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This page was generated on 2025-10-08 12:52 -0400 (Wed, 08 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" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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: 2025-10-07 13:45 -0400 (Tue, 07 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  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'MSnbase' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
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: 2025-10-08 00:02:26 -0400 (Wed, 08 Oct 2025)
EndedAt: 2025-10-08 00:08:37 -0400 (Wed, 08 Oct 2025)
EllapsedTime: 370.3 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
plot_boxplots                5.409  0.049   5.496
plot_intersection_enrichment 0.974  0.046   5.238
* 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_thresholds0.0310.0030.034
detect_outliers_POMA2.0890.0912.193
eigenMSNorm0.6990.0520.756
export_data0.0220.0010.024
extract_consensus_DE_candidates0.0870.0050.093
filter_out_NA_proteins_by_threshold0.2070.0040.212
filter_out_complete_NA_proteins0.0550.0020.057
filter_out_proteins_by_ID0.1790.0030.183
filter_out_proteins_by_value0.1660.0030.171
get_NA_overview0.0340.0030.038
get_normalization_methods000
get_overview_DE0.0590.0040.063
get_proteins_by_value0.1520.0030.156
get_spiked_stats_DE0.0780.0060.086
globalIntNorm0.1540.0030.158
globalMeanNorm0.1430.0030.147
globalMedianNorm0.1500.0050.156
impute_se0.8870.0190.912
irsNorm0.0620.0030.066
limmaNorm0.0760.0030.079
load_data0.0590.0030.063
load_spike_data0.0540.0030.057
loessCycNorm0.1390.0110.154
loessFNorm0.0830.0050.090
meanNorm0.0420.0020.045
medianAbsDevNorm0.1090.0040.115
medianNorm0.0650.0030.068
normalize_se3.9550.1004.079
normalize_se_combination4.5240.1054.657
normalize_se_single3.6890.0623.780
normicsNorm3.5260.0513.609
plot_NA_density0.4550.0060.463
plot_NA_frequency0.2360.0050.243
plot_NA_heatmap1.5980.0971.708
plot_PCA1.5620.0151.586
plot_ROC_AUC_spiked1.4220.0221.456
plot_TP_FP_spiked_bar0.3660.0070.375
plot_TP_FP_spiked_box0.4550.0070.466
plot_TP_FP_spiked_scatter0.5100.0080.521
plot_boxplots5.4090.0495.496
plot_condition_overview0.4500.0380.493
plot_densities3.1270.0473.198
plot_fold_changes_spiked0.5990.0090.611
plot_heatmap4.6170.0454.692
plot_heatmap_DE1.5150.0241.556
plot_histogram_spiked0.4510.0060.460
plot_identified_spiked_proteins0.4940.0070.505
plot_intersection_enrichment0.9740.0465.238
plot_intragroup_PCV0.6650.0060.676
plot_intragroup_PEV0.4690.0050.477
plot_intragroup_PMAD0.4910.0060.499
plot_intragroup_correlation0.5970.0210.630
plot_jaccard_heatmap0.3210.0040.326
plot_logFC_thresholds_spiked0.7840.0150.804
plot_markers_boxplots0.9360.0080.948
plot_nr_prot_samples0.3170.0050.325
plot_overview_DE_bar0.4980.0060.507
plot_overview_DE_tile0.2570.0050.263
plot_profiles_spiked0.8930.0130.910
plot_pvalues_spiked0.5540.0080.565
plot_stats_spiked_heatmap0.4160.0060.425
plot_tot_int_samples0.3090.0040.315
plot_upset0.9980.0161.019
plot_upset_DE0.0330.0020.035
plot_volcano_DE4.8060.0404.870
quantileNorm0.0390.0030.041
readPRONE_example0.0010.0000.002
remove_POMA_outliers0.7020.0060.709
remove_assays_from_SE0.0550.0020.057
remove_reference_samples0.0490.0030.068
remove_samples_manually0.0310.0020.032
rlrMACycNorm0.6940.0060.703
rlrMANorm0.0990.0030.102
rlrNorm0.0850.0030.087
robnormNorm0.1140.0040.120
run_DE2.6480.0342.696
specify_comparisons0.0250.0030.028
subset_SE_by_norm0.0750.0030.078
tmmNorm0.1340.0100.145
vsnNorm0.0730.0030.077