR)
This is peakPantheR version 1.16.1
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1458 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (/tmp/RtmphTyQht/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/tmp/RtmphTyQht/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/tmp/RtmphTyQht/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/tmp/RtmphTyQht/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/home/biocbuild/bbs-3.18-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/home/biocbuild/bbs-3.18-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
>
> proc.time()
user system elapsed
729.184 17.401 900.439
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 12.563 | 0.928 | 13.497 | |
| FIR-peakPantheRAnnotation-method | 0.197 | 0.008 | 0.205 | |
| ROI-peakPantheRAnnotation-method | 0.193 | 0.000 | 0.193 | |
| TIC-peakPantheRAnnotation-method | 0.182 | 0.000 | 0.182 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.172 | 0.000 | 0.172 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.161 | 0.000 | 0.161 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.186 | 0.020 | 0.206 | |
| annotationTable-peakPantheRAnnotation-method | 0.197 | 0.001 | 0.198 | |
| annotation_diagnostic_multiplot_UI_helper | 0.113 | 0.012 | 0.125 | |
| annotation_fit_summary_UI_helper | 0.007 | 0.000 | 0.007 | |
| annotation_showMethod_UI_helper | 0.003 | 0.000 | 0.003 | |
| annotation_showText_UI_helper | 0 | 0 | 0 | |
| cpdID-peakPantheRAnnotation-method | 0.210 | 0.004 | 0.213 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.242 | 0.028 | 0.271 | |
| cpdName-peakPantheRAnnotation-method | 0.184 | 0.008 | 0.192 | |
| dataPoints-peakPantheRAnnotation-method | 0.198 | 0.004 | 0.202 | |
| filename-peakPantheRAnnotation-method | 0.23 | 0.00 | 0.23 | |
| filepath-peakPantheRAnnotation-method | 0.224 | 0.024 | 0.247 | |
| initialise_annotation_from_files_UI_helper | 0.010 | 0.004 | 0.014 | |
| isAnnotated-peakPantheRAnnotation-method | 0.200 | 0.008 | 0.208 | |
| load_annotation_from_file_UI_helper | 0.002 | 0.004 | 0.007 | |
| nbCompounds-peakPantheRAnnotation-method | 0.197 | 0.004 | 0.201 | |
| nbSamples-peakPantheRAnnotation-method | 0.206 | 0.000 | 0.206 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.353 | 0.572 | 15.938 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.005 | 0.000 | 0.005 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.022 | 0.000 | 0.023 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 13.893 | 0.244 | 14.137 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.005 | 0.000 | 0.005 | |
| peakFit-peakPantheRAnnotation-method | 0.156 | 0.000 | 0.157 | |
| peakPantheRAnnotation | 0.165 | 0.000 | 0.165 | |
| peakPantheR_ROIStatistics | 19.577 | 0.344 | 19.925 | |
| peakPantheR_loadAnnotationParamsCSV | 0.006 | 0.000 | 0.006 | |
| peakPantheR_parallelAnnotation | 15.207 | 0.188 | 15.395 | |
| peakPantheR_plotEICFit | 0.292 | 0.000 | 0.292 | |
| peakPantheR_plotPeakwidth | 0.489 | 0.000 | 0.489 | |
| peakPantheR_singleFileSearch | 4.757 | 0.044 | 4.801 | |
| peakPantheR_start_GUI | 0 | 0 | 0 | |
| peakTables-peakPantheRAnnotation-method | 0.134 | 0.004 | 0.138 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.153 | 0.000 | 0.153 | |
| resetFIR-peakPantheRAnnotation-method | 0.005 | 0.000 | 0.005 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 10.47 | 0.14 | 10.61 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.148 | 0.000 | 0.148 | |
| spectraPaths_and_metadata_UI_helper | 0.002 | 0.000 | 0.002 | |
| spectra_metadata_colourScheme_UI_helper | 0.005 | 0.000 | 0.005 | |
| uROI-peakPantheRAnnotation-method | 0.163 | 0.004 | 0.167 | |
| uROIExist-peakPantheRAnnotation-method | 0.144 | 0.008 | 0.152 | |
| useFIR-peakPantheRAnnotation-method | 0.163 | 0.004 | 0.167 | |
| useUROI-peakPantheRAnnotation-method | 0.154 | 0.000 | 0.154 | |