Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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? 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 1114/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.4.0  (landing page)
Tiago Silva
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: RELEASE_3_14
git_last_commit: 4dae66b
git_last_commit_date: 2021-10-26 13:02:56 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MethReg
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethReg.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MethReg_1.4.0.tar.gz
StartedAt: 2022-04-12 22:38:32 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:49:19 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 647.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MethReg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethReg.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MethReg_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MethReg.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
create_triplet_distance_based 32.58   4.85   40.33
create_triplet_regulon_based  24.18   4.14   28.33
get_tf_in_region              21.59   2.90   24.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
create_triplet_distance_based 32.53   2.76   35.39
create_triplet_regulon_based  24.23   1.47   25.72
get_tf_in_region              22.30   1.33   23.63
get_region_target_gene         5.73   0.05    5.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MethReg_1.4.0.tar.gz && rm -rf MethReg.buildbin-libdir && mkdir MethReg.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethReg.buildbin-libdir MethReg_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MethReg_1.4.0.zip && rm MethReg_1.4.0.tar.gz MethReg_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 3625k    0 16009    0     0   135k      0  0:00:26 --:--:--  0:00:26  135k
 41 3625k   41 1513k    0     0  1397k      0  0:00:02  0:00:01  0:00:01 1397k
100 3625k  100 3625k    0     0  1835k      0  0:00:01  0:00:01 --:--:-- 1834k

install for i386

* 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

install for x64

* installing *source* package 'MethReg' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethReg' as MethReg_1.4.0.zip
* DONE (MethReg)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MethReg' successfully unpacked and MD5 sums checked

Tests output

MethReg.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  83.26    9.04   93.00 

MethReg.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

|                                                    |  0%                      
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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 
  87.28    5.15   92.86 

Example timings

MethReg.Rcheck/examples_i386/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.150.000.15
cor_tf_target_gene0.050.000.05
create_triplet_distance_based32.58 4.8540.33
create_triplet_regulon_based24.18 4.1428.33
filter_dnam_by_quant_diff0.190.000.18
filter_exp_by_quant_mean_FC0.950.000.96
get_human_tfs0.970.011.26
get_met_probes_info0.040.000.05
get_promoter_avg000
get_region_target_gene3.550.103.64
get_residuals0.050.000.05
get_tf_ES1.030.111.14
get_tf_in_region21.59 2.9024.50
interaction_model0.180.000.17
make_dnam_se0.100.000.11
make_exp_se0.130.000.12
make_granges_from_names0.020.000.02
make_names_from_granges0.030.000.03
plot_interaction_model1.390.021.41
stratified_model0.120.000.12

MethReg.Rcheck/examples_x64/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.120.000.12
cor_tf_target_gene0.070.000.06
create_triplet_distance_based32.53 2.7635.39
create_triplet_regulon_based24.23 1.4725.72
filter_dnam_by_quant_diff0.210.000.21
filter_exp_by_quant_mean_FC1.010.021.03
get_human_tfs1.110.041.06
get_met_probes_info0.030.000.03
get_promoter_avg000
get_region_target_gene5.730.055.78
get_residuals0.050.000.05
get_tf_ES0.840.110.95
get_tf_in_region22.30 1.3323.63
interaction_model0.230.000.23
make_dnam_se0.110.000.11
make_exp_se0.130.000.13
make_granges_from_names0.030.000.03
make_names_from_granges0.010.000.01
plot_interaction_model1.460.011.47
stratified_model0.120.000.13