Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-02-06 12:10 -0500 (Thu, 06 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4753
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4501
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4524
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4476
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4407
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 1604/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.0.2  (landing page)
Lis Arend
Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: RELEASE_3_20
git_last_commit: b30d6ab
git_last_commit_date: 2025-01-23 11:38:54 -0500 (Thu, 23 Jan 2025)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 kjohnson1

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: 1.0.2
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_1.0.2.tar.gz
StartedAt: 2025-02-05 06:05:19 -0500 (Wed, 05 Feb 2025)
EndedAt: 2025-02-05 06:11:02 -0500 (Wed, 05 Feb 2025)
EllapsedTime: 343.4 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_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PRONE.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PRONE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRONE’ version ‘1.0.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... 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_intersection_enrichment 1.621  0.059   9.154
* 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
  ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘PRONE’ ...
** 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_thresholds0.0430.0040.048
detect_outliers_POMA0.9500.0741.048
eigenMSNorm0.6890.0290.719
export_data0.0420.0040.044
extract_consensus_DE_candidates0.1030.0050.108
filter_out_NA_proteins_by_threshold1.3740.0291.253
filter_out_complete_NA_proteins0.1030.0070.073
filter_out_proteins_by_ID0.1520.0030.155
filter_out_proteins_by_value0.1530.0040.156
get_NA_overview0.0520.0030.055
get_normalization_methods0.0010.0000.000
get_overview_DE0.0530.0040.056
get_proteins_by_value0.1450.0040.149
get_spiked_stats_DE0.1190.0060.125
globalIntNorm0.1540.0160.170
globalMeanNorm0.1530.0180.172
globalMedianNorm0.1530.0180.172
impute_se1.4260.1120.840
irsNorm0.1410.0120.079
limmaNorm0.1050.0060.087
load_data0.0640.0040.069
load_spike_data0.0550.0030.059
loessCycNorm0.1470.0140.162
loessFNorm0.1110.0030.115
meanNorm0.0600.0030.062
medianAbsDevNorm0.1200.0050.124
medianNorm0.0780.0030.082
normalize_se3.3770.1003.480
normalize_se_combination3.2810.0603.345
normalize_se_single3.2320.0473.281
normicsNorm3.1630.0453.210
plot_NA_density0.5020.0330.345
plot_NA_frequency0.3200.0220.206
plot_NA_heatmap1.5820.0781.610
plot_PCA0.9920.0151.008
plot_ROC_AUC_spiked1.1910.0411.045
plot_TP_FP_spiked_bar0.2800.0080.289
plot_TP_FP_spiked_box0.3600.0210.382
plot_TP_FP_spiked_scatter1.5370.0271.565
plot_boxplots4.3990.1383.610
plot_condition_overview0.2130.0050.218
plot_densities3.1500.1522.446
plot_fold_changes_spiked0.6350.0320.478
plot_heatmap3.9060.0653.972
plot_heatmap_DE1.2660.0231.292
plot_histogram_spiked0.4990.0280.338
plot_identified_spiked_proteins0.4280.0090.438
plot_intersection_enrichment1.6210.0599.154
plot_intragroup_PCV0.4940.0070.501
plot_intragroup_PEV0.3390.0060.345
plot_intragroup_PMAD0.3250.0060.330
plot_intragroup_correlation0.3580.0060.364
plot_jaccard_heatmap0.3910.0280.248
plot_logFC_thresholds_spiked0.5640.0120.564
plot_markers_boxplots0.8400.0310.681
plot_nr_prot_samples0.2350.0050.240
plot_overview_DE_bar0.2830.0050.287
plot_overview_DE_tile0.1830.0040.187
plot_profiles_spiked0.9050.0370.738
plot_pvalues_spiked0.4660.0110.477
plot_stats_spiked_heatmap0.3280.0080.337
plot_tot_int_samples0.2570.0060.263
plot_upset0.5670.0100.584
plot_upset_DE0.8080.0190.868
plot_volcano_DE2.0360.0252.081
quantileNorm0.0610.0040.064
readPRONE_example0.0020.0010.003
remove_POMA_outliers0.5350.0060.541
remove_assays_from_SE0.0650.0030.069
remove_reference_samples0.0670.0030.070
remove_samples_manually0.0550.0030.057
rlrMACycNorm0.7590.0090.769
rlrMANorm0.1110.0030.114
rlrNorm0.1050.0030.108
robnormNorm0.0900.0060.097
run_DE2.8410.1032.239
specify_comparisons0.0840.0080.048
subset_SE_by_norm0.1810.0130.103
tmmNorm0.1900.0140.167
vsnNorm0.0820.0030.086