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This page was generated on 2025-08-20 12:05 -0400 (Wed, 20 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
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 1619/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 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 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: 1.3.1
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: 2025-08-19 22:52:25 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 22:58:09 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 343.6 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 (2025-06-13)
* 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 ‘1.3.1’
* 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-x86_64/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_thresholds0.0280.0020.030
detect_outliers_POMA1.7490.0551.816
eigenMSNorm0.6770.0650.744
export_data0.0190.0020.022
extract_consensus_DE_candidates0.0760.0040.081
filter_out_NA_proteins_by_threshold0.2280.0060.237
filter_out_complete_NA_proteins0.0480.0030.051
filter_out_proteins_by_ID0.1740.0040.179
filter_out_proteins_by_value0.1440.0030.147
get_NA_overview0.0310.0020.033
get_normalization_methods0.0000.0010.000
get_overview_DE0.0400.0030.043
get_proteins_by_value0.1690.0030.172
get_spiked_stats_DE0.0760.0050.082
globalIntNorm0.1570.0030.163
globalMeanNorm0.1350.0160.152
globalMedianNorm0.1750.0150.192
impute_se0.8010.0110.817
irsNorm0.0570.0030.060
limmaNorm0.0690.0030.075
load_data0.0640.0040.070
load_spike_data0.0500.0030.054
loessCycNorm0.1380.0120.151
loessFNorm0.0760.0030.079
meanNorm0.0400.0020.043
medianAbsDevNorm0.1000.0040.105
medianNorm0.0610.0020.063
normalize_se3.8640.0733.961
normalize_se_combination3.7630.0443.829
normalize_se_single3.6480.0463.715
normicsNorm3.6580.0423.720
plot_NA_density0.3970.0260.427
plot_NA_frequency0.1850.0040.189
plot_NA_heatmap2.3950.0882.497
plot_PCA1.1460.0221.173
plot_ROC_AUC_spiked1.0980.0201.128
plot_TP_FP_spiked_bar0.3000.0070.308
plot_TP_FP_spiked_box0.3600.0060.368
plot_TP_FP_spiked_scatter0.3850.0060.393
plot_boxplots4.3420.0544.417
plot_condition_overview0.2210.0040.229
plot_densities2.6120.0352.663
plot_fold_changes_spiked0.5040.0100.516
plot_heatmap4.3180.0394.380
plot_heatmap_DE1.3260.0191.358
plot_histogram_spiked0.2880.0040.293
plot_identified_spiked_proteins0.4220.0070.432
plot_intersection_enrichment0.6810.0411.942
plot_intragroup_PCV0.5170.0050.523
plot_intragroup_PEV0.3660.0040.372
plot_intragroup_PMAD0.3520.0040.358
plot_intragroup_correlation0.3580.0050.364
plot_jaccard_heatmap0.2420.0050.249
plot_logFC_thresholds_spiked0.5880.0110.601
plot_markers_boxplots0.6980.0060.707
plot_nr_prot_samples0.2850.0040.291
plot_overview_DE_bar0.3100.0040.316
plot_overview_DE_tile0.1880.0040.192
plot_profiles_spiked0.7370.0090.748
plot_pvalues_spiked0.4800.0090.491
plot_stats_spiked_heatmap0.2930.0060.300
plot_tot_int_samples0.2140.0050.221
plot_upset0.6310.0110.644
plot_upset_DE0.8440.0260.875
plot_volcano_DE3.2590.0353.319
quantileNorm0.0400.0020.043
readPRONE_example0.0010.0000.002
remove_POMA_outliers0.5650.0060.575
remove_assays_from_SE0.0500.0040.055
remove_reference_samples0.0410.0030.044
remove_samples_manually0.0350.0030.037
rlrMACycNorm0.6840.0080.699
rlrMANorm0.0850.0020.088
rlrNorm0.0820.0030.086
robnormNorm0.1950.0100.205
run_DE2.4710.0282.516
specify_comparisons0.0210.0020.022
subset_SE_by_norm0.0790.0030.082
tmmNorm0.1170.0100.126
vsnNorm0.0640.0020.066