Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1197/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.15.0  (landing page)
Tiago Silva
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: devel
git_last_commit: aeb2a7e
git_last_commit_date: 2024-04-30 11:27:17 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation


CHECK results for MethReg on palomino4

To the developers/maintainers of the MethReg package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethReg.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: MethReg
Version: 1.15.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethReg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MethReg_1.15.0.tar.gz
StartedAt: 2024-06-10 05:06:39 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:19:12 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 752.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MethReg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethReg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MethReg_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MethReg.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MethReg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethReg' version '1.15.0'
* 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 whether package 'MethReg' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readRemap2022: no visible binding for global variable 'biotype'
Undefined global functions or variables:
  biotype
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
create_triplet_distance_based 29.95   6.94   69.66
get_tf_in_region              23.19   2.50   25.75
create_triplet_regulon_based  21.43   2.40   23.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/MethReg.Rcheck/00check.log'
for details.


Installation output

MethReg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MethReg
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'MethReg' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (MethReg)

Tests output

MethReg.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MethReg)

> 
> test_check("MethReg")

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 
                   Status freq
1 Regions below threshold    1
2 Regions above threshold    1
                   Status freq
1 Regions below threshold    1
2 Regions above threshold    1
                   Status freq
1 Regions below threshold    1
2 Regions above threshold    1

|                                                    |  0%                      
|==========================                          | 50% ~0 s remaining       
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 
                 Status freq
1 Genes above threshold    1
2                  <NA>    1

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|==========================                          | 50% ~0 s remaining       
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|                                                    |0.8928571% ~0 s remaining 
|                                                    |1.785714% ~0 s remaining  
|=                                                   |2.678571% ~0 s remaining  
|=                                                   |3.571429% ~0 s remaining  
|==                                                  |4.464286% ~0 s remaining  
|==                                                  |5.357143% ~0 s remaining  
|===                                                 |6.25% ~0 s remaining      
|===                                                 |7.142857% ~0 s remaining  
|====                                                |8.035714% ~0 s remaining  
|====                                                |8.928571% ~0 s remaining  
|=====                                               |9.821429% ~0 s remaining  
|=====                                               |10.71429% ~0 s remaining  
|======                                              |11.60714% ~0 s remaining  
|======                                              |12.5% ~0 s remaining      
|======                                              |13.39286% ~0 s remaining  
|=======                                             |14.28571% ~0 s remaining  
|=======                                             |15.17857% ~0 s remaining  
|========                                            |16.07143% ~0 s remaining  
|========                                            |16.96429% ~0 s remaining  
|=========                                           |17.85714% ~0 s remaining  
|=========                                           |18.75% ~0 s remaining     
|==========                                          |19.64286% ~0 s remaining  
|==========                                          |20.53571% ~0 s remaining  
|===========                                         |21.42857% ~0 s remaining  
|===========                                         |22.32143% ~0 s remaining  
|============                                        |23.21429% ~0 s remaining  
|============                                        |24.10714% ~0 s remaining  
|=============                                       | 25% ~0 s remaining       
|=============                                       |25.89286% ~0 s remaining  
|=============                                       |26.78571% ~0 s remaining  
|==============                                      |27.67857% ~0 s remaining  
|==============                                      |28.57143% ~0 s remaining  
|===============                                     |29.46429% ~0 s remaining  
|===============                                     |30.35714% ~0 s remaining  
|================                                    |31.25% ~0 s remaining     
|================                                    |32.14286% ~0 s remaining  
|=================                                   |33.03571% ~0 s remaining  
|=================                                   |33.92857% ~0 s remaining  
|==================                                  |34.82143% ~0 s remaining  
|==================                                  |35.71429% ~0 s remaining  
|===================                                 |36.60714% ~0 s remaining  
|===================                                 |37.5% ~0 s remaining      
|===================                                 |38.39286% ~0 s remaining  
|====================                                |39.28571% ~0 s remaining  
|====================                                |40.17857% ~0 s remaining  
|=====================                               |41.07143% ~0 s remaining  
|=====================                               |41.96429% ~0 s remaining  
|======================                              |42.85714% ~0 s remaining  
|======================                              |43.75% ~0 s remaining     
|=======================                             |44.64286% ~0 s remaining  
|=======================                             |45.53571% ~0 s remaining  
|========================                            |46.42857% ~0 s remaining  
|========================                            |47.32143% ~0 s remaining  
|=========================                           |48.21429% ~0 s remaining  
|=========================                           |49.10714% ~0 s remaining  
|==========================                          | 50% ~0 s remaining       
|==========================                          |50.89286% ~0 s remaining  
|==========================                          |51.78571% ~0 s remaining  
|===========================                         |52.67857% ~0 s remaining  
|===========================                         |53.57143% ~0 s remaining  
|============================                        |54.46429% ~0 s remaining  
|============================                        |55.35714% ~0 s remaining  
|=============================                       |56.25% ~0 s remaining     
|=============================                       |57.14286% ~0 s remaining  
|==============================                      |58.03571% ~0 s remaining  
|==============================                      |58.92857% ~0 s remaining  
|===============================                     |59.82143% ~0 s remaining  
|===============================                     |60.71429% ~0 s remaining  
|================================                    |61.60714% ~0 s remaining  
|================================                    |62.5% ~0 s remaining      
|================================                    |63.39286% ~0 s remaining  
|=================================                   |64.28571% ~0 s remaining  
|=================================                   |65.17857% ~0 s remaining  
|==================================                  |66.07143% ~0 s remaining  
|==================================                  |66.96429% ~0 s remaining  
|===================================                 |67.85714% ~0 s remaining  
|===================================                 |68.75% ~0 s remaining     
|====================================                |69.64286% ~0 s remaining  
|====================================                |70.53571% ~0 s remaining  
|=====================================               |71.42857% ~0 s remaining  
|=====================================               |72.32143% ~0 s remaining  
|======================================              |73.21429% ~0 s remaining  
|======================================              |74.10714% ~0 s remaining  
|=======================================             | 75% ~0 s remaining       
|=======================================             |75.89286% ~0 s remaining  
|=======================================             |76.78571% ~0 s remaining  
|========================================            |77.67857% ~0 s remaining  
|========================================            |78.57143% ~0 s remaining  
|=========================================           |79.46429% ~0 s remaining  
|=========================================           |80.35714% ~0 s remaining  
|==========================================          |81.25% ~0 s remaining     
|==========================================          |82.14286% ~0 s remaining  
|===========================================         |83.03571% ~0 s remaining  
|===========================================         |83.92857% ~0 s remaining  
|============================================        |84.82143% ~0 s remaining  
|============================================        |85.71429% ~0 s remaining  
|=============================================       |86.60714% ~0 s remaining  
|=============================================       |87.5% ~0 s remaining      
|=============================================       |88.39286% ~0 s remaining  
|==============================================      |89.28571% ~0 s remaining  
|==============================================      |90.17857% ~0 s remaining  
|===============================================     |91.07143% ~0 s remaining  
|===============================================     |91.96429% ~0 s remaining  
|================================================    |92.85714% ~0 s remaining  
|================================================    |93.75% ~0 s remaining     
|=================================================   |94.64286% ~0 s remaining  
|=================================================   |95.53571% ~0 s remaining  
|==================================================  |96.42857% ~0 s remaining  
|==================================================  |97.32143% ~0 s remaining  
|=================================================== |98.21429% ~0 s remaining  
|=================================================== |99.10714% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 
[ FAIL 0 | WARN 3 | SKIP 11 | PASS 148 ]

══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On Bioconductor (7): 'test-create_triplet_distance_based.R:2:3',
  'test-get_promoter_avg.R:3:5', 'test-get_promoter_avg.R:15:5',
  'test-get_promoter_avg.R:30:5', 'test-get_promoter_avg.R:47:5',
  'test-plot_interaction_model.R:3:5', 'test-plot_stratified_model.R:3:5'
• On CRAN (2): 'test-get_human_tfs.R:2:5', 'test-get_tf_in_region.R:3:5'
• empty test (2): 'test-get_residuals.R:1:1', 'test-get_tf_in_region.R:16:1'

[ FAIL 0 | WARN 3 | SKIP 11 | PASS 148 ]
> 
> proc.time()
   user  system elapsed 
  70.46   18.06   90.15 

Example timings

MethReg.Rcheck/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.040.110.14
cor_tf_target_gene0.020.020.03
create_triplet_distance_based29.95 6.9469.66
create_triplet_regulon_based21.43 2.4023.97
export_results_to_table1.350.191.64
filter_dnam_by_quant_diff0.110.000.11
filter_exp_by_quant_mean_FC0.950.061.02
get_human_tfs0.450.171.03
get_met_probes_info0.020.000.01
get_promoter_avg000
get_region_target_gene3.000.964.11
get_residuals0.040.000.05
get_tf_ES2.640.903.85
get_tf_in_region23.19 2.5025.75
interaction_model0.190.070.25
make_dnam_se0.060.030.10
make_exp_se0.080.000.08
make_granges_from_names0.010.000.01
make_names_from_granges0.020.000.02
plot_interaction_model1.700.171.90
stratified_model0.070.030.10