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This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1653/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.2  (landing page)
Lis Arend
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 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 12.7.6 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    NA    NA  


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: 2025-10-24 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

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
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.


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_thresholds0.0240.0020.027
detect_outliers_POMA1.9380.0722.020
eigenMSNorm0.6750.0590.738
export_data0.0190.0020.021
extract_consensus_DE_candidates0.0980.0050.104
filter_out_NA_proteins_by_threshold0.2370.0050.243
filter_out_complete_NA_proteins0.0510.0030.054
filter_out_proteins_by_ID0.1670.0040.171
filter_out_proteins_by_value0.1650.0040.170
get_NA_overview0.0290.0030.031
get_normalization_methods0.0000.0010.000
get_overview_DE0.0410.0030.045
get_proteins_by_value0.1530.0030.157
get_spiked_stats_DE0.0790.0050.085
globalIntNorm0.1620.0040.166
globalMeanNorm0.1410.0040.145
globalMedianNorm0.1490.0040.153
impute_se0.8380.0160.860
irsNorm0.0570.0030.060
limmaNorm0.0710.0030.074
load_data0.0600.0040.064
load_spike_data0.0490.0030.053
loessCycNorm0.1340.0090.144
loessFNorm0.0820.0030.088
meanNorm0.0340.0020.036
medianAbsDevNorm0.0940.0030.099
medianNorm0.0540.0020.056
normalize_se3.8840.0903.996
normalize_se_combination5.3930.1195.541
normalize_se_single3.5200.0603.604
normicsNorm3.5600.0523.642
plot_NA_density0.4730.0080.484
plot_NA_frequency0.2430.0060.252
plot_NA_heatmap1.5580.1001.672
plot_PCA1.5910.0141.613
plot_ROC_AUC_spiked1.3320.0201.361
plot_TP_FP_spiked_bar0.3620.0060.372
plot_TP_FP_spiked_box0.4520.0080.464
plot_TP_FP_spiked_scatter0.4510.0070.462
plot_boxplots5.2330.0495.328
plot_condition_overview0.3060.0050.313
plot_densities3.1320.0413.202
plot_fold_changes_spiked0.6250.0090.639
plot_heatmap4.4270.0454.494
plot_heatmap_DE1.4150.0201.441
plot_histogram_spiked0.4340.0060.442
plot_identified_spiked_proteins0.5220.0080.533
plot_intersection_enrichment0.9320.0432.396
plot_intragroup_PCV0.6550.0060.662
plot_intragroup_PEV0.5080.0050.513
plot_intragroup_PMAD0.4500.0050.456
plot_intragroup_correlation0.4700.0050.477
plot_jaccard_heatmap0.3460.0060.356
plot_logFC_thresholds_spiked0.7390.0080.751
plot_markers_boxplots0.9070.0090.921
plot_nr_prot_samples0.2930.0040.299
plot_overview_DE_bar0.4600.0040.465
plot_overview_DE_tile0.2920.0040.298
plot_profiles_spiked0.8620.0100.875
plot_pvalues_spiked0.6060.0110.621
plot_stats_spiked_heatmap0.4170.0070.427
plot_tot_int_samples0.2940.0050.301
plot_upset0.9650.0150.984
plot_upset_DE0.0320.0030.035
plot_volcano_DE4.6840.0444.759
quantileNorm0.0360.0020.037
readPRONE_example0.0010.0010.001
remove_POMA_outliers0.6940.0060.705
remove_assays_from_SE0.0420.0020.045
remove_reference_samples0.0370.0020.039
remove_samples_manually0.0360.0010.038
rlrMACycNorm0.6270.0070.689
rlrMANorm0.0990.0030.102
rlrNorm0.0810.0020.084
robnormNorm0.0820.0040.086
run_DE2.5750.0212.607
specify_comparisons0.0220.0020.024
subset_SE_by_norm0.0790.0030.082
tmmNorm0.1260.0080.136
vsnNorm0.0690.0020.072