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This page was generated on 2025-10-07 12:05 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1637/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.2  (landing page)
Lis Arend
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: devel
git_last_commit: a875b50
git_last_commit_date: 2025-09-25 06:07:44 -0400 (Thu, 25 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for PRONE on lconway

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.

raw results


Summary

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: 2025-10-06 23:56:43 -0400 (Mon, 06 Oct 2025)
EndedAt: 2025-10-07 00:02:52 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 369.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 5.324  0.051   5.407
* 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.


Installation output

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)

Tests output


Example timings

PRONE.Rcheck/PRONE-Ex.timings

nameusersystemelapsed
apply_thresholds0.0270.0030.030
detect_outliers_POMA2.0230.0872.121
eigenMSNorm0.7030.0550.762
export_data0.0210.0030.025
extract_consensus_DE_candidates0.0860.0070.095
filter_out_NA_proteins_by_threshold0.2230.0040.228
filter_out_complete_NA_proteins0.0540.0030.056
filter_out_proteins_by_ID0.1750.0040.180
filter_out_proteins_by_value0.1910.0040.196
get_NA_overview0.0300.0030.032
get_normalization_methods000
get_overview_DE0.0640.0050.070
get_proteins_by_value0.1580.0040.162
get_spiked_stats_DE0.0760.0050.081
globalIntNorm0.1400.0030.144
globalMeanNorm0.1340.0020.137
globalMedianNorm0.1370.0030.142
impute_se0.8420.0190.869
irsNorm0.0510.0030.054
limmaNorm0.0730.0020.075
load_data0.0590.0040.065
load_spike_data0.0500.0030.053
loessCycNorm0.1460.0120.160
loessFNorm0.0840.0030.088
meanNorm0.0350.0020.038
medianAbsDevNorm0.1140.0040.119
medianNorm0.0580.0030.062
normalize_se4.0340.0984.172
normalize_se_combination4.4160.0954.534
normalize_se_single3.6630.0553.747
normicsNorm3.5430.0433.607
plot_NA_density0.4830.0090.494
plot_NA_frequency0.2320.0040.238
plot_NA_heatmap1.6090.0971.721
plot_PCA1.6300.0151.656
plot_ROC_AUC_spiked1.4000.0221.433
plot_TP_FP_spiked_bar0.3590.0060.367
plot_TP_FP_spiked_box0.4670.0070.476
plot_TP_FP_spiked_scatter0.4730.0060.481
plot_boxplots5.3240.0515.407
plot_condition_overview0.4380.0450.487
plot_densities3.1140.0523.185
plot_fold_changes_spiked0.6170.0090.630
plot_heatmap4.3780.0404.442
plot_heatmap_DE1.4140.0221.447
plot_histogram_spiked0.4470.0050.455
plot_identified_spiked_proteins0.5320.0080.542
plot_intersection_enrichment0.9110.0442.094
plot_intragroup_PCV0.6920.0070.702
plot_intragroup_PEV0.4610.0040.468
plot_intragroup_PMAD0.4810.0050.488
plot_intragroup_correlation0.6000.0190.624
plot_jaccard_heatmap0.3550.0050.364
plot_logFC_thresholds_spiked0.7510.0190.773
plot_markers_boxplots0.8710.0090.884
plot_nr_prot_samples0.3060.0050.312
plot_overview_DE_bar0.5260.0070.535
plot_overview_DE_tile0.2780.0050.286
plot_profiles_spiked0.9550.0120.975
plot_pvalues_spiked0.5980.0090.610
plot_stats_spiked_heatmap0.4290.0070.439
plot_tot_int_samples0.3080.0050.315
plot_upset0.9470.0160.968
plot_upset_DE0.0210.0020.024
plot_volcano_DE4.8740.0404.933
quantileNorm0.0380.0020.041
readPRONE_example0.0010.0000.002
remove_POMA_outliers0.7230.0060.733
remove_assays_from_SE0.0440.0020.048
remove_reference_samples0.0400.0020.042
remove_samples_manually0.0370.0030.039
rlrMACycNorm0.6950.0070.705
rlrMANorm0.0960.0020.098
rlrNorm0.0840.0030.088
robnormNorm0.1000.0030.105
run_DE2.5800.0242.613
specify_comparisons0.0220.0030.025
subset_SE_by_norm0.0870.0040.096
tmmNorm0.1230.0090.133
vsnNorm0.0670.0020.069