Tiago Silva
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MethReg |
| git_branch: RELEASE_3_17 |
| git_last_commit: 21c4a4d |
| git_last_commit_date: 2023-07-24 12:45:17 -0400 (Mon, 24 Jul 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:30 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1192/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethReg 1.10.2 (landing page) Tiago Silva
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: MethReg |
| Version: 1.10.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MethReg_1.10.2.tar.gz |
| StartedAt: 2023-10-15 22:40:58 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:50:38 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 580.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MethReg.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MethReg_1.10.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MethReg.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.10.2’
* 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 ‘MethReg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘downloader’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘downloader::download.file’
* 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 30.401 0.935 31.359
get_tf_in_region 23.829 0.608 24.437
create_triplet_regulon_based 23.543 0.588 24.130
* 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 ...
‘MethReg.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MethReg.Rcheck/00check.log’
for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 ** 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)
MethReg.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
| | 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%
|======= |14.28571% ~0 s remaining
|============== |28.57143% ~0 s remaining
|====================== |42.85714% ~0 s remaining
|============================= |57.14286% ~0 s remaining
|===================================== |71.42857% ~0 s remaining
|============================================ |85.71429% ~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
65.643 2.210 69.270
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.035 | 0.004 | 0.040 | |
| cor_tf_target_gene | 0.016 | 0.001 | 0.016 | |
| create_triplet_distance_based | 30.401 | 0.935 | 31.359 | |
| create_triplet_regulon_based | 23.543 | 0.588 | 24.130 | |
| filter_dnam_by_quant_diff | 0.133 | 0.000 | 0.132 | |
| filter_exp_by_quant_mean_FC | 0.691 | 0.064 | 0.755 | |
| get_human_tfs | 0.370 | 0.060 | 0.422 | |
| get_met_probes_info | 0.016 | 0.000 | 0.016 | |
| get_promoter_avg | 0 | 0 | 0 | |
| get_region_target_gene | 2.654 | 0.052 | 2.705 | |
| get_residuals | 0.037 | 0.004 | 0.040 | |
| get_tf_ES | 1.299 | 0.136 | 1.435 | |
| get_tf_in_region | 23.829 | 0.608 | 24.437 | |
| interaction_model | 0.222 | 0.020 | 0.242 | |
| make_dnam_se | 0.061 | 0.008 | 0.069 | |
| make_exp_se | 0.076 | 0.008 | 0.084 | |
| make_granges_from_names | 0.014 | 0.000 | 0.014 | |
| make_names_from_granges | 0.015 | 0.000 | 0.015 | |
| plot_interaction_model | 1.533 | 0.104 | 1.637 | |
| stratified_model | 0.036 | 0.004 | 0.039 | |