Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1604/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.0.0  (landing page)
Lis Arend
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: RELEASE_3_20
git_last_commit: 0833b5f
git_last_commit_date: 2024-10-29 11:34:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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


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: 1.0.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PRONE_1.0.0.tar.gz
StartedAt: 2024-12-20 04:22:51 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:29:59 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 427.4 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PRONE_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PRONE.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* 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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 1.603  0.035  13.997
* 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-3.20-bioc/meat/PRONE.Rcheck/00check.log’
for details.


Installation output

PRONE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL PRONE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘PRONE’ ...
** 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_thresholds0.0330.0000.033
detect_outliers_POMA1.6770.0291.706
eigenMSNorm0.6000.0720.672
export_data0.0260.0020.028
extract_consensus_DE_candidates0.0750.0030.079
filter_out_NA_proteins_by_threshold0.2030.0000.195
filter_out_complete_NA_proteins0.0500.0010.051
filter_out_proteins_by_ID0.1520.0100.162
filter_out_proteins_by_value0.1490.0040.153
get_NA_overview0.0330.0040.036
get_normalization_methods0.0010.0000.000
get_overview_DE0.0410.0010.043
get_proteins_by_value0.1410.0020.144
get_spiked_stats_DE0.0830.0040.087
globalIntNorm0.1430.0080.150
globalMeanNorm0.1240.0010.125
globalMedianNorm0.1270.0040.130
impute_se0.7320.0060.690
irsNorm0.0550.0020.057
limmaNorm0.0680.0000.068
load_data0.0440.0050.049
load_spike_data0.040.000.04
loessCycNorm0.1190.0090.127
loessFNorm0.0820.0020.085
meanNorm0.0430.0000.043
medianAbsDevNorm0.0930.0030.095
medianNorm0.060.000.06
normalize_se3.2910.0503.341
normalize_se_combination3.1860.0793.265
normalize_se_single3.8350.1083.943
normicsNorm2.9010.0022.903
plot_NA_density0.2930.0070.293
plot_NA_frequency0.1670.0000.160
plot_NA_heatmap1.1650.0311.196
plot_PCA0.9420.0020.944
plot_ROC_AUC_spiked0.9000.0040.887
plot_TP_FP_spiked_bar0.2480.0040.251
plot_TP_FP_spiked_box1.1980.0021.200
plot_TP_FP_spiked_scatter0.3310.0010.331
plot_boxplots3.6540.1333.721
plot_condition_overview0.1720.0030.176
plot_densities2.3020.0112.213
plot_fold_changes_spiked0.4230.0130.429
plot_heatmap3.5090.0193.528
plot_heatmap_DE1.1440.0021.146
plot_histogram_spiked0.3050.0220.320
plot_identified_spiked_proteins0.3590.0040.363
plot_intersection_enrichment 1.603 0.03513.997
plot_intragroup_PCV0.4490.0020.451
plot_intragroup_PEV0.3320.0000.332
plot_intragroup_PMAD0.3030.0020.305
plot_intragroup_correlation0.3120.0020.314
plot_jaccard_heatmap0.2310.0000.221
plot_logFC_thresholds_spiked0.5010.0000.501
plot_markers_boxplots0.6570.0280.677
plot_nr_prot_samples0.2170.0030.220
plot_overview_DE_bar0.2700.0020.272
plot_overview_DE_tile0.1650.0000.164
plot_profiles_spiked0.6370.0070.632
plot_pvalues_spiked0.3910.0040.395
plot_stats_spiked_heatmap0.2770.0020.280
plot_tot_int_samples0.2050.0040.209
plot_upset0.5100.0030.513
plot_upset_DE0.7390.0040.745
plot_volcano_DE2.6540.0802.735
quantileNorm0.0430.0010.045
readPRONE_example0.0000.0010.001
remove_POMA_outliers0.4550.0000.456
remove_assays_from_SE0.0450.0020.047
remove_reference_samples0.0450.0010.046
remove_samples_manually0.040.000.04
rlrMACycNorm0.5710.0040.576
rlrMANorm0.1230.0020.125
rlrNorm0.0840.0010.084
robnormNorm0.0750.0010.075
run_DE2.2280.0442.242
specify_comparisons0.0340.0000.030
subset_SE_by_norm0.0740.0020.076
tmmNorm0.1210.0040.125
vsnNorm0.0700.0020.072