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This page was generated on 2025-08-11 12:08 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 1619/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 palomino8

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: 1.3.1
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PRONE.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings PRONE_1.3.1.tar.gz
StartedAt: 2025-08-11 05:37:12 -0400 (Mon, 11 Aug 2025)
EndedAt: 2025-08-11 05:43:35 -0400 (Mon, 11 Aug 2025)
EllapsedTime: 382.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PRONE.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings PRONE_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 ... 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
plot_boxplots 4.97   0.07    5.05
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log'
for details.


Installation output

PRONE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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_thresholds0.030.000.03
detect_outliers_POMA2.160.092.25
eigenMSNorm0.880.131.00
export_data0.030.000.03
extract_consensus_DE_candidates0.100.030.13
filter_out_NA_proteins_by_threshold0.230.030.26
filter_out_complete_NA_proteins0.070.000.07
filter_out_proteins_by_ID0.140.000.17
filter_out_proteins_by_value0.150.000.15
get_NA_overview0.030.010.05
get_normalization_methods000
get_overview_DE0.030.020.05
get_proteins_by_value0.150.000.14
get_spiked_stats_DE0.070.010.09
globalIntNorm0.100.020.11
globalMeanNorm0.110.000.11
globalMedianNorm0.110.020.12
impute_se0.850.040.89
irsNorm0.060.000.06
limmaNorm0.040.020.07
load_data0.080.000.09
load_spike_data0.050.000.05
loessCycNorm0.140.000.14
loessFNorm0.110.000.11
meanNorm0.050.000.05
medianAbsDevNorm0.070.020.09
medianNorm0.050.020.07
normalize_se4.300.144.43
normalize_se_combination3.810.093.91
normalize_se_single3.920.084.00
normicsNorm4.500.114.61
plot_NA_density0.360.000.36
plot_NA_frequency0.140.030.17
plot_NA_heatmap2.100.891.80
plot_PCA1.450.051.47
plot_ROC_AUC_spiked1.250.091.36
plot_TP_FP_spiked_bar0.320.020.35
plot_TP_FP_spiked_box0.330.040.37
plot_TP_FP_spiked_scatter0.440.030.47
plot_boxplots4.970.075.05
plot_condition_overview0.170.010.18
plot_densities3.120.083.21
plot_fold_changes_spiked0.500.050.54
plot_heatmap4.690.144.85
plot_heatmap_DE1.410.031.43
plot_histogram_spiked0.390.000.40
plot_identified_spiked_proteins0.620.000.63
plot_intersection_enrichment0.800.102.37
plot_intragroup_PCV0.660.010.67
plot_intragroup_PEV0.510.000.52
plot_intragroup_PMAD0.300.020.32
plot_intragroup_correlation0.490.000.49
plot_jaccard_heatmap0.250.010.26
plot_logFC_thresholds_spiked0.780.020.80
plot_markers_boxplots0.820.020.84
plot_nr_prot_samples0.240.010.25
plot_overview_DE_bar0.340.000.35
plot_overview_DE_tile0.250.030.28
plot_profiles_spiked0.750.070.81
plot_pvalues_spiked0.640.030.67
plot_stats_spiked_heatmap0.390.000.39
plot_tot_int_samples0.310.000.31
plot_upset0.640.010.65
plot_upset_DE1.250.021.30
plot_volcano_DE3.620.043.67
quantileNorm0.070.000.06
readPRONE_example000
remove_POMA_outliers0.770.080.84
remove_assays_from_SE0.030.020.05
remove_reference_samples0.030.010.05
remove_samples_manually0.020.020.03
rlrMACycNorm0.780.050.83
rlrMANorm0.090.000.09
rlrNorm0.080.000.08
robnormNorm0.120.000.12
run_DE3.020.093.11
specify_comparisons0.010.000.02
subset_SE_by_norm0.100.000.09
tmmNorm0.200.000.21
vsnNorm0.100.000.09