| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1645/2353 | 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 | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: PRONE |
| Version: 1.3.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PRONE_1.3.2.tar.gz |
| StartedAt: 2025-10-17 12:23:01 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 12:30:23 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 441.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PRONE.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PRONE_1.3.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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
plot_boxplots 7.116 0.144 7.280
plot_volcano_DE 6.418 0.276 6.714
normalize_se_combination 6.269 0.183 6.471
normalize_se 5.840 0.159 6.017
plot_heatmap 5.776 0.107 5.904
normalize_se_single 5.467 0.112 5.595
normicsNorm 5.210 0.048 5.274
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log’
for details.
PRONE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL PRONE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 | 0.033 | 0.000 | 0.033 | |
| detect_outliers_POMA | 2.278 | 0.116 | 2.402 | |
| eigenMSNorm | 0.927 | 0.063 | 0.993 | |
| export_data | 0.023 | 0.000 | 0.024 | |
| extract_consensus_DE_candidates | 0.100 | 0.004 | 0.105 | |
| filter_out_NA_proteins_by_threshold | 0.291 | 0.000 | 0.290 | |
| filter_out_complete_NA_proteins | 0.057 | 0.000 | 0.057 | |
| filter_out_proteins_by_ID | 0.242 | 0.000 | 0.243 | |
| filter_out_proteins_by_value | 0.229 | 0.004 | 0.233 | |
| get_NA_overview | 0.036 | 0.000 | 0.036 | |
| get_normalization_methods | 0 | 0 | 0 | |
| get_overview_DE | 0.073 | 0.004 | 0.077 | |
| get_proteins_by_value | 0.198 | 0.000 | 0.198 | |
| get_spiked_stats_DE | 0.085 | 0.000 | 0.085 | |
| globalIntNorm | 0.188 | 0.004 | 0.193 | |
| globalMeanNorm | 0.198 | 0.000 | 0.198 | |
| globalMedianNorm | 0.187 | 0.004 | 0.191 | |
| impute_se | 1.063 | 0.015 | 1.076 | |
| irsNorm | 0.065 | 0.000 | 0.065 | |
| limmaNorm | 0.087 | 0.000 | 0.087 | |
| load_data | 0.067 | 0.000 | 0.070 | |
| load_spike_data | 0.051 | 0.000 | 0.054 | |
| loessCycNorm | 0.170 | 0.016 | 0.186 | |
| loessFNorm | 0.126 | 0.000 | 0.127 | |
| meanNorm | 0.047 | 0.000 | 0.047 | |
| medianAbsDevNorm | 0.129 | 0.004 | 0.134 | |
| medianNorm | 0.068 | 0.004 | 0.073 | |
| normalize_se | 5.840 | 0.159 | 6.017 | |
| normalize_se_combination | 6.269 | 0.183 | 6.471 | |
| normalize_se_single | 5.467 | 0.112 | 5.595 | |
| normicsNorm | 5.210 | 0.048 | 5.274 | |
| plot_NA_density | 0.573 | 0.012 | 0.586 | |
| plot_NA_frequency | 0.314 | 0.004 | 0.318 | |
| plot_NA_heatmap | 1.908 | 0.035 | 1.949 | |
| plot_PCA | 2.051 | 0.016 | 2.073 | |
| plot_ROC_AUC_spiked | 1.739 | 0.028 | 1.779 | |
| plot_TP_FP_spiked_bar | 0.454 | 0.004 | 0.458 | |
| plot_TP_FP_spiked_box | 0.634 | 0.024 | 0.660 | |
| plot_TP_FP_spiked_scatter | 0.660 | 0.016 | 0.678 | |
| plot_boxplots | 7.116 | 0.144 | 7.280 | |
| plot_condition_overview | 0.372 | 0.016 | 0.389 | |
| plot_densities | 4.049 | 0.032 | 4.090 | |
| plot_fold_changes_spiked | 0.836 | 0.004 | 0.842 | |
| plot_heatmap | 5.776 | 0.107 | 5.904 | |
| plot_heatmap_DE | 1.866 | 0.032 | 1.903 | |
| plot_histogram_spiked | 0.585 | 0.004 | 0.591 | |
| plot_identified_spiked_proteins | 0.696 | 0.032 | 0.731 | |
| plot_intersection_enrichment | 1.213 | 0.016 | 3.567 | |
| plot_intragroup_PCV | 0.996 | 0.072 | 1.071 | |
| plot_intragroup_PEV | 0.683 | 0.059 | 0.745 | |
| plot_intragroup_PMAD | 0.708 | 0.072 | 0.783 | |
| plot_intragroup_correlation | 0.641 | 0.060 | 0.704 | |
| plot_jaccard_heatmap | 0.460 | 0.056 | 0.516 | |
| plot_logFC_thresholds_spiked | 1.048 | 0.119 | 1.172 | |
| plot_markers_boxplots | 1.246 | 0.108 | 1.359 | |
| plot_nr_prot_samples | 0.491 | 0.048 | 0.540 | |
| plot_overview_DE_bar | 0.618 | 0.043 | 0.664 | |
| plot_overview_DE_tile | 0.361 | 0.024 | 0.386 | |
| plot_profiles_spiked | 1.268 | 0.100 | 1.368 | |
| plot_pvalues_spiked | 0.716 | 0.052 | 0.774 | |
| plot_stats_spiked_heatmap | 0.582 | 0.032 | 0.616 | |
| plot_tot_int_samples | 0.456 | 0.032 | 0.490 | |
| plot_upset | 1.285 | 0.063 | 1.353 | |
| plot_upset_DE | 0.032 | 0.000 | 0.032 | |
| plot_volcano_DE | 6.418 | 0.276 | 6.714 | |
| quantileNorm | 0.050 | 0.000 | 0.051 | |
| readPRONE_example | 0.002 | 0.000 | 0.002 | |
| remove_POMA_outliers | 1.068 | 0.020 | 1.092 | |
| remove_assays_from_SE | 0.053 | 0.000 | 0.053 | |
| remove_reference_samples | 0.036 | 0.000 | 0.036 | |
| remove_samples_manually | 0.037 | 0.004 | 0.042 | |
| rlrMACycNorm | 1.012 | 0.043 | 1.061 | |
| rlrMANorm | 0.261 | 0.056 | 0.319 | |
| rlrNorm | 0.115 | 0.004 | 0.119 | |
| robnormNorm | 0.104 | 0.004 | 0.109 | |
| run_DE | 3.583 | 0.080 | 3.675 | |
| specify_comparisons | 0.027 | 0.000 | 0.027 | |
| subset_SE_by_norm | 0.110 | 0.004 | 0.114 | |
| tmmNorm | 0.187 | 0.004 | 0.192 | |
| vsnNorm | 0.084 | 0.000 | 0.085 | |