| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1653/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PRONE 1.3.2 (landing page) Lis Arend
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
To the developers/maintainers of the PRONE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PRONE.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: PRONE |
| Version: 1.3.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PRONE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PRONE_1.3.2.tar.gz |
| StartedAt: 2025-10-24 23:27:35 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 23:33:31 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 356.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PRONE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PRONE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PRONE_1.3.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘PRONE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRONE’ version ‘1.3.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘PRONE’ 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 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 ... NOTE
Unexported objects imported by ':::' calls:
‘NormalyzerDE:::calculateAvgMadMem’
‘NormalyzerDE:::calculateAvgReplicateVariation’
‘NormalyzerDE:::calculatePercentageAvgDiffInMat’
‘NormalyzerDE:::calculateReplicateCV’
‘NormalyzerDE:::calculateSummarizedCorrelationVector’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_upset_DE: no visible global function definition for
‘packageVersion’
Undefined global functions or variables:
packageVersion
Consider adding
importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normalize_se_combination 5.393 0.119 5.541
plot_boxplots 5.233 0.049 5.328
* 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-3.22-bioc/meat/PRONE.Rcheck/00check.log’
for details.
PRONE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PRONE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘PRONE’ ... ** this is package ‘PRONE’ version ‘1.3.2’ ** using staged installation ** R ** data ** 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 (PRONE)
PRONE.Rcheck/PRONE-Ex.timings
| name | user | system | elapsed | |
| apply_thresholds | 0.024 | 0.002 | 0.027 | |
| detect_outliers_POMA | 1.938 | 0.072 | 2.020 | |
| eigenMSNorm | 0.675 | 0.059 | 0.738 | |
| export_data | 0.019 | 0.002 | 0.021 | |
| extract_consensus_DE_candidates | 0.098 | 0.005 | 0.104 | |
| filter_out_NA_proteins_by_threshold | 0.237 | 0.005 | 0.243 | |
| filter_out_complete_NA_proteins | 0.051 | 0.003 | 0.054 | |
| filter_out_proteins_by_ID | 0.167 | 0.004 | 0.171 | |
| filter_out_proteins_by_value | 0.165 | 0.004 | 0.170 | |
| get_NA_overview | 0.029 | 0.003 | 0.031 | |
| get_normalization_methods | 0.000 | 0.001 | 0.000 | |
| get_overview_DE | 0.041 | 0.003 | 0.045 | |
| get_proteins_by_value | 0.153 | 0.003 | 0.157 | |
| get_spiked_stats_DE | 0.079 | 0.005 | 0.085 | |
| globalIntNorm | 0.162 | 0.004 | 0.166 | |
| globalMeanNorm | 0.141 | 0.004 | 0.145 | |
| globalMedianNorm | 0.149 | 0.004 | 0.153 | |
| impute_se | 0.838 | 0.016 | 0.860 | |
| irsNorm | 0.057 | 0.003 | 0.060 | |
| limmaNorm | 0.071 | 0.003 | 0.074 | |
| load_data | 0.060 | 0.004 | 0.064 | |
| load_spike_data | 0.049 | 0.003 | 0.053 | |
| loessCycNorm | 0.134 | 0.009 | 0.144 | |
| loessFNorm | 0.082 | 0.003 | 0.088 | |
| meanNorm | 0.034 | 0.002 | 0.036 | |
| medianAbsDevNorm | 0.094 | 0.003 | 0.099 | |
| medianNorm | 0.054 | 0.002 | 0.056 | |
| normalize_se | 3.884 | 0.090 | 3.996 | |
| normalize_se_combination | 5.393 | 0.119 | 5.541 | |
| normalize_se_single | 3.520 | 0.060 | 3.604 | |
| normicsNorm | 3.560 | 0.052 | 3.642 | |
| plot_NA_density | 0.473 | 0.008 | 0.484 | |
| plot_NA_frequency | 0.243 | 0.006 | 0.252 | |
| plot_NA_heatmap | 1.558 | 0.100 | 1.672 | |
| plot_PCA | 1.591 | 0.014 | 1.613 | |
| plot_ROC_AUC_spiked | 1.332 | 0.020 | 1.361 | |
| plot_TP_FP_spiked_bar | 0.362 | 0.006 | 0.372 | |
| plot_TP_FP_spiked_box | 0.452 | 0.008 | 0.464 | |
| plot_TP_FP_spiked_scatter | 0.451 | 0.007 | 0.462 | |
| plot_boxplots | 5.233 | 0.049 | 5.328 | |
| plot_condition_overview | 0.306 | 0.005 | 0.313 | |
| plot_densities | 3.132 | 0.041 | 3.202 | |
| plot_fold_changes_spiked | 0.625 | 0.009 | 0.639 | |
| plot_heatmap | 4.427 | 0.045 | 4.494 | |
| plot_heatmap_DE | 1.415 | 0.020 | 1.441 | |
| plot_histogram_spiked | 0.434 | 0.006 | 0.442 | |
| plot_identified_spiked_proteins | 0.522 | 0.008 | 0.533 | |
| plot_intersection_enrichment | 0.932 | 0.043 | 2.396 | |
| plot_intragroup_PCV | 0.655 | 0.006 | 0.662 | |
| plot_intragroup_PEV | 0.508 | 0.005 | 0.513 | |
| plot_intragroup_PMAD | 0.450 | 0.005 | 0.456 | |
| plot_intragroup_correlation | 0.470 | 0.005 | 0.477 | |
| plot_jaccard_heatmap | 0.346 | 0.006 | 0.356 | |
| plot_logFC_thresholds_spiked | 0.739 | 0.008 | 0.751 | |
| plot_markers_boxplots | 0.907 | 0.009 | 0.921 | |
| plot_nr_prot_samples | 0.293 | 0.004 | 0.299 | |
| plot_overview_DE_bar | 0.460 | 0.004 | 0.465 | |
| plot_overview_DE_tile | 0.292 | 0.004 | 0.298 | |
| plot_profiles_spiked | 0.862 | 0.010 | 0.875 | |
| plot_pvalues_spiked | 0.606 | 0.011 | 0.621 | |
| plot_stats_spiked_heatmap | 0.417 | 0.007 | 0.427 | |
| plot_tot_int_samples | 0.294 | 0.005 | 0.301 | |
| plot_upset | 0.965 | 0.015 | 0.984 | |
| plot_upset_DE | 0.032 | 0.003 | 0.035 | |
| plot_volcano_DE | 4.684 | 0.044 | 4.759 | |
| quantileNorm | 0.036 | 0.002 | 0.037 | |
| readPRONE_example | 0.001 | 0.001 | 0.001 | |
| remove_POMA_outliers | 0.694 | 0.006 | 0.705 | |
| remove_assays_from_SE | 0.042 | 0.002 | 0.045 | |
| remove_reference_samples | 0.037 | 0.002 | 0.039 | |
| remove_samples_manually | 0.036 | 0.001 | 0.038 | |
| rlrMACycNorm | 0.627 | 0.007 | 0.689 | |
| rlrMANorm | 0.099 | 0.003 | 0.102 | |
| rlrNorm | 0.081 | 0.002 | 0.084 | |
| robnormNorm | 0.082 | 0.004 | 0.086 | |
| run_DE | 2.575 | 0.021 | 2.607 | |
| specify_comparisons | 0.022 | 0.002 | 0.024 | |
| subset_SE_by_norm | 0.079 | 0.003 | 0.082 | |
| tmmNorm | 0.126 | 0.008 | 0.136 | |
| vsnNorm | 0.069 | 0.002 | 0.072 | |