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This page was generated on 2025-08-21 12:06 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 1620/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 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: 2025-08-20 20:58:37 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 21:00:38 -0400 (Wed, 20 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_thresholds0.0130.0010.015
detect_outliers_POMA0.6290.0120.642
eigenMSNorm0.1890.0160.205
export_data0.0140.0010.015
extract_consensus_DE_candidates0.0330.0020.035
filter_out_NA_proteins_by_threshold0.0650.0010.066
filter_out_complete_NA_proteins0.0210.0010.022
filter_out_proteins_by_ID0.0480.0010.050
filter_out_proteins_by_value0.0490.0010.050
get_NA_overview0.0150.0010.016
get_normalization_methods000
get_overview_DE0.0160.0010.018
get_proteins_by_value0.0460.0020.047
get_spiked_stats_DE0.0370.0020.040
globalIntNorm0.0480.0020.049
globalMeanNorm0.0490.0040.053
globalMedianNorm0.0570.0040.061
impute_se0.2250.0040.229
irsNorm0.0220.0010.023
limmaNorm0.0260.0020.027
load_data0.0190.0010.022
load_spike_data0.0150.0010.017
loessCycNorm0.0460.0020.048
loessFNorm0.0350.0010.036
meanNorm0.0180.0010.019
medianAbsDevNorm0.0370.0020.038
medianNorm0.0240.0010.026
normalize_se1.1190.0281.147
normalize_se_combination1.0950.0211.116
normalize_se_single1.0810.0261.107
normicsNorm1.0350.0181.053
plot_NA_density0.1250.0090.134
plot_NA_frequency0.0600.0020.061
plot_NA_heatmap0.9210.0290.949
plot_PCA0.3230.0160.339
plot_ROC_AUC_spiked0.3180.0080.330
plot_TP_FP_spiked_bar0.0960.0040.100
plot_TP_FP_spiked_box0.1100.0020.115
plot_TP_FP_spiked_scatter0.1190.0030.122
plot_boxplots1.1640.0451.226
plot_condition_overview0.0650.0010.067
plot_densities0.7540.0220.781
plot_fold_changes_spiked0.1440.0040.149
plot_heatmap1.2980.0331.332
plot_heatmap_DE0.3910.0070.399
plot_histogram_spiked0.0990.0020.102
plot_identified_spiked_proteins0.1290.0030.132
plot_intersection_enrichment0.2150.0131.411
plot_intragroup_PCV0.1610.0030.165
plot_intragroup_PEV0.1160.0020.118
plot_intragroup_PMAD0.1060.0010.107
plot_intragroup_correlation0.1060.0020.108
plot_jaccard_heatmap0.0780.0030.080
plot_logFC_thresholds_spiked0.1810.0050.189
plot_markers_boxplots0.2020.0030.205
plot_nr_prot_samples0.0740.0020.076
plot_overview_DE_bar0.1090.0020.110
plot_overview_DE_tile0.0570.0010.058
plot_profiles_spiked0.2130.0050.216
plot_pvalues_spiked0.1560.0030.159
plot_stats_spiked_heatmap0.0990.0030.101
plot_tot_int_samples0.0710.0020.073
plot_upset0.1860.0050.191
plot_upset_DE0.2420.0070.249
plot_volcano_DE0.9820.0110.999
quantileNorm0.0200.0020.021
readPRONE_example0.0010.0010.000
remove_POMA_outliers0.1660.0030.168
remove_assays_from_SE0.0200.0010.021
remove_reference_samples0.0210.0010.022
remove_samples_manually0.0180.0010.019
rlrMACycNorm0.1890.0040.193
rlrMANorm0.0350.0020.037
rlrNorm0.0310.0020.032
robnormNorm0.0410.0040.046
run_DE1.1480.0151.177
specify_comparisons0.0140.0010.016
subset_SE_by_norm0.0280.0010.030
tmmNorm0.0480.0030.052
vsnNorm0.0260.0020.027