Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-21 12:08 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
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 1620/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 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: 2025-08-19 11:14:02 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 11:20:57 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 415.3 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             5.970  0.123   6.107
plot_boxplots            5.819  0.056   5.880
plot_heatmap             5.753  0.064   5.830
normalize_se_single      5.705  0.068   5.783
normalize_se_combination 5.642  0.076   5.730
normicsNorm              5.487  0.028   5.525
* 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_thresholds0.0330.0000.033
detect_outliers_POMA1.8490.0801.932
eigenMSNorm0.8720.1321.006
export_data0.0230.0000.023
extract_consensus_DE_candidates0.0990.0000.100
filter_out_NA_proteins_by_threshold0.2710.0080.278
filter_out_complete_NA_proteins0.0560.0000.056
filter_out_proteins_by_ID0.2170.0000.217
filter_out_proteins_by_value0.2150.0000.215
get_NA_overview0.0350.0000.034
get_normalization_methods000
get_overview_DE0.0460.0000.045
get_proteins_by_value0.1940.0040.198
get_spiked_stats_DE0.0850.0000.085
globalIntNorm0.1890.0040.194
globalMeanNorm0.2030.0080.211
globalMedianNorm0.2010.0200.222
impute_se1.0660.0281.091
irsNorm0.0750.0000.076
limmaNorm0.0860.0040.091
load_data0.0670.0040.074
load_spike_data0.0550.0000.058
loessCycNorm0.1790.0000.180
loessFNorm0.1220.0040.126
meanNorm0.0460.0000.046
medianAbsDevNorm0.1260.0080.134
medianNorm0.0680.0040.072
normalize_se5.9700.1236.107
normalize_se_combination5.6420.0765.730
normalize_se_single5.7050.0685.783
normicsNorm5.4870.0285.525
plot_NA_density0.4790.0080.487
plot_NA_frequency0.2360.0030.239
plot_NA_heatmap2.7990.0722.877
plot_PCA1.4690.0201.493
plot_ROC_AUC_spiked1.3260.0121.343
plot_TP_FP_spiked_bar0.3140.0040.319
plot_TP_FP_spiked_box0.4460.0000.447
plot_TP_FP_spiked_scatter0.4770.0000.478
plot_boxplots5.8190.0565.880
plot_condition_overview0.2920.0000.292
plot_densities3.5390.0443.585
plot_fold_changes_spiked0.6360.0160.653
plot_heatmap5.7530.0645.830
plot_heatmap_DE1.7640.0121.779
plot_histogram_spiked0.4140.0120.427
plot_identified_spiked_proteins0.5800.0110.594
plot_intersection_enrichment0.8570.0513.077
plot_intragroup_PCV0.7200.0040.726
plot_intragroup_PEV0.5540.0000.557
plot_intragroup_PMAD0.4690.0000.471
plot_intragroup_correlation0.5140.0040.520
plot_jaccard_heatmap0.3100.0040.314
plot_logFC_thresholds_spiked0.7650.0120.779
plot_markers_boxplots0.9700.0040.976
plot_nr_prot_samples0.3340.0000.335
plot_overview_DE_bar0.390.000.39
plot_overview_DE_tile0.2330.0000.234
plot_profiles_spiked0.9540.0040.957
plot_pvalues_spiked0.5770.0040.583
plot_stats_spiked_heatmap0.3810.0000.382
plot_tot_int_samples0.2970.0000.298
plot_upset0.8390.0080.849
plot_upset_DE1.1320.0201.161
plot_volcano_DE4.3090.0364.357
quantileNorm0.0460.0000.048
readPRONE_example0.0010.0000.002
remove_POMA_outliers0.7780.0160.796
remove_assays_from_SE0.0560.0000.055
remove_reference_samples0.0360.0000.036
remove_samples_manually0.0400.0000.041
rlrMACycNorm0.9360.0080.947
rlrMANorm0.1250.0040.130
rlrNorm0.1080.0000.108
robnormNorm0.2220.0000.223
run_DE3.4420.0563.502
specify_comparisons0.0240.0020.026
subset_SE_by_norm0.1010.0010.102
tmmNorm0.1660.0080.175
vsnNorm0.0820.0000.082