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This page was generated on 2025-08-23 12:06 -0400 (Sat, 23 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" 4553
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: 2025-08-22 13:45 -0400 (Fri, 22 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: 2025-08-22 20:57:10 -0400 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 20:59:11 -0400 (Fri, 22 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_thresholds0.0130.0020.015
detect_outliers_POMA0.6300.0130.643
eigenMSNorm0.1910.0150.207
export_data0.0120.0010.014
extract_consensus_DE_candidates0.0300.0020.034
filter_out_NA_proteins_by_threshold0.0680.0020.070
filter_out_complete_NA_proteins0.0230.0010.024
filter_out_proteins_by_ID0.0500.0010.052
filter_out_proteins_by_value0.0500.0010.052
get_NA_overview0.0160.0010.018
get_normalization_methods000
get_overview_DE0.0160.0020.017
get_proteins_by_value0.0450.0010.047
get_spiked_stats_DE0.0370.0020.039
globalIntNorm0.0480.0010.049
globalMeanNorm0.0480.0040.053
globalMedianNorm0.0560.0050.061
impute_se0.2300.0060.237
irsNorm0.0240.0010.025
limmaNorm0.0280.0010.029
load_data0.0220.0010.024
load_spike_data0.0190.0010.020
loessCycNorm0.0460.0040.050
loessFNorm0.0350.0010.036
meanNorm0.0180.0010.019
medianAbsDevNorm0.0360.0010.038
medianNorm0.0230.0010.025
normalize_se1.1270.0351.162
normalize_se_combination1.0820.0201.102
normalize_se_single1.0790.0241.136
normicsNorm1.0440.0211.072
plot_NA_density0.1270.0110.140
plot_NA_frequency0.0600.0010.062
plot_NA_heatmap0.9020.0260.930
plot_PCA0.3240.0070.331
plot_ROC_AUC_spiked0.310.010.32
plot_TP_FP_spiked_bar0.0970.0030.101
plot_TP_FP_spiked_box0.1110.0020.114
plot_TP_FP_spiked_scatter0.1220.0020.125
plot_boxplots1.1820.0251.242
plot_condition_overview0.0650.0010.067
plot_densities0.7470.0160.772
plot_fold_changes_spiked0.1440.0040.148
plot_heatmap1.2460.0151.261
plot_heatmap_DE0.3950.0070.406
plot_histogram_spiked0.1000.0030.103
plot_identified_spiked_proteins0.1390.0030.142
plot_intersection_enrichment0.1960.0121.343
plot_intragroup_PCV0.1770.0020.181
plot_intragroup_PEV0.1040.0020.105
plot_intragroup_PMAD0.1040.0020.106
plot_intragroup_correlation0.1060.0010.107
plot_jaccard_heatmap0.1370.0060.143
plot_logFC_thresholds_spiked0.1780.0040.186
plot_markers_boxplots0.2270.0090.245
plot_nr_prot_samples0.0780.0020.089
plot_overview_DE_bar0.0880.0020.093
plot_overview_DE_tile0.0570.0010.059
plot_profiles_spiked0.2320.0070.294
plot_pvalues_spiked0.1450.0040.153
plot_stats_spiked_heatmap0.1020.0030.104
plot_tot_int_samples0.0750.0020.077
plot_upset0.1970.0050.203
plot_upset_DE0.2600.0060.267
plot_volcano_DE0.9040.0090.913
quantileNorm0.0190.0020.020
readPRONE_example000
remove_POMA_outliers0.1810.0030.184
remove_assays_from_SE0.0220.0020.024
remove_reference_samples0.0220.0010.023
remove_samples_manually0.0170.0010.018
rlrMACycNorm0.1710.0030.173
rlrMANorm0.0370.0020.038
rlrNorm0.0460.0020.050
robnormNorm0.0280.0020.031
run_DE0.7410.0120.755
specify_comparisons0.0140.0010.015
subset_SE_by_norm0.0290.0010.030
tmmNorm0.0500.0030.053
vsnNorm0.0260.0010.027