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This page was generated on 2025-10-18 12:06 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1645/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.2  (landing page)
Lis Arend
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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    OK    OK  


CHECK results for PRONE on kjohnson3

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: 2025-10-17 21:31:31 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 21:33:40 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 129.5 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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
* 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-arm64/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_thresholds0.0140.0010.014
detect_outliers_POMA0.7290.0200.763
eigenMSNorm0.1940.0140.209
export_data0.0130.0010.013
extract_consensus_DE_candidates0.0310.0020.036
filter_out_NA_proteins_by_threshold0.0690.0010.073
filter_out_complete_NA_proteins0.0230.0010.024
filter_out_proteins_by_ID0.0500.0010.052
filter_out_proteins_by_value0.0500.0020.055
get_NA_overview0.0160.0010.022
get_normalization_methods0.0010.0000.000
get_overview_DE0.0160.0020.024
get_proteins_by_value0.0460.0010.048
get_spiked_stats_DE0.0370.0020.040
globalIntNorm0.0560.0020.058
globalMeanNorm0.0480.0010.054
globalMedianNorm0.0480.0010.050
impute_se0.2520.0050.313
irsNorm0.0290.0010.030
limmaNorm0.0260.0010.028
load_data0.0200.0010.022
load_spike_data0.0170.0000.019
loessCycNorm0.0510.0030.060
loessFNorm0.0350.0010.037
meanNorm0.0180.0010.022
medianAbsDevNorm0.0400.0020.042
medianNorm0.0250.0020.025
normalize_se1.1680.0351.203
normalize_se_combination1.9100.0601.995
normalize_se_single1.0660.0251.113
normicsNorm1.0330.0201.065
plot_NA_density0.1330.0030.184
plot_NA_frequency0.0790.0030.081
plot_NA_heatmap0.4990.0270.529
plot_PCA0.4500.0060.456
plot_ROC_AUC_spiked0.3930.0100.410
plot_TP_FP_spiked_bar0.1210.0040.125
plot_TP_FP_spiked_box0.1400.0030.143
plot_TP_FP_spiked_scatter0.1470.0030.161
plot_boxplots1.3540.0181.472
plot_condition_overview0.0820.0010.084
plot_densities0.8460.0160.939
plot_fold_changes_spiked0.1850.0040.197
plot_heatmap1.3500.0201.395
plot_heatmap_DE0.4120.0130.460
plot_histogram_spiked0.1360.0030.140
plot_identified_spiked_proteins0.1560.0020.161
plot_intersection_enrichment0.2930.0131.447
plot_intragroup_PCV0.1940.0020.203
plot_intragroup_PEV0.1480.0020.158
plot_intragroup_PMAD0.1370.0020.144
plot_intragroup_correlation0.1390.0020.141
plot_jaccard_heatmap0.1100.0020.118
plot_logFC_thresholds_spiked0.2270.0050.241
plot_markers_boxplots0.2540.0030.264
plot_nr_prot_samples0.0880.0010.090
plot_overview_DE_bar0.1320.0020.134
plot_overview_DE_tile0.0890.0020.091
plot_profiles_spiked0.2620.0050.269
plot_pvalues_spiked0.1900.0040.194
plot_stats_spiked_heatmap0.1310.0020.133
plot_tot_int_samples0.0870.0020.089
plot_upset0.2780.0050.291
plot_upset_DE0.0130.0010.014
plot_volcano_DE1.2930.0081.339
quantileNorm0.0190.0010.020
readPRONE_example0.0000.0000.001
remove_POMA_outliers0.2110.0020.213
remove_assays_from_SE0.0200.0010.021
remove_reference_samples0.0210.0010.022
remove_samples_manually0.0180.0010.018
rlrMACycNorm0.1870.0040.192
rlrMANorm0.0380.0010.039
rlrNorm0.0330.0010.034
robnormNorm0.0300.0020.033
run_DE0.6850.0080.694
specify_comparisons0.0150.0010.016
subset_SE_by_norm0.0300.0010.031
tmmNorm0.0520.0030.055
vsnNorm0.0260.0020.027