Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-11 12:04 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1623/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PRONE_1.3.1.tar.gz
StartedAt: 2025-09-11 03:56:31 -0400 (Thu, 11 Sep 2025)
EndedAt: 2025-09-11 04:04:25 -0400 (Thu, 11 Sep 2025)
EllapsedTime: 473.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PRONE_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log’
for details.


Installation output

PRONE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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_thresholds0.0310.0010.033
detect_outliers_POMA1.6390.0551.692
eigenMSNorm0.6110.0810.693
export_data0.0270.0000.028
extract_consensus_DE_candidates0.0800.0010.080
filter_out_NA_proteins_by_threshold0.2430.0000.208
filter_out_complete_NA_proteins0.0540.0010.055
filter_out_proteins_by_ID0.1570.0010.158
filter_out_proteins_by_value0.1570.0020.159
get_NA_overview0.0370.0000.038
get_normalization_methods000
get_overview_DE0.0430.0010.045
get_proteins_by_value0.1420.0020.144
get_spiked_stats_DE0.0840.0030.087
globalIntNorm0.1310.0020.133
globalMeanNorm0.1330.0240.159
globalMedianNorm0.1500.0030.154
impute_se1.0080.0170.727
irsNorm0.0590.0010.060
limmaNorm0.0680.0010.070
load_data0.0460.0040.049
load_spike_data0.0590.0040.063
loessCycNorm0.1020.0000.102
loessFNorm0.0860.0010.087
meanNorm0.0440.0000.044
medianAbsDevNorm0.0950.0050.099
medianNorm0.0590.0020.061
normalize_se3.4520.0663.517
normalize_se_combination3.3010.0413.342
normalize_se_single3.2380.0743.312
normicsNorm3.1630.0433.206
plot_NA_density0.3810.0110.350
plot_NA_frequency0.2140.0030.174
plot_NA_heatmap2.2530.1022.355
plot_PCA1.0140.0001.014
plot_ROC_AUC_spiked1.0140.0110.959
plot_TP_FP_spiked_bar0.2550.0050.260
plot_TP_FP_spiked_box0.3300.0010.330
plot_TP_FP_spiked_scatter0.3510.0020.354
plot_boxplots4.1440.0213.847
plot_condition_overview0.1950.0010.196
plot_densities2.6820.0062.365
plot_fold_changes_spiked0.4900.0050.447
plot_heatmap3.6040.0033.609
plot_heatmap_DE1.2040.0041.209
plot_histogram_spiked0.3840.0030.295
plot_identified_spiked_proteins0.3920.0000.392
plot_intersection_enrichment0.6940.0062.999
plot_intragroup_PCV0.4740.0010.475
plot_intragroup_PEV0.3840.0020.386
plot_intragroup_PMAD0.3190.0010.320
plot_intragroup_correlation0.3320.0020.334
plot_jaccard_heatmap0.2290.0010.217
plot_logFC_thresholds_spiked0.5520.0010.553
plot_markers_boxplots0.7400.0010.706
plot_nr_prot_samples0.2590.0020.261
plot_overview_DE_bar0.3050.0020.308
plot_overview_DE_tile0.1770.0120.190
plot_profiles_spiked0.8470.0290.765
plot_pvalues_spiked0.4250.0270.452
plot_stats_spiked_heatmap0.3090.0310.341
plot_tot_int_samples0.2290.0140.243
plot_upset0.6200.0490.669
plot_upset_DE0.7910.0300.822
plot_volcano_DE2.9060.1913.099
quantileNorm0.0410.0080.051
readPRONE_example0.0010.0000.001
remove_POMA_outliers0.4830.0260.509
remove_assays_from_SE0.0480.0030.050
remove_reference_samples0.0470.0040.051
remove_samples_manually0.0420.0020.043
rlrMACycNorm0.6320.0620.694
rlrMANorm0.1020.0050.108
rlrNorm0.0890.0050.093
robnormNorm0.2460.0270.273
run_DE2.4210.0212.381
specify_comparisons0.0390.0000.031
subset_SE_by_norm0.0830.0000.083
tmmNorm0.1380.0060.144
vsnNorm0.0750.0030.078