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This page was generated on 2025-08-22 12:06 -0400 (Fri, 22 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1621/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-08-21 13:45 -0400 (Thu, 21 Aug 2025)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: devel
git_last_commit: 6288796
git_last_commit_date: 2025-05-26 09:22:53 -0400 (Mon, 26 May 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 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: 1.3.1
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_1.3.1.tar.gz
StartedAt: 2025-08-21 20:58:01 -0400 (Thu, 21 Aug 2025)
EndedAt: 2025-08-21 21:00:02 -0400 (Thu, 21 Aug 2025)
EllapsedTime: 121.4 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_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 ‘1.3.1’
* 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 ... OK
* 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: 1 NOTE
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 ‘1.3.1’
** 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_thresholds0.0140.0020.015
detect_outliers_POMA0.6420.0150.657
eigenMSNorm0.1900.0150.205
export_data0.0130.0010.014
extract_consensus_DE_candidates0.0320.0010.033
filter_out_NA_proteins_by_threshold0.0690.0010.071
filter_out_complete_NA_proteins0.0210.0010.023
filter_out_proteins_by_ID0.0490.0010.051
filter_out_proteins_by_value0.0500.0020.051
get_NA_overview0.0160.0010.017
get_normalization_methods000
get_overview_DE0.0170.0020.018
get_proteins_by_value0.0460.0010.048
get_spiked_stats_DE0.0380.0030.040
globalIntNorm0.0480.0010.050
globalMeanNorm0.0490.0050.053
globalMedianNorm0.0580.0040.062
impute_se0.2300.0040.253
irsNorm0.0230.0020.025
limmaNorm0.0280.0010.029
load_data0.0220.0010.024
load_spike_data0.0180.0010.019
loessCycNorm0.0510.0030.054
loessFNorm0.0360.0020.037
meanNorm0.0190.0010.020
medianAbsDevNorm0.0400.0020.042
medianNorm0.0250.0010.026
normalize_se1.1260.0221.150
normalize_se_combination1.0980.0171.115
normalize_se_single1.0770.0241.102
normicsNorm1.0580.0241.109
plot_NA_density0.1260.0170.142
plot_NA_frequency0.0640.0020.066
plot_NA_heatmap0.9270.0320.990
plot_PCA0.3350.0170.353
plot_ROC_AUC_spiked0.3120.0090.320
plot_TP_FP_spiked_bar0.0960.0040.100
plot_TP_FP_spiked_box0.1080.0030.111
plot_TP_FP_spiked_scatter0.1170.0030.120
plot_boxplots1.1810.0361.253
plot_condition_overview0.0650.0010.066
plot_densities0.7410.0170.778
plot_fold_changes_spiked0.1520.0040.160
plot_heatmap1.2490.0121.325
plot_heatmap_DE0.3970.0070.431
plot_histogram_spiked0.1020.0020.104
plot_identified_spiked_proteins0.1340.0030.141
plot_intersection_enrichment0.2490.0151.498
plot_intragroup_PCV0.1680.0020.170
plot_intragroup_PEV0.1240.0020.134
plot_intragroup_PMAD0.1070.0020.109
plot_intragroup_correlation0.1080.0010.110
plot_jaccard_heatmap0.0730.0020.075
plot_logFC_thresholds_spiked0.1890.0040.197
plot_markers_boxplots0.2060.0020.209
plot_nr_prot_samples0.0880.0020.089
plot_overview_DE_bar0.0930.0020.094
plot_overview_DE_tile0.0590.0020.061
plot_profiles_spiked0.2150.0050.219
plot_pvalues_spiked0.1650.0030.168
plot_stats_spiked_heatmap0.1020.0030.104
plot_tot_int_samples0.0700.0010.072
plot_upset0.1910.0050.196
plot_upset_DE0.2500.0070.257
plot_volcano_DE0.9160.0080.941
quantileNorm0.0190.0010.020
readPRONE_example0.0000.0000.001
remove_POMA_outliers0.1680.0010.169
remove_assays_from_SE0.0200.0020.021
remove_reference_samples0.0200.0010.022
remove_samples_manually0.0170.0010.019
rlrMACycNorm0.1890.0020.192
rlrMANorm0.0340.0020.036
rlrNorm0.0890.0070.095
robnormNorm0.0300.0020.032
run_DE0.7000.0120.712
specify_comparisons0.0140.0010.015
subset_SE_by_norm0.0300.0020.031
tmmNorm0.0520.0030.056
vsnNorm0.0260.0010.027