Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-16 11:07:55 -0400 (Wed, 16 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4060
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4081
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4133
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

CHECK results for MethReg on riesling1


To the developers/maintainers of the MethReg package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1119/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.5.3  (landing page)
Tiago Silva
Snapshot Date: 2022-03-15 13:55:23 -0400 (Tue, 15 Mar 2022)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: master
git_last_commit: 667bc66
git_last_commit_date: 2022-03-08 14:25:39 -0400 (Tue, 08 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MethReg
Version: 1.5.3
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethReg.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MethReg_1.5.3.tar.gz
StartedAt: 2022-03-15 19:24:35 -0400 (Tue, 15 Mar 2022)
EndedAt: 2022-03-15 19:30:14 -0400 (Tue, 15 Mar 2022)
EllapsedTime: 339.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MethReg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethReg.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MethReg_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MethReg.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethReg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethReg' version '1.5.3'
* 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 R 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 ... 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 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 25.37   4.50   29.87
get_tf_in_region              20.61   2.67   23.28
create_triplet_regulon_based  19.78   3.31   23.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MethReg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MethReg
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'MethReg'
    finding HTML links ... done
    MethReg                                 html  
    clinical                                html  
    cor_dnam_target_gene                    html  
    cor_tf_target_gene                      html  
    create_triplet_distance_based           html  
    create_triplet_regulon_based            html  
    dna.met.chr21                           html  
    filter_dnam_by_quant_diff               html  
    filter_exp_by_quant_mean_FC             html  
    filter_genes_zero_expression            html  
    gene.exp.chr21.log2                     html  
    get_human_tfs                           html  
    get_met_probes_info                     html  
    get_promoter_avg                        html  
    get_region_target_gene                  html  
    get_residuals                           html  
    get_tf_ES                               html  
    get_tf_in_region                        html  
    interaction_model                       html  
    make_dnam_se                            html  
    make_exp_se                             html  
    make_granges_from_names                 html  
    make_names_from_granges                 html  
    plot_interaction_model                  html  
    plot_stratified_model                   html  
    stratified_model                        html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'InterCellar' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'TADCompare' is missing or broken
 done

Tests output

MethReg.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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")

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                   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

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                 Status freq
1 Genes above threshold    1
2                  <NA>    1

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[ FAIL 0 | WARN 0 | SKIP 10 | PASS 152 ]

== Skipped tests ===============================================================
* On Bioconductor (6)
* On CRAN (2)
* empty test (2)

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 152 ]
> 
> proc.time()
   user  system elapsed 
  70.76    8.53   80.59 

Example timings

MethReg.Rcheck/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.550.010.57
cor_tf_target_gene0.030.000.03
create_triplet_distance_based25.37 4.5029.87
create_triplet_regulon_based19.78 3.3123.09
filter_dnam_by_quant_diff0.090.000.10
filter_exp_by_quant_mean_FC0.770.020.78
get_human_tfs0.440.110.56
get_met_probes_info0.010.000.01
get_promoter_avg000
get_region_target_gene3.490.033.52
get_residuals0.040.000.05
get_tf_ES1.990.172.15
get_tf_in_region20.61 2.6723.28
interaction_model0.260.000.27
make_dnam_se0.030.020.05
make_exp_se0.070.000.06
make_granges_from_names0.010.000.02
make_names_from_granges0.020.000.01
plot_interaction_model1.340.051.39
stratified_model0.130.010.14