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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1215/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.17.0  (landing page)
Tiago Silva
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: devel
git_last_commit: ba3e766
git_last_commit_date: 2024-10-29 10:50:40 -0500 (Tue, 29 Oct 2024)
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  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MethReg on nebbiolo1

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: 1.17.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MethReg_1.17.0.tar.gz
StartedAt: 2024-12-23 23:38:23 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:54:52 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 989.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MethReg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MethReg_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 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 ‘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 loading without being on the library search path ... 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 27.047  1.960  29.049
create_triplet_regulon_based  22.698  0.844  23.560
get_tf_in_region              20.714  0.358  21.072
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck/00check.log’
for details.


Installation output

MethReg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MethReg
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘MethReg’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’
** testing if installed package can be loaded from final location
No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’
** testing if installed package keeps a record of temporary installation path
* DONE (MethReg)

Tests output

MethReg.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)

No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools'
> 
> 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 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 
 79.085   3.966  83.861 

Example timings

MethReg.Rcheck/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.0310.0010.032
cor_tf_target_gene0.0160.0010.017
create_triplet_distance_based27.047 1.96029.049
create_triplet_regulon_based22.698 0.84423.560
export_results_to_table1.3040.0251.342
filter_dnam_by_quant_diff0.0800.0000.081
filter_exp_by_quant_mean_FC0.7190.0410.761
get_human_tfs0.6350.0511.560
get_met_probes_info0.0140.0010.015
get_promoter_avg0.0000.0000.001
get_region_target_gene3.8320.1744.007
get_residuals0.0360.0010.038
get_tf_ES1.1640.0391.203
get_tf_in_region20.714 0.35821.072
interaction_model0.1890.0170.205
make_dnam_se0.0580.0040.061
make_exp_se0.0800.0010.081
make_granges_from_names0.0150.0000.014
make_names_from_granges0.0160.0000.017
plot_interaction_model1.5140.0391.554
stratified_model0.0420.0010.044