Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-08 12:52 -0400 (Wed, 08 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4641 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4586 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 1637/2341 | 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 12.7.1 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. |
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: 2025-10-08 00:02:26 -0400 (Wed, 08 Oct 2025) |
EndedAt: 2025-10-08 00:08:37 -0400 (Wed, 08 Oct 2025) |
EllapsedTime: 370.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PRONE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 plot_boxplots 5.409 0.049 5.496 plot_intersection_enrichment 0.974 0.046 5.238 * 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 | 0.031 | 0.003 | 0.034 | |
detect_outliers_POMA | 2.089 | 0.091 | 2.193 | |
eigenMSNorm | 0.699 | 0.052 | 0.756 | |
export_data | 0.022 | 0.001 | 0.024 | |
extract_consensus_DE_candidates | 0.087 | 0.005 | 0.093 | |
filter_out_NA_proteins_by_threshold | 0.207 | 0.004 | 0.212 | |
filter_out_complete_NA_proteins | 0.055 | 0.002 | 0.057 | |
filter_out_proteins_by_ID | 0.179 | 0.003 | 0.183 | |
filter_out_proteins_by_value | 0.166 | 0.003 | 0.171 | |
get_NA_overview | 0.034 | 0.003 | 0.038 | |
get_normalization_methods | 0 | 0 | 0 | |
get_overview_DE | 0.059 | 0.004 | 0.063 | |
get_proteins_by_value | 0.152 | 0.003 | 0.156 | |
get_spiked_stats_DE | 0.078 | 0.006 | 0.086 | |
globalIntNorm | 0.154 | 0.003 | 0.158 | |
globalMeanNorm | 0.143 | 0.003 | 0.147 | |
globalMedianNorm | 0.150 | 0.005 | 0.156 | |
impute_se | 0.887 | 0.019 | 0.912 | |
irsNorm | 0.062 | 0.003 | 0.066 | |
limmaNorm | 0.076 | 0.003 | 0.079 | |
load_data | 0.059 | 0.003 | 0.063 | |
load_spike_data | 0.054 | 0.003 | 0.057 | |
loessCycNorm | 0.139 | 0.011 | 0.154 | |
loessFNorm | 0.083 | 0.005 | 0.090 | |
meanNorm | 0.042 | 0.002 | 0.045 | |
medianAbsDevNorm | 0.109 | 0.004 | 0.115 | |
medianNorm | 0.065 | 0.003 | 0.068 | |
normalize_se | 3.955 | 0.100 | 4.079 | |
normalize_se_combination | 4.524 | 0.105 | 4.657 | |
normalize_se_single | 3.689 | 0.062 | 3.780 | |
normicsNorm | 3.526 | 0.051 | 3.609 | |
plot_NA_density | 0.455 | 0.006 | 0.463 | |
plot_NA_frequency | 0.236 | 0.005 | 0.243 | |
plot_NA_heatmap | 1.598 | 0.097 | 1.708 | |
plot_PCA | 1.562 | 0.015 | 1.586 | |
plot_ROC_AUC_spiked | 1.422 | 0.022 | 1.456 | |
plot_TP_FP_spiked_bar | 0.366 | 0.007 | 0.375 | |
plot_TP_FP_spiked_box | 0.455 | 0.007 | 0.466 | |
plot_TP_FP_spiked_scatter | 0.510 | 0.008 | 0.521 | |
plot_boxplots | 5.409 | 0.049 | 5.496 | |
plot_condition_overview | 0.450 | 0.038 | 0.493 | |
plot_densities | 3.127 | 0.047 | 3.198 | |
plot_fold_changes_spiked | 0.599 | 0.009 | 0.611 | |
plot_heatmap | 4.617 | 0.045 | 4.692 | |
plot_heatmap_DE | 1.515 | 0.024 | 1.556 | |
plot_histogram_spiked | 0.451 | 0.006 | 0.460 | |
plot_identified_spiked_proteins | 0.494 | 0.007 | 0.505 | |
plot_intersection_enrichment | 0.974 | 0.046 | 5.238 | |
plot_intragroup_PCV | 0.665 | 0.006 | 0.676 | |
plot_intragroup_PEV | 0.469 | 0.005 | 0.477 | |
plot_intragroup_PMAD | 0.491 | 0.006 | 0.499 | |
plot_intragroup_correlation | 0.597 | 0.021 | 0.630 | |
plot_jaccard_heatmap | 0.321 | 0.004 | 0.326 | |
plot_logFC_thresholds_spiked | 0.784 | 0.015 | 0.804 | |
plot_markers_boxplots | 0.936 | 0.008 | 0.948 | |
plot_nr_prot_samples | 0.317 | 0.005 | 0.325 | |
plot_overview_DE_bar | 0.498 | 0.006 | 0.507 | |
plot_overview_DE_tile | 0.257 | 0.005 | 0.263 | |
plot_profiles_spiked | 0.893 | 0.013 | 0.910 | |
plot_pvalues_spiked | 0.554 | 0.008 | 0.565 | |
plot_stats_spiked_heatmap | 0.416 | 0.006 | 0.425 | |
plot_tot_int_samples | 0.309 | 0.004 | 0.315 | |
plot_upset | 0.998 | 0.016 | 1.019 | |
plot_upset_DE | 0.033 | 0.002 | 0.035 | |
plot_volcano_DE | 4.806 | 0.040 | 4.870 | |
quantileNorm | 0.039 | 0.003 | 0.041 | |
readPRONE_example | 0.001 | 0.000 | 0.002 | |
remove_POMA_outliers | 0.702 | 0.006 | 0.709 | |
remove_assays_from_SE | 0.055 | 0.002 | 0.057 | |
remove_reference_samples | 0.049 | 0.003 | 0.068 | |
remove_samples_manually | 0.031 | 0.002 | 0.032 | |
rlrMACycNorm | 0.694 | 0.006 | 0.703 | |
rlrMANorm | 0.099 | 0.003 | 0.102 | |
rlrNorm | 0.085 | 0.003 | 0.087 | |
robnormNorm | 0.114 | 0.004 | 0.120 | |
run_DE | 2.648 | 0.034 | 2.696 | |
specify_comparisons | 0.025 | 0.003 | 0.028 | |
subset_SE_by_norm | 0.075 | 0.003 | 0.078 | |
tmmNorm | 0.134 | 0.010 | 0.145 | |
vsnNorm | 0.073 | 0.003 | 0.077 | |