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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-16 11:07:55 -0400 (Wed, 16 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4060 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4081 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R 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 | ||||
|
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. |
| Package 1119/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethReg 1.5.3 (landing page) Tiago Silva
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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 |
##############################################################################
##############################################################################
###
### 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
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
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
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2 Regions above threshold 1
Status freq
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2 Regions above threshold 1
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Status freq
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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
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.55 | 0.01 | 0.57 | |
| cor_tf_target_gene | 0.03 | 0.00 | 0.03 | |
| create_triplet_distance_based | 25.37 | 4.50 | 29.87 | |
| create_triplet_regulon_based | 19.78 | 3.31 | 23.09 | |
| filter_dnam_by_quant_diff | 0.09 | 0.00 | 0.10 | |
| filter_exp_by_quant_mean_FC | 0.77 | 0.02 | 0.78 | |
| get_human_tfs | 0.44 | 0.11 | 0.56 | |
| get_met_probes_info | 0.01 | 0.00 | 0.01 | |
| get_promoter_avg | 0 | 0 | 0 | |
| get_region_target_gene | 3.49 | 0.03 | 3.52 | |
| get_residuals | 0.04 | 0.00 | 0.05 | |
| get_tf_ES | 1.99 | 0.17 | 2.15 | |
| get_tf_in_region | 20.61 | 2.67 | 23.28 | |
| interaction_model | 0.26 | 0.00 | 0.27 | |
| make_dnam_se | 0.03 | 0.02 | 0.05 | |
| make_exp_se | 0.07 | 0.00 | 0.06 | |
| make_granges_from_names | 0.01 | 0.00 | 0.02 | |
| make_names_from_granges | 0.02 | 0.00 | 0.01 | |
| plot_interaction_model | 1.34 | 0.05 | 1.39 | |
| stratified_model | 0.13 | 0.01 | 0.14 | |