Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1645/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.2  (landing page)
Lis Arend
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: devel
git_last_commit: a875b50
git_last_commit_date: 2025-09-25 06:07:44 -0400 (Thu, 25 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: PRONE
Version: 1.3.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PRONE_1.3.2.tar.gz
StartedAt: 2025-10-17 12:23:01 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 12:30:23 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 441.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PRONE_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PRONE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRONE’ version ‘1.3.2’
* 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 ... NOTE
plot_upset_DE: no visible global function definition for
  ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plot_boxplots            7.116  0.144   7.280
plot_volcano_DE          6.418  0.276   6.714
normalize_se_combination 6.269  0.183   6.471
normalize_se             5.840  0.159   6.017
plot_heatmap             5.776  0.107   5.904
normalize_se_single      5.467  0.112   5.595
normicsNorm              5.210  0.048   5.274
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log’
for details.


Installation output

PRONE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘PRONE’ ...
** this is package ‘PRONE’ version ‘1.3.2’
** 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_thresholds0.0330.0000.033
detect_outliers_POMA2.2780.1162.402
eigenMSNorm0.9270.0630.993
export_data0.0230.0000.024
extract_consensus_DE_candidates0.1000.0040.105
filter_out_NA_proteins_by_threshold0.2910.0000.290
filter_out_complete_NA_proteins0.0570.0000.057
filter_out_proteins_by_ID0.2420.0000.243
filter_out_proteins_by_value0.2290.0040.233
get_NA_overview0.0360.0000.036
get_normalization_methods000
get_overview_DE0.0730.0040.077
get_proteins_by_value0.1980.0000.198
get_spiked_stats_DE0.0850.0000.085
globalIntNorm0.1880.0040.193
globalMeanNorm0.1980.0000.198
globalMedianNorm0.1870.0040.191
impute_se1.0630.0151.076
irsNorm0.0650.0000.065
limmaNorm0.0870.0000.087
load_data0.0670.0000.070
load_spike_data0.0510.0000.054
loessCycNorm0.1700.0160.186
loessFNorm0.1260.0000.127
meanNorm0.0470.0000.047
medianAbsDevNorm0.1290.0040.134
medianNorm0.0680.0040.073
normalize_se5.8400.1596.017
normalize_se_combination6.2690.1836.471
normalize_se_single5.4670.1125.595
normicsNorm5.2100.0485.274
plot_NA_density0.5730.0120.586
plot_NA_frequency0.3140.0040.318
plot_NA_heatmap1.9080.0351.949
plot_PCA2.0510.0162.073
plot_ROC_AUC_spiked1.7390.0281.779
plot_TP_FP_spiked_bar0.4540.0040.458
plot_TP_FP_spiked_box0.6340.0240.660
plot_TP_FP_spiked_scatter0.6600.0160.678
plot_boxplots7.1160.1447.280
plot_condition_overview0.3720.0160.389
plot_densities4.0490.0324.090
plot_fold_changes_spiked0.8360.0040.842
plot_heatmap5.7760.1075.904
plot_heatmap_DE1.8660.0321.903
plot_histogram_spiked0.5850.0040.591
plot_identified_spiked_proteins0.6960.0320.731
plot_intersection_enrichment1.2130.0163.567
plot_intragroup_PCV0.9960.0721.071
plot_intragroup_PEV0.6830.0590.745
plot_intragroup_PMAD0.7080.0720.783
plot_intragroup_correlation0.6410.0600.704
plot_jaccard_heatmap0.4600.0560.516
plot_logFC_thresholds_spiked1.0480.1191.172
plot_markers_boxplots1.2460.1081.359
plot_nr_prot_samples0.4910.0480.540
plot_overview_DE_bar0.6180.0430.664
plot_overview_DE_tile0.3610.0240.386
plot_profiles_spiked1.2680.1001.368
plot_pvalues_spiked0.7160.0520.774
plot_stats_spiked_heatmap0.5820.0320.616
plot_tot_int_samples0.4560.0320.490
plot_upset1.2850.0631.353
plot_upset_DE0.0320.0000.032
plot_volcano_DE6.4180.2766.714
quantileNorm0.0500.0000.051
readPRONE_example0.0020.0000.002
remove_POMA_outliers1.0680.0201.092
remove_assays_from_SE0.0530.0000.053
remove_reference_samples0.0360.0000.036
remove_samples_manually0.0370.0040.042
rlrMACycNorm1.0120.0431.061
rlrMANorm0.2610.0560.319
rlrNorm0.1150.0040.119
robnormNorm0.1040.0040.109
run_DE3.5830.0803.675
specify_comparisons0.0270.0000.027
subset_SE_by_norm0.1100.0040.114
tmmNorm0.1870.0040.192
vsnNorm0.0840.0000.085