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This page was generated on 2025-09-11 12:07 -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 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: 2025-09-09 10:04:55 -0000 (Tue, 09 Sep 2025)
EndedAt: 2025-09-09 10:11:56 -0000 (Tue, 09 Sep 2025)
EllapsedTime: 421.4 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_1.3.1.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             5.823  0.151   5.992
plot_boxplots            5.850  0.032   5.894
plot_heatmap             5.756  0.056   5.834
normalize_se_combination 5.674  0.076   5.768
normalize_se_single      5.657  0.080   5.754
normicsNorm              5.633  0.075   5.726
* 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_thresholds0.0290.0040.033
detect_outliers_POMA1.9410.0962.043
eigenMSNorm0.9120.1041.019
export_data0.0230.0000.024
extract_consensus_DE_candidates0.0970.0040.102
filter_out_NA_proteins_by_threshold0.2760.0040.280
filter_out_complete_NA_proteins0.0570.0000.057
filter_out_proteins_by_ID0.2170.0000.218
filter_out_proteins_by_value0.2220.0000.223
get_NA_overview0.0360.0000.035
get_normalization_methods000
get_overview_DE0.0460.0000.046
get_proteins_by_value0.2230.0000.223
get_spiked_stats_DE0.0890.0000.089
globalIntNorm0.1960.0000.196
globalMeanNorm0.1860.0200.205
globalMedianNorm0.2150.0040.219
impute_se0.9790.0000.976
irsNorm0.0680.0000.069
limmaNorm0.0900.0000.089
load_data0.0580.0120.076
load_spike_data0.0770.0040.084
loessCycNorm0.1530.0000.153
loessFNorm0.1240.0030.128
meanNorm0.0470.0000.047
medianAbsDevNorm0.1270.0000.128
medianNorm0.0660.0030.070
normalize_se5.8230.1515.992
normalize_se_combination5.6740.0765.768
normalize_se_single5.6570.0805.754
normicsNorm5.6330.0755.726
plot_NA_density0.4300.0080.439
plot_NA_frequency0.2640.0000.264
plot_NA_heatmap2.7960.0602.865
plot_PCA1.4750.0081.488
plot_ROC_AUC_spiked1.3530.0201.380
plot_TP_FP_spiked_bar0.3290.0080.338
plot_TP_FP_spiked_box0.4580.0000.460
plot_TP_FP_spiked_scatter0.4920.0040.497
plot_boxplots5.8500.0325.894
plot_condition_overview0.2640.0080.273
plot_densities3.3890.0393.435
plot_fold_changes_spiked0.6290.0310.662
plot_heatmap5.7560.0565.834
plot_heatmap_DE1.8250.0041.836
plot_histogram_spiked0.4170.0120.430
plot_identified_spiked_proteins0.6050.0160.623
plot_intersection_enrichment0.8930.0362.700
plot_intragroup_PCV0.7440.0000.747
plot_intragroup_PEV0.5420.0000.544
plot_intragroup_PMAD0.5020.0000.504
plot_intragroup_correlation0.5130.0000.515
plot_jaccard_heatmap0.3350.0000.337
plot_logFC_thresholds_spiked0.7720.0040.778
plot_markers_boxplots1.0210.0001.025
plot_nr_prot_samples0.3540.0080.364
plot_overview_DE_bar0.4060.0000.407
plot_overview_DE_tile0.2470.0000.248
plot_profiles_spiked1.0260.0041.031
plot_pvalues_spiked0.5730.0000.575
plot_stats_spiked_heatmap0.4040.0000.405
plot_tot_int_samples0.3180.0000.319
plot_upset0.8650.0200.889
plot_upset_DE1.1720.0121.196
plot_volcano_DE4.3010.0604.377
quantileNorm0.0400.0070.049
readPRONE_example0.0020.0010.001
remove_POMA_outliers0.7430.0510.798
remove_assays_from_SE0.0520.0000.052
remove_reference_samples0.0350.0000.036
remove_samples_manually0.0400.0000.041
rlrMACycNorm0.9540.0080.966
rlrMANorm0.1320.0040.136
rlrNorm0.1120.0000.112
robnormNorm0.2290.0040.233
run_DE3.5270.0043.539
specify_comparisons0.0270.0000.027
subset_SE_by_norm0.110.000.11
tmmNorm0.1660.0080.174
vsnNorm0.0810.0000.082