Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1622/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.3.1  (landing page)
Lis Arend
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PRONE_1.3.1.tar.gz
StartedAt: 2025-08-30 01:55:58 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 02:03:42 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 463.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PRONE_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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_thresholds0.0320.0000.033
detect_outliers_POMA1.5490.0431.592
eigenMSNorm0.6000.0990.699
export_data0.0280.0000.029
extract_consensus_DE_candidates0.0810.0010.083
filter_out_NA_proteins_by_threshold0.2030.0000.197
filter_out_complete_NA_proteins0.0500.0020.053
filter_out_proteins_by_ID0.1530.0020.155
filter_out_proteins_by_value0.1550.0000.156
get_NA_overview0.0370.0000.037
get_normalization_methods0.0000.0000.001
get_overview_DE0.0420.0010.043
get_proteins_by_value0.1480.0010.148
get_spiked_stats_DE0.0900.0010.091
globalIntNorm0.1340.0000.135
globalMeanNorm0.1290.0300.159
globalMedianNorm0.1480.0050.153
impute_se0.7690.0170.724
irsNorm0.0590.0000.059
limmaNorm0.0700.0010.071
load_data0.0510.0020.055
load_spike_data0.0650.0040.069
loessCycNorm0.1050.0010.106
loessFNorm0.0840.0020.086
meanNorm0.0390.0040.044
medianAbsDevNorm0.0940.0050.099
medianNorm0.0620.0010.062
normalize_se3.3720.0713.444
normalize_se_combination3.2930.0423.335
normalize_se_single3.2700.0743.344
normicsNorm3.2540.0333.287
plot_NA_density0.3020.0060.300
plot_NA_frequency0.1860.0020.182
plot_NA_heatmap2.2710.0902.361
plot_PCA1.0300.0011.031
plot_ROC_AUC_spiked0.9460.0070.945
plot_TP_FP_spiked_bar0.2570.0020.259
plot_TP_FP_spiked_box0.3420.0020.343
plot_TP_FP_spiked_scatter0.3740.0000.374
plot_boxplots3.8440.0193.811
plot_condition_overview0.1920.0020.195
plot_densities2.3320.0072.288
plot_fold_changes_spiked0.4410.0050.439
plot_heatmap3.6360.0043.640
plot_heatmap_DE1.2530.0031.257
plot_histogram_spiked0.3090.0010.304
plot_identified_spiked_proteins0.4060.0000.407
plot_intersection_enrichment0.6460.0122.924
plot_intragroup_PCV0.4820.0000.481
plot_intragroup_PEV0.3710.0020.373
plot_intragroup_PMAD0.3240.0020.326
plot_intragroup_correlation0.3380.0010.339
plot_jaccard_heatmap0.2370.0020.218
plot_logFC_thresholds_spiked0.5670.0010.569
plot_markers_boxplots0.6940.0030.681
plot_nr_prot_samples0.2460.0000.247
plot_overview_DE_bar0.2830.0020.286
plot_overview_DE_tile0.1770.0010.178
plot_profiles_spiked0.7140.0000.692
plot_pvalues_spiked0.4200.0030.423
plot_stats_spiked_heatmap0.2960.0040.299
plot_tot_int_samples0.2170.0010.218
plot_upset0.5780.0030.582
plot_upset_DE0.7720.0060.780
plot_volcano_DE2.8290.0052.833
quantileNorm0.0440.0010.045
readPRONE_example0.0010.0000.001
remove_POMA_outliers0.5090.0010.510
remove_assays_from_SE0.0470.0000.047
remove_reference_samples0.0450.0010.047
remove_samples_manually0.0390.0010.040
rlrMACycNorm0.5890.0000.588
rlrMANorm0.0970.0000.096
rlrNorm0.0850.0010.085
robnormNorm0.1860.0000.185
run_DE2.5150.0022.317
specify_comparisons0.0350.0010.031
subset_SE_by_norm0.0790.0010.081
tmmNorm0.1270.0040.131
vsnNorm0.0710.0010.072