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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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: 2025-10-09 13:45 -0400 (Thu, 09 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: 2025-10-10 00:17:41 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 00:24:03 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 381.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
normalize_se_combination 5.548  0.142   5.734
plot_boxplots            5.308  0.048   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_thresholds0.0260.0020.029
detect_outliers_POMA2.0510.0832.149
eigenMSNorm0.6980.0670.775
export_data0.0210.0020.023
extract_consensus_DE_candidates0.0930.0040.097
filter_out_NA_proteins_by_threshold0.2250.0050.233
filter_out_complete_NA_proteins0.0500.0020.053
filter_out_proteins_by_ID0.1760.0040.181
filter_out_proteins_by_value0.1880.0050.198
get_NA_overview0.0310.0030.035
get_normalization_methods000
get_overview_DE0.0370.0030.041
get_proteins_by_value0.1630.0040.169
get_spiked_stats_DE0.0740.0050.079
globalIntNorm0.1580.0050.163
globalMeanNorm0.1460.0030.151
globalMedianNorm0.1460.0040.152
impute_se0.9310.0260.978
irsNorm0.0640.0030.066
limmaNorm0.0780.0060.087
load_data0.0580.0040.064
load_spike_data0.0500.0040.055
loessCycNorm0.1490.0120.165
loessFNorm0.0860.0030.092
meanNorm0.0430.0040.048
medianAbsDevNorm0.0980.0050.107
medianNorm0.0590.0020.062
normalize_se4.2270.1214.390
normalize_se_combination5.5480.1425.734
normalize_se_single3.7870.0713.878
normicsNorm3.6810.0473.755
plot_NA_density0.4550.0070.465
plot_NA_frequency0.2340.0050.240
plot_NA_heatmap1.5670.1071.687
plot_PCA1.5850.0121.604
plot_ROC_AUC_spiked1.3770.0191.402
plot_TP_FP_spiked_bar0.3680.0070.377
plot_TP_FP_spiked_box0.4710.0070.479
plot_TP_FP_spiked_scatter0.5100.0080.520
plot_boxplots5.3080.0485.377
plot_condition_overview0.2880.0040.293
plot_densities3.1250.0343.170
plot_fold_changes_spiked0.6060.0100.619
plot_heatmap4.5840.0744.678
plot_heatmap_DE1.4970.0361.544
plot_histogram_spiked0.4830.0070.495
plot_identified_spiked_proteins0.5540.0090.565
plot_intersection_enrichment1.0020.0492.171
plot_intragroup_PCV0.6610.0050.669
plot_intragroup_PEV0.5470.0060.557
plot_intragroup_PMAD0.5040.0060.513
plot_intragroup_correlation0.5040.0050.511
plot_jaccard_heatmap0.3890.0060.398
plot_logFC_thresholds_spiked0.7520.0110.769
plot_markers_boxplots0.9370.0080.950
plot_nr_prot_samples0.2980.0040.304
plot_overview_DE_bar0.5080.0050.516
plot_overview_DE_tile0.3130.0040.322
plot_profiles_spiked0.9140.0110.928
plot_pvalues_spiked0.6240.0110.640
plot_stats_spiked_heatmap0.4380.0070.447
plot_tot_int_samples0.3170.0050.325
plot_upset1.0160.0161.035
plot_upset_DE0.0290.0030.032
plot_volcano_DE4.7660.0374.823
quantileNorm0.0420.0030.045
readPRONE_example0.0010.0010.002
remove_POMA_outliers0.7610.0060.770
remove_assays_from_SE0.0430.0020.045
remove_reference_samples0.0460.0020.048
remove_samples_manually0.0380.0020.041
rlrMACycNorm0.6970.0070.707
rlrMANorm0.1470.0050.152
rlrNorm0.0890.0030.092
robnormNorm0.0820.0040.087
run_DE2.6150.0222.649
specify_comparisons0.0240.0020.027
subset_SE_by_norm0.1210.0040.126
tmmNorm0.1390.0100.149
vsnNorm0.0710.0030.075