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This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1637/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.2  (landing page)
Lis Arend
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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 12.7.1 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 lconway

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: 1.3.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PRONE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PRONE_1.3.2.tar.gz
StartedAt: 2025-10-03 23:51:53 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 23:58:02 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 368.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PRONE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PRONE_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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 5.267  0.084   5.377
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log’
for details.


Installation output

PRONE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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_thresholds0.0350.0040.039
detect_outliers_POMA2.0910.0912.200
eigenMSNorm0.6630.0550.726
export_data0.0220.0020.023
extract_consensus_DE_candidates0.0820.0050.086
filter_out_NA_proteins_by_threshold0.2240.0060.231
filter_out_complete_NA_proteins0.0530.0020.055
filter_out_proteins_by_ID0.1810.0040.189
filter_out_proteins_by_value0.1710.0030.176
get_NA_overview0.0340.0020.036
get_normalization_methods000
get_overview_DE0.0610.0050.066
get_proteins_by_value0.1550.0030.159
get_spiked_stats_DE0.0710.0040.076
globalIntNorm0.1410.0030.145
globalMeanNorm0.1360.0040.140
globalMedianNorm0.1480.0030.153
impute_se0.8570.0200.883
irsNorm0.0560.0040.061
limmaNorm0.0660.0030.071
load_data0.0620.0040.068
load_spike_data0.0510.0040.056
loessCycNorm0.1490.0110.162
loessFNorm0.0800.0040.084
meanNorm0.0410.0030.044
medianAbsDevNorm0.1020.0070.112
medianNorm0.0600.0040.064
normalize_se4.0100.0984.141
normalize_se_combination4.3960.0994.518
normalize_se_single3.2890.0453.352
normicsNorm3.5260.0423.587
plot_NA_density0.4960.0080.507
plot_NA_frequency0.2410.0050.248
plot_NA_heatmap1.7400.1071.864
plot_PCA1.5920.0151.617
plot_ROC_AUC_spiked1.3640.0231.394
plot_TP_FP_spiked_bar0.3510.0070.361
plot_TP_FP_spiked_box0.4680.0070.476
plot_TP_FP_spiked_scatter0.5110.0070.521
plot_boxplots5.2670.0845.377
plot_condition_overview0.3320.0070.342
plot_densities3.0070.0363.059
plot_fold_changes_spiked0.6100.0110.624
plot_heatmap3.9520.0323.998
plot_heatmap_DE1.4090.0201.439
plot_histogram_spiked0.4820.0070.492
plot_identified_spiked_proteins0.5350.0090.549
plot_intersection_enrichment0.9890.0562.210
plot_intragroup_PCV0.6110.0060.622
plot_intragroup_PEV0.5560.0160.575
plot_intragroup_PMAD0.4670.0050.474
plot_intragroup_correlation0.5000.0070.510
plot_jaccard_heatmap0.3780.0080.387
plot_logFC_thresholds_spiked0.7550.0080.766
plot_markers_boxplots0.9540.0090.967
plot_nr_prot_samples0.3220.0050.330
plot_overview_DE_bar0.5210.0060.532
plot_overview_DE_tile0.3170.0040.323
plot_profiles_spiked0.8890.0090.901
plot_pvalues_spiked0.6290.0100.645
plot_stats_spiked_heatmap0.3980.0060.408
plot_tot_int_samples0.2960.0040.302
plot_upset0.9640.0150.986
plot_upset_DE0.0250.0020.028
plot_volcano_DE4.7450.0414.812
quantileNorm0.0410.0030.044
readPRONE_example0.0010.0000.002
remove_POMA_outliers0.7020.0060.712
remove_assays_from_SE0.0480.0030.050
remove_reference_samples0.0410.0020.043
remove_samples_manually0.0310.0010.033
rlrMACycNorm0.6900.0070.703
rlrMANorm0.0930.0020.096
rlrNorm0.0820.0020.085
robnormNorm0.1670.0150.187
run_DE3.5980.0253.636
specify_comparisons0.0190.0020.022
subset_SE_by_norm0.0840.0030.087
tmmNorm0.1400.0090.150
vsnNorm0.0730.0020.074