Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-23 12:07 -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 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: 1.3.1
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_1.3.1.tar.gz
StartedAt: 2025-08-22 11:12:15 -0000 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 11:19:08 -0000 (Fri, 22 Aug 2025)
EllapsedTime: 412.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.3.1.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 ‘1.3.1’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
normalize_se_single      5.856  0.586   6.463
plot_boxplots            6.269  0.136   6.424
normalize_se             5.939  0.140   6.097
plot_heatmap             5.877  0.083   5.983
normalize_se_combination 5.735  0.223   5.976
normicsNorm              5.489  0.232   5.743
* 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
  ‘/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 ‘1.3.1’
** 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_thresholds0.0340.0000.034
detect_outliers_POMA2.0630.0552.125
eigenMSNorm1.0020.0681.073
export_data0.0240.0000.024
extract_consensus_DE_candidates0.1110.0000.112
filter_out_NA_proteins_by_threshold0.3160.0080.324
filter_out_complete_NA_proteins0.0590.0000.059
filter_out_proteins_by_ID0.240.000.24
filter_out_proteins_by_value0.2350.0040.240
get_NA_overview0.0340.0030.037
get_normalization_methods000
get_overview_DE0.0480.0000.047
get_proteins_by_value0.2140.0000.214
get_spiked_stats_DE0.0820.0040.087
globalIntNorm0.1840.0000.185
globalMeanNorm0.1930.0160.209
globalMedianNorm0.2230.0040.228
impute_se1.0930.0361.129
irsNorm0.070.000.07
limmaNorm0.0910.0000.091
load_data0.0700.0040.078
load_spike_data0.0560.0000.059
loessCycNorm0.1830.0000.183
loessFNorm0.1290.0000.128
meanNorm0.0460.0040.049
medianAbsDevNorm0.1290.0040.140
medianNorm0.0690.0040.073
normalize_se5.9390.1406.097
normalize_se_combination5.7350.2235.976
normalize_se_single5.8560.5866.463
normicsNorm5.4890.2325.743
plot_NA_density0.4670.0280.496
plot_NA_frequency0.2420.0000.242
plot_NA_heatmap2.8180.0752.902
plot_PCA1.5040.0161.524
plot_ROC_AUC_spiked1.3950.0321.437
plot_TP_FP_spiked_bar0.3370.0080.345
plot_TP_FP_spiked_box0.4820.0120.494
plot_TP_FP_spiked_scatter0.5150.0000.518
plot_boxplots6.2690.1366.424
plot_condition_overview0.2840.0000.286
plot_densities3.7420.0923.843
plot_fold_changes_spiked0.6390.0160.657
plot_heatmap5.8770.0835.983
plot_heatmap_DE2.0040.0322.042
plot_histogram_spiked0.4810.0160.498
plot_identified_spiked_proteins0.6270.0200.649
plot_intersection_enrichment0.9460.0402.762
plot_intragroup_PCV0.7840.0120.799
plot_intragroup_PEV0.5980.0160.615
plot_intragroup_PMAD0.5280.0080.537
plot_intragroup_correlation0.5400.0160.558
plot_jaccard_heatmap0.3480.0000.348
plot_logFC_thresholds_spiked0.7860.0160.805
plot_markers_boxplots1.0700.0121.084
plot_nr_prot_samples0.3690.0080.378
plot_overview_DE_bar0.4210.0000.422
plot_overview_DE_tile0.2550.0000.254
plot_profiles_spiked1.0410.0081.052
plot_pvalues_spiked0.6200.0080.630
plot_stats_spiked_heatmap0.4220.0120.436
plot_tot_int_samples0.3180.0040.322
plot_upset0.8830.0000.889
plot_upset_DE1.2100.0481.267
plot_volcano_DE4.4970.0914.600
quantileNorm0.0440.0040.049
readPRONE_example0.0010.0000.001
remove_POMA_outliers0.8150.0080.824
remove_assays_from_SE0.0510.0040.056
remove_reference_samples0.0340.0040.038
remove_samples_manually0.0430.0000.044
rlrMACycNorm1.0630.0201.087
rlrMANorm0.1400.0000.141
rlrNorm0.1150.0080.122
robnormNorm0.2260.0160.242
run_DE3.6130.0163.638
specify_comparisons0.0260.0000.027
subset_SE_by_norm0.1010.0080.110
tmmNorm0.1750.0040.179
vsnNorm0.0850.0000.085