Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 1635/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.2.2  (landing page)
Lis Arend
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: RELEASE_3_21
git_last_commit: 4daae2c
git_last_commit_date: 2025-09-25 06:05:12 -0400 (Thu, 25 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for PRONE on nebbiolo1

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: 1.2.2
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PRONE_1.2.2.tar.gz
StartedAt: 2025-10-13 02:29:58 -0400 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 02:38:10 -0400 (Mon, 13 Oct 2025)
EllapsedTime: 492.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PRONE_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘1.2.2’
* 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 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 ... 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_volcano_DE 5.124  0.424   5.549
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/PRONE.Rcheck/00check.log’
for details.


Installation output

PRONE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘PRONE’ ...
** this is package ‘PRONE’ version ‘1.2.2’
** 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_thresholds0.0310.0020.033
detect_outliers_POMA1.0390.1321.171
eigenMSNorm0.5630.0010.564
export_data0.0270.0020.028
extract_consensus_DE_candidates0.0810.0010.082
filter_out_NA_proteins_by_threshold0.2080.0040.205
filter_out_complete_NA_proteins0.0710.0020.073
filter_out_proteins_by_ID0.1530.0010.154
filter_out_proteins_by_value0.1580.0000.158
get_NA_overview0.0350.0020.037
get_normalization_methods0.0010.0000.001
get_overview_DE0.0430.0000.043
get_proteins_by_value0.1440.0020.146
get_spiked_stats_DE0.0840.0040.088
globalIntNorm0.1340.0010.135
globalMeanNorm0.1360.0110.147
globalMedianNorm0.1320.0030.135
impute_se0.7430.0530.753
irsNorm0.0570.0020.059
limmaNorm0.0700.0000.071
load_data0.0480.0020.053
load_spike_data0.0380.0040.044
loessCycNorm0.1160.0030.119
loessFNorm0.0850.0020.086
meanNorm0.0450.0000.045
medianAbsDevNorm0.1030.0060.108
medianNorm0.0590.0020.061
normalize_se3.4240.0633.488
normalize_se_combination4.1270.1794.306
normalize_se_single3.2520.0783.331
normicsNorm3.0020.0243.027
plot_NA_density0.4090.0090.403
plot_NA_frequency0.2160.0020.203
plot_NA_heatmap1.2380.0431.282
plot_PCA1.3360.0021.338
plot_ROC_AUC_spiked1.1610.0091.151
plot_TP_FP_spiked_bar0.3350.0020.337
plot_TP_FP_spiked_box0.4190.0030.423
plot_TP_FP_spiked_scatter0.4260.0120.439
plot_boxplots4.5230.0214.461
plot_condition_overview0.2510.0010.252
plot_densities2.7540.0132.718
plot_fold_changes_spiked0.5750.0040.572
plot_heatmap3.6940.0033.697
plot_heatmap_DE1.1910.0041.195
plot_histogram_spiked0.3910.0010.385
plot_identified_spiked_proteins0.4790.0050.484
plot_intersection_enrichment0.8140.0092.102
plot_intragroup_PCV0.5870.0020.588
plot_intragroup_PEV0.4170.0040.421
plot_intragroup_PMAD0.4420.0010.443
plot_intragroup_correlation0.4110.0000.410
plot_jaccard_heatmap0.2950.0010.284
plot_logFC_thresholds_spiked0.6820.0070.689
plot_markers_boxplots0.8450.0540.893
plot_nr_prot_samples0.2740.0260.301
plot_overview_DE_bar0.4380.0460.483
plot_overview_DE_tile0.2460.0210.267
plot_profiles_spiked0.8430.0670.887
plot_pvalues_spiked0.5300.0290.559
plot_stats_spiked_heatmap0.5210.0710.592
plot_tot_int_samples0.2890.0180.307
plot_upset0.8850.0530.938
plot_upset_DE0.0320.0010.033
plot_volcano_DE5.1240.4245.549
quantileNorm0.0440.0020.047
readPRONE_example0.0000.0020.002
remove_POMA_outliers0.6010.0350.635
remove_assays_from_SE0.0470.0020.048
remove_reference_samples0.0440.0030.046
remove_samples_manually0.0390.0010.040
rlrMACycNorm0.5840.0170.600
rlrMANorm0.0940.0010.095
rlrNorm0.0820.0010.084
robnormNorm0.0770.0030.080
run_DE2.2810.1272.375
specify_comparisons0.0330.0020.031
subset_SE_by_norm0.0770.0080.084
tmmNorm0.1300.0110.141
vsnNorm0.0690.0050.074