Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-02-15 11:40 -0500 (Sat, 15 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4720
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4482
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4493
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4446
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 1607/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.1.2  (landing page)
Lis Arend
Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 Feb 2025)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: devel
git_last_commit: bca70b6
git_last_commit_date: 2025-01-23 12:01:15 -0500 (Thu, 23 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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


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: 1.1.2
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_1.1.2.tar.gz
StartedAt: 2025-02-15 01:09:38 -0500 (Sat, 15 Feb 2025)
EndedAt: 2025-02-15 01:17:13 -0500 (Sat, 15 Feb 2025)
EllapsedTime: 454.7 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PRONE.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘PRONE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRONE’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 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
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
plot_intersection_enrichment 1.705  0.028  13.278
* 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-3.21-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 ‘1.1.2’
** 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_thresholds0.0320.0010.034
detect_outliers_POMA1.7310.0481.779
eigenMSNorm0.5660.0430.610
export_data0.0280.0010.029
extract_consensus_DE_candidates0.0820.0070.089
filter_out_NA_proteins_by_threshold0.1940.0380.225
filter_out_complete_NA_proteins0.0480.0080.057
filter_out_proteins_by_ID0.1480.0270.175
filter_out_proteins_by_value0.1490.0270.175
get_NA_overview0.0540.0040.059
get_normalization_methods0.0000.0000.001
get_overview_DE0.0430.0000.043
get_proteins_by_value0.1390.0010.140
get_spiked_stats_DE0.0840.0030.088
globalIntNorm0.1270.0010.128
globalMeanNorm0.1260.0000.127
globalMedianNorm0.1330.0000.133
impute_se0.7610.0110.708
irsNorm0.0560.0060.062
limmaNorm0.0840.0020.085
load_data0.0460.0040.052
load_spike_data0.0380.0020.042
loessCycNorm0.0980.0060.105
loessFNorm0.0870.0010.087
meanNorm0.0430.0010.044
medianAbsDevNorm0.0950.0040.098
medianNorm0.0790.0020.081
normalize_se3.3070.0043.312
normalize_se_combination3.2200.0123.232
normalize_se_single3.1890.0183.208
normicsNorm3.1070.0013.108
plot_NA_density0.3120.0030.300
plot_NA_frequency0.1880.0010.182
plot_NA_heatmap1.3820.0231.405
plot_PCA1.9810.0001.981
plot_ROC_AUC_spiked0.9130.0170.913
plot_TP_FP_spiked_bar0.2700.0030.273
plot_TP_FP_spiked_box0.3250.0050.331
plot_TP_FP_spiked_scatter0.3580.0040.362
plot_boxplots3.8160.0313.745
plot_condition_overview0.1950.0010.197
plot_densities2.3750.0062.314
plot_fold_changes_spiked0.4360.0050.434
plot_heatmap3.6980.0443.743
plot_heatmap_DE1.1980.0071.205
plot_histogram_spiked0.3320.0020.328
plot_identified_spiked_proteins0.3900.0050.395
plot_intersection_enrichment 1.705 0.02813.278
plot_intragroup_PCV0.4980.0010.500
plot_intragroup_PEV0.3140.0010.315
plot_intragroup_PMAD0.3320.0020.334
plot_intragroup_correlation0.3490.0010.350
plot_jaccard_heatmap0.2530.0030.243
plot_logFC_thresholds_spiked0.5280.0030.532
plot_markers_boxplots0.6830.0020.677
plot_nr_prot_samples0.2090.0010.211
plot_overview_DE_bar0.2700.0000.271
plot_overview_DE_tile0.1700.0010.172
plot_profiles_spiked0.8160.0030.805
plot_pvalues_spiked0.4030.0050.409
plot_stats_spiked_heatmap0.2870.0040.290
plot_tot_int_samples0.2110.0000.211
plot_upset0.5710.0370.608
plot_upset_DE0.7810.0220.803
plot_volcano_DE2.7650.0062.771
quantileNorm0.0440.0000.045
readPRONE_example0.0000.0010.001
remove_POMA_outliers0.5150.0030.518
remove_assays_from_SE0.0450.0030.049
remove_reference_samples0.0470.0020.049
remove_samples_manually0.0410.0010.042
rlrMACycNorm0.5750.0010.576
rlrMANorm0.0980.0000.098
rlrNorm0.0860.0010.087
robnormNorm0.1000.0010.101
run_DE2.3420.0012.309
specify_comparisons0.0340.0020.031
subset_SE_by_norm0.0730.0020.075
tmmNorm0.1270.0010.129
vsnNorm0.0710.0000.071