Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-02-03 12:37 -0500 (Mon, 03 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
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 1601/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.1.2  (landing page)
Lis Arend
Snapshot Date: 2025-02-02 13:40 -0500 (Sun, 02 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


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: 2025-02-03 01:20:59 -0500 (Mon, 03 Feb 2025)
EndedAt: 2025-02-03 01:28:40 -0500 (Mon, 03 Feb 2025)
EllapsedTime: 461.5 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_1.1.2.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 24.04.1 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 1.821   0.02   12.66
* 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_thresholds0.0320.0010.033
detect_outliers_POMA1.7970.0381.835
eigenMSNorm0.6030.0550.658
export_data0.0280.0000.030
extract_consensus_DE_candidates0.0860.0100.096
filter_out_NA_proteins_by_threshold0.2030.0380.234
filter_out_complete_NA_proteins0.0540.0050.059
filter_out_proteins_by_ID0.1520.0270.179
filter_out_proteins_by_value0.1690.0020.171
get_NA_overview0.0360.0000.036
get_normalization_methods0.0010.0010.000
get_overview_DE0.0410.0000.042
get_proteins_by_value0.1390.0010.140
get_spiked_stats_DE0.0800.0060.085
globalIntNorm0.1250.0030.127
globalMeanNorm0.1280.0020.130
globalMedianNorm0.1340.0010.136
impute_se0.7770.0460.781
irsNorm0.0570.0000.057
limmaNorm0.0650.0040.068
load_data0.0520.0020.056
load_spike_data0.0440.0000.046
loessCycNorm0.1080.0060.113
loessFNorm0.1010.0030.103
meanNorm0.0420.0020.044
medianAbsDevNorm0.0950.0030.098
medianNorm0.0560.0020.058
normalize_se3.3100.0443.354
normalize_se_combination3.2990.0393.338
normalize_se_single3.2070.1013.309
normicsNorm3.0850.0143.100
plot_NA_density0.3030.0120.303
plot_NA_frequency0.2110.0080.204
plot_NA_heatmap1.3060.0331.339
plot_PCA1.9580.0962.053
plot_ROC_AUC_spiked0.9410.0170.949
plot_TP_FP_spiked_bar0.2580.0040.261
plot_TP_FP_spiked_box0.3190.0040.323
plot_TP_FP_spiked_scatter0.3410.0020.343
plot_boxplots3.8300.0633.846
plot_condition_overview0.1880.0030.191
plot_densities2.3610.0662.379
plot_fold_changes_spiked0.4170.0040.414
plot_heatmap3.6630.0423.706
plot_heatmap_DE1.2450.0091.262
plot_histogram_spiked0.2990.0020.294
plot_identified_spiked_proteins0.3870.0050.392
plot_intersection_enrichment 1.821 0.02012.660
plot_intragroup_PCV0.4450.0070.452
plot_intragroup_PEV0.3270.0000.327
plot_intragroup_PMAD0.3300.0010.330
plot_intragroup_correlation0.3390.0030.341
plot_jaccard_heatmap0.2320.0030.224
plot_logFC_thresholds_spiked0.6010.0030.604
plot_markers_boxplots0.6830.0030.671
plot_nr_prot_samples0.2560.0010.260
plot_overview_DE_bar0.3010.0030.304
plot_overview_DE_tile0.1720.0010.173
plot_profiles_spiked0.7160.0260.720
plot_pvalues_spiked0.4390.0340.473
plot_stats_spiked_heatmap0.2850.0370.322
plot_tot_int_samples0.2070.0310.237
plot_upset0.5930.0670.659
plot_upset_DE0.7910.0350.827
plot_volcano_DE2.9560.1873.142
quantileNorm0.0460.0050.052
readPRONE_example0.0010.0010.002
remove_POMA_outliers0.5090.0480.556
remove_assays_from_SE0.0490.0030.052
remove_reference_samples0.0500.0020.052
remove_samples_manually0.0400.0020.042
rlrMACycNorm0.6420.0610.702
rlrMANorm0.1040.0050.110
rlrNorm0.0900.0030.093
robnormNorm0.1050.0120.117
run_DE2.4930.0952.540
specify_comparisons0.0320.0020.031
subset_SE_by_norm0.0760.0130.090
tmmNorm0.1330.0120.145
vsnNorm0.0730.0020.074